From: m.doering Date: Fri, 2 Nov 2007 17:36:25 +0000 (+0000) Subject: Major update to the latest CDM definition 2.Nov.2007 X-Git-Tag: rel_1.1.0~788 X-Git-Url: https://dev.e-taxonomy.eu/gitweb/cdmlib.git/commitdiff_plain/bd9a5b0515d6eddb1f5a0066c922ba3ded5e33f9 Major update to the latest CDM definition 2.Nov.2007 --- diff --git a/.gitattributes b/.gitattributes index 9921ade43a..b71e90e072 100644 --- a/.gitattributes +++ b/.gitattributes @@ -60,61 +60,152 @@ cdmlibrary/src/main/java/eu/etaxonomy/cdm/aspectj/PropertyChangeAspect.aj -text cdmlibrary/src/main/java/eu/etaxonomy/cdm/database/DbType.java -text cdmlibrary/src/main/java/eu/etaxonomy/cdm/database/LocalHsqldb.java -text cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/PropertyChangeBean.java -text +cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/Address.java -text +cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/Contact.java -text +cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/Institution.java -text +cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/InstitutionType.java -text +cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/InstitutionalMembership.java -text cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/Person.java -text +cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/PersonInSource.java -text cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/Team.java -text +cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/TeamInSource.java -text +cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/AnnotatableEntity.java -text +cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Annotation.java -text +cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/AudioFile.java -text cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/CdmBase.java -text -cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Fact.java -text -cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/FactBase.java -text +cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/DatePeriodTerm.java -text +cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/DefinedTermBase.java -text +cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/EntityInSourceBase.java -text +cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/EnumeratedTermBase.java -text +cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Enumeration.java -text +cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Extension.java -text +cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/ExtensionType.java -text +cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Figure.java -text +cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/IReferencedEntity.java -text cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/IdentifiableEntity.java -text +cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/ImageFile.java -text +cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Keyword.java -text 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-cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonFactType.java -text +cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonInSource.java -text cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonRelationship.java -text -cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/view/Group.java -text cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/view/User.java -text cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/view/View.java -text cdmlibrary/src/main/java/eu/etaxonomy/cdm/persistence/dao/AgentDaoHibernateImpl.java -text diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/Address.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/Address.java new file mode 100644 index 0000000000..42cdc6901a --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/Address.java @@ -0,0 +1,130 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.agent; + + +import etaxonomy.cdm.model.location.WaterbodyOrCountry; +import etaxonomy.cdm.model.location.Point; +import etaxonomy.cdm.model.common.VersionableEntity; +import org.apache.log4j.Logger; + +/** + * taken from TDWG & VCard + * + * http://rs.tdwg.org/ontology/voc/ContactDetails#Address + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:33 + */ +public class Address extends VersionableEntity { + static Logger logger = Logger.getLogger(Address.class); + + //Post Office Box + @Description("Post Office Box") + private String pobox; + //including number + @Description("including number") + private String street; + @Description("") + private String postcode; + //town,locality,suburb + @Description("town,locality,suburb") + private String locality; + //Region/State + @Description("Region/State") + private String region; + private Point location; + private WaterbodyOrCountry country; + + public WaterbodyOrCountry getCountry(){ + return country; + } + + /** + * + * @param newVal + */ + public void setCountry(WaterbodyOrCountry newVal){ + country = newVal; + } + + public Point getLocation(){ + return location; + } + + /** + * + * @param newVal + */ + public void setLocation(Point newVal){ + location = newVal; + } + + public String getPobox(){ + return pobox; + } + + /** + * + * @param newVal + */ + public void setPobox(String newVal){ + pobox = newVal; + } + + public String getStreet(){ + return street; + } + + /** + * + * @param newVal + */ + public void setStreet(String newVal){ + street = newVal; + } + + public String getPostcode(){ + return postcode; + } + + /** + * + * @param newVal + */ + public void setPostcode(String newVal){ + postcode = newVal; + } + + public String getLocality(){ + return locality; + } + + /** + * + * @param newVal + */ + public void setLocality(String newVal){ + locality = newVal; + } + + public String getRegion(){ + return region; + } + + /** + * + * @param newVal + */ + public void setRegion(String newVal){ + region = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/Contact.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/Contact.java new file mode 100644 index 0000000000..c697245a26 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/Contact.java @@ -0,0 +1,95 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.agent; + + +import etaxonomy.cdm.model.common.VersionableEntity; +import org.apache.log4j.Logger; + +/** + * http://rs.tdwg.org/ontology/voc/ContactDetails#ContactDetails + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:41 + */ +public class Contact extends VersionableEntity { + static Logger logger = Logger.getLogger(Contact.class); + + @Description("") + private String email; + @Description("") + private String url; + @Description("") + private String phone; + @Description("") + private String fax; + private ArrayList addresses; + + public ArrayList getAddresses(){ + return addresses; + } + + /** + * + * @param newVal + */ + public void setAddresses(ArrayList newVal){ + addresses = newVal; + } + + public String getEmail(){ + return email; + } + + /** + * + * @param newVal + */ + public void setEmail(String newVal){ + email = newVal; + } + + public String getUrl(){ + return url; + } + + /** + * + * @param newVal + */ + public void setUrl(String newVal){ + url = newVal; + } + + public String getPhone(){ + return phone; + } + + /** + * + * @param newVal + */ + public void setPhone(String newVal){ + phone = newVal; + } + + public String getFax(){ + return fax; + } + + /** + * + * @param newVal + */ + public void setFax(String newVal){ + fax = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/Institution.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/Institution.java new file mode 100644 index 0000000000..dbfc8d5819 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/Institution.java @@ -0,0 +1,94 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.agent; + + +import etaxonomy.cdm.model.common.IdentifiableEntity; +import org.apache.log4j.Logger; + +/** + * http://rs.tdwg.org/ontology/voc/Institution.rdf + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:54 + */ +public class Institution extends IdentifiableEntity { + static Logger logger = Logger.getLogger(Institution.class); + + //Acronym, code or initialism by which the insitution is generally known + @Description("Acronym, code or initialism by which the insitution is generally known") + private String code; + @Description("") + private String name; + private ArrayList types; + private Institution isPartOf; + private Contact contact; + + public Contact getContact(){ + return contact; + } + + /** + * + * @param newVal + */ + public void setContact(Contact newVal){ + contact = newVal; + } + + public ArrayList getTypes(){ + return types; + } + + /** + * + * @param newVal + */ + public void setTypes(ArrayList newVal){ + types = newVal; + } + + public Institution getIsPartOf(){ + return isPartOf; + } + + /** + * + * @param newVal + */ + public void setIsPartOf(Institution newVal){ + isPartOf = newVal; + } + + public String getCode(){ + return code; + } + + /** + * + * @param newVal + */ + public void setCode(String newVal){ + code = newVal; + } + + public String getName(){ + return name; + } + + /** + * + * @param newVal + */ + public void setName(String newVal){ + name = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/InstitutionType.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/InstitutionType.java new file mode 100644 index 0000000000..4b0b37b878 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/InstitutionType.java @@ -0,0 +1,25 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.agent; + + +import etaxonomy.cdm.model.common.EnumeratedTermBase; +import org.apache.log4j.Logger; + +/** + * http://rs.tdwg.org/ontology/voc/InstitutionType + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:55 + */ +public class InstitutionType extends EnumeratedTermBase { + static Logger logger = Logger.getLogger(InstitutionType.class); + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/InstitutionalMembership.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/InstitutionalMembership.java new file mode 100644 index 0000000000..250a3618f6 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/InstitutionalMembership.java @@ -0,0 +1,86 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.agent; + + +import etaxonomy.cdm.model.common.VersionableEntity; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:54 + */ +public class InstitutionalMembership extends VersionableEntity { + static Logger logger = Logger.getLogger(InstitutionalMembership.class); + + //Time period a person belonged to the institution + @Description("Time period a person belonged to the institution") + private TimePeriod period; + //Department of the institution this person was working in + @Description("Department of the institution this person was working in") + private String department; + //Role this person had in the institution + @Description("Role this person had in the institution") + private String role; + /** + * current institute the person belongs to + */ + private Institution institute; + + public Institution getInstitute(){ + return institute; + } + + /** + * + * @param newVal + */ + public void setInstitute(Institution newVal){ + institute = newVal; + } + + public TimePeriod getPeriod(){ + return period; + } + + /** + * + * @param newVal + */ + public void setPeriod(TimePeriod newVal){ + period = newVal; + } + + public String getDepartment(){ + return department; + } + + /** + * + * @param newVal + */ + public void setDepartment(String newVal){ + department = newVal; + } + + public String getRole(){ + return role; + } + + /** + * + * @param newVal + */ + public void setRole(String newVal){ + role = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/Person.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/Person.java index a2b4070ce3..d09925df84 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/Person.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/Person.java @@ -1,94 +1,158 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.agent; - - -import eu.etaxonomy.cdm.model.common.VersionableEntity; -import eu.etaxonomy.cdm.model.common.NameAlias; -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:10 - */ -@Entity -public class Person extends VersionableEntity { - static Logger logger = Logger.getLogger(Person.class); - - private String forenames; - private String lifespan; - private String subjectScope; - private String surname; - private ArrayList standardForms; - - public String getForenames(){ - return forenames; - } - - public String getLifespan(){ - return lifespan; - } - - public ArrayList getStandardForms(){ - return standardForms; - } - - public String getSubjectScope(){ - return subjectScope; - } - - public String getSurname(){ - return surname; - } - - /** - * - * @param newVal - */ - public void setForenames(String newVal){ - forenames = newVal; - } - - /** - * - * @param newVal - */ - public void setLifespan(String newVal){ - lifespan = newVal; - } - - /** - * - * @param newVal - */ - public void setStandardForms(ArrayList newVal){ - standardForms = newVal; - } - - /** - * - * @param newVal - */ - public void setSubjectScope(String newVal){ - subjectScope = newVal; - } - - /** - * - * @param newVal - */ - public void setSurname(String newVal){ - surname = newVal; - } - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.agent; + + +import etaxonomy.cdm.model.common.Keyword; +import etaxonomy.cdm.model.common.IdentifiableEntity; +import org.apache.log4j.Logger; + +/** + * http://rs.tdwg.org/ontology/voc/Person.rdf + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:07 + */ +public class Person extends IdentifiableEntity { + static Logger logger = Logger.getLogger(Person.class); + + //e.g. the title + @Description("e.g. the title") + private String prefix; + //All other names not included in the surname. May be just initials, all forenames in full or a combination of expanded + //names and initials. + @Description("All other names not included in the surname. May be just initials, all forenames in full or a combination of expanded names and initials.") + private String firstname; + //A hereditary name common to all members of a family, as distinct from a given name or forename + @Description("A hereditary name common to all members of a family, as distinct from a given name or forename") + private String lastname; + //e.g. junior + @Description("e.g. junior") + private String suffix; + //The period for which this person was alive represented as a TimePeriod datatype, i.e. start - end date. + //Alternative suggestion as a flexible String. the form birthdate - deathdate (XXXX - YYYY; XXXX - or - YYYY as + //appropriate) is prefered, or as simple flourished date (fl. XXXX) may be given where that is all that is known + @Description("The period for which this person was alive represented as a TimePeriod datatype, i.e. start - end date. + Alternative suggestion as a flexible String. the form birthdate - deathdate (XXXX - YYYY; XXXX - or - YYYY as appropriate) is prefered, or as simple flourished date (fl. XXXX) may be given where that is all that is known") + private TimePeriod lifespan; + private ArrayList institutionalMemberships; + private Contact contact; + private ArrayList personInSources; + private ArrayList keywords; + + public ArrayList getInstitutionalMemberships(){ + return institutionalMemberships; + } + + /** + * + * @param newVal + */ + public void setInstitutionalMemberships(ArrayList newVal){ + institutionalMemberships = newVal; + } + + public ArrayList getPersonInSources(){ + return personInSources; + } + + /** + * + * @param newVal + */ + public void setPersonInSources(ArrayList newVal){ + personInSources = newVal; + } + + public ArrayList getKeywords(){ + return keywords; + } + + /** + * + * @param newVal + */ + public void setKeywords(ArrayList newVal){ + keywords = newVal; + } + + public Contact getContact(){ + return contact; + } + + /** + * + * @param newVal + */ + public void setContact(Contact newVal){ + contact = newVal; + } + + public String getPrefix(){ + return prefix; + } + + /** + * + * @param newVal + */ + public void setPrefix(String newVal){ + prefix = newVal; + } + + public String getFirstname(){ + return firstname; + } + + /** + * + * @param newVal + */ + public void setFirstname(String newVal){ + firstname = newVal; + } + + public String getLastname(){ + return lastname; + } + + /** + * + * @param newVal + */ + public void setLastname(String newVal){ + lastname = newVal; + } + + public String getSuffix(){ + return suffix; + } + + /** + * + * @param newVal + */ + public void setSuffix(String newVal){ + suffix = newVal; + } + + public TimePeriod getLifespan(){ + return lifespan; + } + + /** + * + * @param newVal + */ + public void setLifespan(TimePeriod newVal){ + lifespan = newVal; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/PersonInSource.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/PersonInSource.java new file mode 100644 index 0000000000..7c98a44dc2 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/PersonInSource.java @@ -0,0 +1,24 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.agent; + + +import etaxonomy.cdm.model.common.EntityInSourceBase; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:08 + */ +public class PersonInSource extends EntityInSourceBase { + static Logger logger = Logger.getLogger(PersonInSource.class); + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/Team.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/Team.java index 1268c81638..e2fa7d5935 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/Team.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/Team.java @@ -1,70 +1,71 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.agent; - - -import eu.etaxonomy.cdm.model.common.VersionableEntity; -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * This author team class note explains everything there is to authors and - * includes explanation why certain attributes have been dropped or are dealt with - * elsewhere. - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:16 - */ -@Entity -public class Team extends VersionableEntity { - static Logger logger = Logger.getLogger(Team.class); - - private String fullName; - private String shortName; - private java.util.ArrayList teamMembers; - - public String getFullName(){ - return fullName; - } - - public String getShortName(){ - return shortName; - } - - public java.util.ArrayList getTeamMembers(){ - return teamMembers; - } - - /** - * - * @param newVal - */ - public void setFullName(String newVal){ - fullName = newVal; - } - - /** - * - * @param newVal - */ - public void setShortName(String newVal){ - shortName = newVal; - } - - /** - * - * @param newVal - */ - public void setTeamMembers(java.util.ArrayList newVal){ - teamMembers = newVal; - } - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.agent; + + +import etaxonomy.cdm.model.common.VersionableEntity; +import org.apache.log4j.Logger; + +/** + * An author team may exist for itself or may be built with the persons who belong + * to it. + * {At least one otf the attributes shortName or fullName must exist.} + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:23 + */ +public class Team extends VersionableEntity { + static Logger logger = Logger.getLogger(Team.class); + + //An abreviated name for the team (e. g. in case of nomenclatural authorteams). + //A non abreviated name for the team (e. g. in case of some bibliographical references) + @Description("An abreviated name for the team (e. g. in case of nomenclatural authorteams). + A non abreviated name for the team (e. g. in case of some bibliographical references)") + private String originalCitation; + private ArrayList teamInSource; + private java.util.ArrayList teamMembers; + + public java.util.ArrayList getTeamMembers(){ + return teamMembers; + } + + /** + * + * @param newVal + */ + public void setTeamMembers(java.util.ArrayList newVal){ + teamMembers = newVal; + } + + public ArrayList getTeamInSource(){ + return teamInSource; + } + + /** + * + * @param newVal + */ + public void setTeamInSource(ArrayList newVal){ + teamInSource = newVal; + } + + public String getOriginalCitation(){ + return originalCitation; + } + + /** + * + * @param newVal + */ + public void setOriginalCitation(String newVal){ + originalCitation = newVal; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/TeamInSource.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/TeamInSource.java new file mode 100644 index 0000000000..c7bcca10f3 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/agent/TeamInSource.java @@ -0,0 +1,24 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.agent; + + +import etaxonomy.cdm.model.common.EntityInSourceBase; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:23 + */ +public class TeamInSource extends EntityInSourceBase { + static Logger logger = Logger.getLogger(TeamInSource.class); + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/AnnotatableEntity.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/AnnotatableEntity.java new file mode 100644 index 0000000000..8c6e91b07c --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/AnnotatableEntity.java @@ -0,0 +1,51 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:34 + */ +@MappedSuperclass +public abstract class AnnotatableEntity extends VersionableEntity { + static Logger logger = Logger.getLogger(AnnotatableEntity.class); + + private ArrayList markers; + private ArrayList annotations; + + public ArrayList getMarkers(){ + return markers; + } + + /** + * + * @param newVal + */ + public void setMarkers(ArrayList newVal){ + markers = newVal; + } + + public ArrayList getAnnotations(){ + return annotations; + } + + /** + * + * @param newVal + */ + public void setAnnotations(ArrayList newVal){ + annotations = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Annotation.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Annotation.java new file mode 100644 index 0000000000..b11094a6f8 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Annotation.java @@ -0,0 +1,66 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import etaxonomy.cdm.model.agent.Person; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:34 + */ +public class Annotation extends VersionableEntity { + static Logger logger = Logger.getLogger(Annotation.class); + + //Human annotation + @Description("Human annotation") + private String note; + private Language language; + private Person commentator; + + public Person getCommentator(){ + return commentator; + } + + /** + * + * @param newVal + */ + public void setCommentator(Person newVal){ + commentator = newVal; + } + + public Language getLanguage(){ + return language; + } + + /** + * + * @param newVal + */ + public void setLanguage(Language newVal){ + language = newVal; + } + + public String getNote(){ + return note; + } + + /** + * + * @param newVal + */ + public void setNote(String newVal){ + note = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/AudioFile.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/AudioFile.java new file mode 100644 index 0000000000..5a0fdf5629 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/AudioFile.java @@ -0,0 +1,39 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:35 + */ +public class AudioFile extends MediaInstance { + static Logger logger = Logger.getLogger(AudioFile.class); + + //length of recording in seconds + @Description("length of recording in seconds") + private int duration; + + public int getDuration(){ + return duration; + } + + /** + * + * @param newVal + */ + public void setDuration(int newVal){ + duration = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Generic.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/DatePeriodTerm.java similarity index 57% rename from cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Generic.java rename to cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/DatePeriodTerm.java index df1caf6d2a..32e68c11db 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Generic.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/DatePeriodTerm.java @@ -1,23 +1,24 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.publication; - - -import org.apache.log4j.Logger; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:04 - */ -public class Generic extends PublicationBase { - static Logger logger = Logger.getLogger(Generic.class); - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import etaxonomy.cdm.model.description.Scope; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:43 + */ +public class DatePeriodTerm extends Scope { + static Logger logger = Logger.getLogger(DatePeriodTerm.class); + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/DefinedTermBase.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/DefinedTermBase.java new file mode 100644 index 0000000000..5c3fee23d4 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/DefinedTermBase.java @@ -0,0 +1,160 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import org.apache.log4j.Logger; + +/** + * workaround for enumerations, base type according to TDWG. + * + * For linear ordering use partOf relation and BreadthFirst. + * Default iterator order should therefore be BreadthFirst (not DepthFirst) + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:43 + */ +public abstract class DefinedTermBase extends VersionableEntity { + static Logger logger = Logger.getLogger(DefinedTermBase.class); + + //URI used as an ID for the term. In the case of TDWG ontology derived terms the URL to the term! + @Description("URI used as an ID for the term. In the case of TDWG ontology derived terms the URL to the term!") + private String uri; + //The RDF ontology source defining the terms to be loaded when a database is created for the first time. + // + //Software can go and grap these terms incl labels and description. UUID needed? Furhter vocs can be setup through our + //own ontology. + @Description("The RDF ontology source defining the terms to be loaded when a database is created for the first time. + + Software can go and grap these terms incl labels and description. UUID needed? Furhter vocs can be setup through our own ontology.") + private static final int initializationClassUri; + private DefinedTermBase partOf; + private ArrayList includes; + private ArrayList representations; + private DefinedTermBase kindOf; + private ArrayList generalizationOf; + private java.util.ArrayList media; + + public ArrayList getRepresentations(){ + return representations; + } + + /** + * + * @param newVal + */ + public void setRepresentations(ArrayList newVal){ + representations = newVal; + } + + public DefinedTermBase getKindOf(){ + return kindOf; + } + + /** + * + * @param newVal + */ + public void setKindOf(DefinedTermBase newVal){ + kindOf = newVal; + } + + public ArrayList getGeneralizationOf(){ + return generalizationOf; + } + + /** + * + * @param newVal + */ + public void setGeneralizationOf(ArrayList newVal){ + generalizationOf = newVal; + } + + public DefinedTermBase getPartOf(){ + return partOf; + } + + /** + * + * @param newVal + */ + public void setPartOf(DefinedTermBase newVal){ + partOf = newVal; + } + + public ArrayList getIncludes(){ + return includes; + } + + /** + * + * @param newVal + */ + public void setIncludes(ArrayList newVal){ + includes = newVal; + } + + public java.util.ArrayList getMedia(){ + return media; + } + + /** + * + * @param newVal + */ + public void setMedia(java.util.ArrayList newVal){ + media = newVal; + } + + public String getUri(){ + return uri; + } + + /** + * + * @param newVal + */ + public void setUri(String newVal){ + uri = newVal; + } + + public getInitializationClassUri(){ + return initializationClassUri; + } + + /** + * + * @param newVal + */ + public void setInitializationClassUri(newVal){ + initializationClassUri = newVal; + } + + /** + * + * @param uri + */ + @Transient + public static defined terms getDefinedTermByUri(String uri){ + return null; + } + + /** + * add new terms from a vocabulary to which uri points. By default this is the + * initializationClassUri + * + * @param uri + */ + public void addTermsFromInitializationClass(String uri){ + + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/EntityInSourceBase.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/EntityInSourceBase.java new file mode 100644 index 0000000000..ac2db58602 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/EntityInSourceBase.java @@ -0,0 +1,41 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import org.apache.log4j.Logger; + +/** + * Other names/labels/titles (abreviated or not) for the same object (person, + * reference, source, etc.) + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:46 + */ +public abstract class EntityInSourceBase extends ReferencedEntityBase { + static Logger logger = Logger.getLogger(EntityInSourceBase.class); + + //The object's ID in the source, where the alternative string comes from + @Description("The object's ID in the source, where the alternative string comes from") + private String idInSource; + + public String getIdInSource(){ + return idInSource; + } + + /** + * + * @param newVal + */ + public void setIdInSource(String newVal){ + idInSource = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/EnumeratedTermBase.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/EnumeratedTermBase.java new file mode 100644 index 0000000000..73119a94d2 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/EnumeratedTermBase.java @@ -0,0 +1,37 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:47 + */ +public abstract class EnumeratedTermBase extends DefinedTermBase { + static Logger logger = Logger.getLogger(EnumeratedTermBase.class); + + private Enumeration enumeration; + + public Enumeration getEnumeration(){ + return enumeration; + } + + /** + * + * @param newVal + */ + public void setEnumeration(Enumeration newVal){ + enumeration = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Enumeration.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Enumeration.java new file mode 100644 index 0000000000..3b5a74b451 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Enumeration.java @@ -0,0 +1,42 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import org.apache.log4j.Logger; + +/** + * A single enumeration must only contain DefinedTerm instances of one kind + * (=class) + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:47 + */ +public class Enumeration extends DefinedTermBase { + static Logger logger = Logger.getLogger(Enumeration.class); + + //The order of the enumeration list is a linear order that can be used for statistical purposes. Measurement scale = + //ordinal + @Description("The order of the enumeration list is a linear order that can be used for statistical purposes. Measurement scale = ordinal") + private boolean isOrdinal; + + public boolean isOrdinal(){ + return isOrdinal; + } + + /** + * + * @param newVal + */ + public void setOrdinal(boolean newVal){ + isOrdinal = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Extension.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Extension.java new file mode 100644 index 0000000000..aefa2f5c6c --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Extension.java @@ -0,0 +1,55 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import org.apache.log4j.Logger; + +/** + * This class aims to make available more "attributes" for identifiable entities + * in a flexible way. Application developers (and even users) can define their own + * "attrributes" as an ExtensionType and add data to Identifiable instances via + * Extension instances. + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:47 + */ +public class Extension extends VersionableEntity { + static Logger logger = Logger.getLogger(Extension.class); + + @Description("") + private String value; + private ExtensionType type; + + public ExtensionType getType(){ + return type; + } + + /** + * + * @param newVal + */ + public void setType(ExtensionType newVal){ + type = newVal; + } + + public String getValue(){ + return value; + } + + /** + * + * @param newVal + */ + public void setValue(String newVal){ + value = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/ExtensionType.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/ExtensionType.java new file mode 100644 index 0000000000..ec1b37e01c --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/ExtensionType.java @@ -0,0 +1,34 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import org.apache.log4j.Logger; + +/** + * Extension types similar to dynamically defined attributes. These are not data + * types, but rather content types like "DOI", "2nd nomenclatural reference", "3rd + * hybrid parent" or specific local identifiers. + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:48 + */ +public class ExtensionType extends DefinedTermBase { + static Logger logger = Logger.getLogger(ExtensionType.class); + + public static final ExtensionType XML_FRAGMENT(){ + return null; + } + + public static final ExtensionType RDF_FRAGMENT(){ + return null; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/FactBase.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/FactBase.java deleted file mode 100644 index 61dfcf3f0d..0000000000 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/FactBase.java +++ /dev/null @@ -1,53 +0,0 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.common; - - -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:03 - */ -@Entity -public abstract class FactBase extends VersionableEntity { - static Logger logger = Logger.getLogger(FactBase.class); - - private String citationMicroReference; - private String fact; - - public String getCitationMicroReference(){ - return citationMicroReference; - } - - public String getFact(){ - return fact; - } - - /** - * - * @param newVal - */ - public void setCitationMicroReference(String newVal){ - citationMicroReference = newVal; - } - - /** - * - * @param newVal - */ - public void setFact(String newVal){ - fact = newVal; - } - -} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Report.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Figure.java similarity index 58% rename from cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Report.java rename to cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Figure.java index f5b9546c1a..dcb99e6aeb 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Report.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Figure.java @@ -1,23 +1,23 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.publication; - - -import org.apache.log4j.Logger; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:12 - */ -public class Report extends PublicationBase { - static Logger logger = Logger.getLogger(Report.class); - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:49 + */ +public class Figure extends ReferencedMedia { + static Logger logger = Logger.getLogger(Figure.class); + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/IReferencedEntity.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/IReferencedEntity.java new file mode 100644 index 0000000000..130bc64457 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/IReferencedEntity.java @@ -0,0 +1,29 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import etaxonomy.cdm.model.reference.StrictReferenceBase; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:55 + */ +public interface IReferencedEntity { + + @Transient + public StrictReferenceBase getCitation(); + + @Transient + public String getCitation(); + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/IdentifiableEntity.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/IdentifiableEntity.java index e31cafc3b5..16d7dd2526 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/IdentifiableEntity.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/IdentifiableEntity.java @@ -1,40 +1,147 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.common; - - -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:04 - */ -@MappedSuperclass -public abstract class IdentifiableEntity extends VersionableEntity { - static Logger logger = Logger.getLogger(IdentifiableEntity.class); - - private String lsid; - - public String getLsid(){ - return lsid; - } - - /** - * - * @param newVal - */ - public void setLsid(String newVal){ - lsid = newVal; - } - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:52 + */ +@MappedSuperclass +public abstract class IdentifiableEntity extends AnnotatableEntity { + static Logger logger = Logger.getLogger(IdentifiableEntity.class); + + @Description("") + private String lsid; + @Description("") + private String titleCache; + //if true titleCache will not be automatically generated/updated + @Description("if true titleCache will not be automatically generated/updated") + private boolean hasProtectedTitleCache; + private ArrayList rights; + private ArrayList extensions; + + public ArrayList getExtensions(){ + return extensions; + } + + /** + * + * @param newVal + */ + public void setExtensions(ArrayList newVal){ + extensions = newVal; + } + + public ArrayList getRights(){ + return rights; + } + + /** + * + * @param newVal + */ + public void setRights(ArrayList newVal){ + rights = newVal; + } + + public String getLsid(){ + return lsid; + } + + /** + * + * @param newVal + */ + public void setLsid(String newVal){ + lsid = newVal; + } + + public String getTitleCache(){ + return titleCache; + } + + /** + * + * @param newVal + */ + public void setTitleCache(String newVal){ + titleCache = newVal; + } + + public boolean getHasProtectedTitleCache(){ + return hasProtectedTitleCache; + } + + /** + * + * @param newVal + */ + public void setHasProtectedTitleCache(boolean newVal){ + hasProtectedTitleCache = newVal; + } + + @Transient + public String getTitle(){ + return ""; + } + + public abstract String generateTitle(); + + public boolean hasProtectedTitleCache(){ + return false; + } + + @Transient + public Extension[] getExtensions(){ + return null; + } + + @Transient + public Marker[] getMarkers(){ + return null; + } + + /** + * + * @param extension + */ + public void addExtension(Extension extension){ + + } + + /** + * + * @param marker + */ + public void addMarker(Marker marker){ + + } + + /** + * + * @param extension + */ + public void removeExtension(Extension extension){ + + } + + /** + * + * @param marker + */ + public void removeMarker(Marker marker){ + + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/ImageFile.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/ImageFile.java new file mode 100644 index 0000000000..49b5fc36a1 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/ImageFile.java @@ -0,0 +1,54 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:53 + */ +public class ImageFile extends MediaInstance { + static Logger logger = Logger.getLogger(ImageFile.class); + + //image height in pixel + @Description("image height in pixel") + private int height; + //image width in pixel + @Description("image width in pixel") + private int width; + + public int getHeight(){ + return height; + } + + /** + * + * @param newVal + */ + public void setHeight(int newVal){ + height = newVal; + } + + public int getWidth(){ + return width; + } + + /** + * + * @param newVal + */ + public void setWidth(int newVal){ + width = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Keyword.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Keyword.java new file mode 100644 index 0000000000..3c49da3f6c --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Keyword.java @@ -0,0 +1,24 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import org.apache.log4j.Logger; + +/** + * simple keywords. could be taxonomic scope, geographic scope or anything else + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:56 + */ +public class Keyword extends EnumeratedTermBase { + static Logger logger = Logger.getLogger(Keyword.class); + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Language.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Language.java new file mode 100644 index 0000000000..a58095200b --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Language.java @@ -0,0 +1,69 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import org.apache.log4j.Logger; + +/** + * list of languages according to current internet best practices as given by IANA + * or ISO codes. + * + * http://www.ietf.org/rfc/rfc4646.txt + * http://www.loc.gov/standards/iso639-2/php/English_list.php + * + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:56 + */ +public class Language extends DefinedTermBase { + static Logger logger = Logger.getLogger(Language.class); + + public static final Language CHINESE(){ + return null; + } + + public static final Language ENGLISH(){ + return null; + } + + public static final Language SPANISH(){ + return null; + } + + public static final Language HINDI(){ + return null; + } + + public static final Language ARABIC(){ + return null; + } + + public static final Language BENGALI(){ + return null; + } + + public static final Language RUSSIAN(){ + return null; + } + + public static final Language PORTUGUESE(){ + return null; + } + + public static final Language JAPANESE(){ + return null; + } + + public static final Language GERMAN(){ + return null; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/LanguageString.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/LanguageString.java new file mode 100644 index 0000000000..344f40f0d2 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/LanguageString.java @@ -0,0 +1,51 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:57 + */ +public class LanguageString { + static Logger logger = Logger.getLogger(LanguageString.class); + + @Description("") + private char text; + private Language language; + + public Language getLanguage(){ + return language; + } + + /** + * + * @param newVal + */ + public void setLanguage(Language newVal){ + language = newVal; + } + + public char getText(){ + return text; + } + + /** + * + * @param newVal + */ + public void setText(char newVal){ + text = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Marker.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Marker.java new file mode 100644 index 0000000000..bcc5d4af3c --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Marker.java @@ -0,0 +1,54 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import org.apache.log4j.Logger; + +/** + * This class aims to make available some "flags" for identifiable entities in a + * flexible way. Application developers (and even users) can define their own + * "flags" as a MarkerType. + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:58 + */ +public class Marker extends VersionableEntity { + static Logger logger = Logger.getLogger(Marker.class); + + @Description("") + private boolean flag; + private MarkerType type; + + public MarkerType getType(){ + return type; + } + + /** + * + * @param newVal + */ + public void setType(MarkerType newVal){ + type = newVal; + } + + public boolean getFlag(){ + return flag; + } + + /** + * + * @param newVal + */ + public void setFlag(boolean newVal){ + flag = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/MarkerType.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/MarkerType.java new file mode 100644 index 0000000000..5910868c79 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/MarkerType.java @@ -0,0 +1,41 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import org.apache.log4j.Logger; + +/** + * Marker types similar to dynamically defined attributes. These content types + * like "IS_DOUBTFUL", "COMPLETE" or specific local flags. + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:59 + */ +public class MarkerType extends DefinedTermBase { + static Logger logger = Logger.getLogger(MarkerType.class); + + public static final MarkerType IMPORTED(){ + return null; + } + + public static final MarkerType TO_BE_CHECKED(){ + return null; + } + + public static final MarkerType IS_DOUBTFUL(){ + return null; + } + + public static final MarkerType COMPLETE(){ + return null; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Media.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Media.java index 7af994b0d1..d0a94401c8 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Media.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Media.java @@ -1,53 +1,111 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.common; - - -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:07 - */ -@Entity -public class Media extends VersionableEntity { - static Logger logger = Logger.getLogger(Media.class); - - private String description; - private String location; - - public String getDescription(){ - return description; - } - - public String getLocation(){ - return location; - } - - /** - * - * @param newVal - */ - public void setDescription(String newVal){ - description = newVal; - } - - /** - * - * @param newVal - */ - public void setLocation(String newVal){ - location = newVal; - } - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import etaxonomy.cdm.model.agent.Team; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:59 + */ +public class Media extends AnnotatableEntity { + static Logger logger = Logger.getLogger(Media.class); + + @Description("") + private MultilanguageString title; + //creation date of the media (not of the record) + @Description("creation date of the media (not of the record)") + private Calendar mediaCreated; + @Description("") + private MultilanguageString description; + /** + * A single medium such as a picture can have multiple representations in files. + * Common are multiple resolutions or file formats for images for example + */ + private ArrayList instances; + private ArrayList rights; + private Team artist; + + public ArrayList getInstances(){ + return instances; + } + + /** + * + * @param newVal + */ + public void setInstances(ArrayList newVal){ + instances = newVal; + } + + public Team getArtist(){ + return artist; + } + + /** + * + * @param newVal + */ + public void setArtist(Team newVal){ + artist = newVal; + } + + public ArrayList getRights(){ + return rights; + } + + /** + * + * @param newVal + */ + public void setRights(ArrayList newVal){ + rights = newVal; + } + + public MultilanguageString getTitle(){ + return title; + } + + /** + * + * @param newVal + */ + public void setTitle(MultilanguageString newVal){ + title = newVal; + } + + public Calendar getMediaCreated(){ + return mediaCreated; + } + + /** + * + * @param newVal + */ + public void setMediaCreated(Calendar newVal){ + mediaCreated = newVal; + } + + public MultilanguageString getDescription(){ + return description; + } + + /** + * + * @param newVal + */ + public void setDescription(MultilanguageString newVal){ + description = newVal; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/MediaInstance.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/MediaInstance.java new file mode 100644 index 0000000000..f7753e986e --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/MediaInstance.java @@ -0,0 +1,86 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import org.apache.log4j.Logger; + +/** + * metadata for an external file such as images, phylogenetic trees, or audio + * recordings available through the location attribute! + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:00 + */ +public class MediaInstance extends VersionableEntity { + static Logger logger = Logger.getLogger(MediaInstance.class); + + //http://www.iana.org/assignments/media-types/ + @Description("http://www.iana.org/assignments/media-types/") + private String mimeType; + //filename suffix defining the media-type as an alternative to the proper MIME type + @Description("filename suffix defining the media-type as an alternative to the proper MIME type") + private String suffix; + //where the media file is stored + @Description("where the media file is stored") + private String uri; + //in bytes + @Description("in bytes") + private int size; + + public String getMimeType(){ + return mimeType; + } + + /** + * + * @param newVal + */ + public void setMimeType(String newVal){ + mimeType = newVal; + } + + public String getSuffix(){ + return suffix; + } + + /** + * + * @param newVal + */ + public void setSuffix(String newVal){ + suffix = newVal; + } + + public String getUri(){ + return uri; + } + + /** + * + * @param newVal + */ + public void setUri(String newVal){ + uri = newVal; + } + + public int getSize(){ + return size; + } + + /** + * + * @param newVal + */ + public void setSize(int newVal){ + size = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/MovieFile.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/MovieFile.java new file mode 100644 index 0000000000..5abebcd063 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/MovieFile.java @@ -0,0 +1,39 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:01 + */ +public class MovieFile extends ImageFile { + static Logger logger = Logger.getLogger(MovieFile.class); + + //Length of movie in seconds + @Description("Length of movie in seconds") + private int duration; + + public int getDuration(){ + return duration; + } + + /** + * + * @param newVal + */ + public void setDuration(int newVal){ + duration = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/MultilanguageString.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/MultilanguageString.java new file mode 100644 index 0000000000..b4f95d50d5 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/MultilanguageString.java @@ -0,0 +1,37 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:01 + */ +public class MultilanguageString { + static Logger logger = Logger.getLogger(MultilanguageString.class); + + private ArrayList representations; + + public ArrayList getRepresentations(){ + return representations; + } + + /** + * + * @param newVal + */ + public void setRepresentations(ArrayList newVal){ + representations = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/NameAlias.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/NameAlias.java deleted file mode 100644 index ffc80bab87..0000000000 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/NameAlias.java +++ /dev/null @@ -1,53 +0,0 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.common; - - -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:07 - */ -@Entity -public class NameAlias extends VersionableEntity { - static Logger logger = Logger.getLogger(NameAlias.class); - - private String alias; - private ArrayList sources; - - public String getAlias(){ - return alias; - } - - public ArrayList getSources(){ - return sources; - } - - /** - * - * @param newVal - */ - public void setAlias(String newVal){ - alias = newVal; - } - - /** - * - * @param newVal - */ - public void setSources(ArrayList newVal){ - sources = newVal; - } - -} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/ReferencedEntityBase.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/ReferencedEntityBase.java new file mode 100644 index 0000000000..f550027e14 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/ReferencedEntityBase.java @@ -0,0 +1,70 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import etaxonomy.cdm.model.reference.StrictReferenceBase; +import org.apache.log4j.Logger; + +/** + * abstract class for all objects that may have a reference + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:12 + */ +public abstract class ReferencedEntityBase extends AnnotatableEntity implements IReferencedEntity { + static Logger logger = Logger.getLogger(ReferencedEntityBase.class); + + //Details of the reference. These are mostly (implicitly) pages but can also be tables or any other element of a + //publication. + //{if the citationMicroReference exists then there must be also a reference} + + @Description("Details of the reference. These are mostly (implicitly) pages but can also be tables or any other element of a publication. + {if the citationMicroReference exists then there must be also a reference} + ") + private String citationMicroReference; + @Description("") + private String originalNameString; + + public String getCitationMicroReference(){ + return citationMicroReference; + } + + /** + * + * @param newVal + */ + public void setCitationMicroReference(String newVal){ + citationMicroReference = newVal; + } + + public String getOriginalNameString(){ + return originalNameString; + } + + /** + * + * @param newVal + */ + public void setOriginalNameString(String newVal){ + originalNameString = newVal; + } + + @Transient + public String getCitation(){ + return ""; + } + + @Transient + public StrictReferenceBase getCitation(){ + return null; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/ReferencedMedia.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/ReferencedMedia.java new file mode 100644 index 0000000000..38710e43d5 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/ReferencedMedia.java @@ -0,0 +1,63 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import etaxonomy.cdm.model.reference.ReferenceBase; +import etaxonomy.cdm.model.reference.StrictReferenceBase; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:13 + */ +public abstract class ReferencedMedia extends Media implements IReferencedEntity { + static Logger logger = Logger.getLogger(ReferencedMedia.class); + + @Description("") + private String citationMicroReference; + private ReferenceBase citation; + + public ReferenceBase getCitation(){ + return citation; + } + + /** + * + * @param newVal + */ + public void setCitation(ReferenceBase newVal){ + citation = newVal; + } + + public String getCitationMicroReference(){ + return citationMicroReference; + } + + /** + * + * @param newVal + */ + public void setCitationMicroReference(String newVal){ + citationMicroReference = newVal; + } + + @Transient + public String getCitation(){ + return ""; + } + + @Transient + public StrictReferenceBase getCitation(){ + return null; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Representation.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Representation.java new file mode 100644 index 0000000000..886c5a9208 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Representation.java @@ -0,0 +1,80 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import org.apache.log4j.Logger; + +/** + * workaround for enumerations + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:14 + */ +public class Representation extends VersionableEntity { + static Logger logger = Logger.getLogger(Representation.class); + + @Description("") + private String label; + @Description("") + private String abbreviatedLabel; + @Description("") + private String description; + private Language language; + + public Language getLanguage(){ + return language; + } + + /** + * + * @param newVal + */ + public void setLanguage(Language newVal){ + language = newVal; + } + + public String getLabel(){ + return label; + } + + /** + * + * @param newVal + */ + public void setLabel(String newVal){ + label = newVal; + } + + public String getAbbreviatedLabel(){ + return abbreviatedLabel; + } + + /** + * + * @param newVal + */ + public void setAbbreviatedLabel(String newVal){ + abbreviatedLabel = newVal; + } + + public String getDescription(){ + return description; + } + + /** + * + * @param newVal + */ + public void setDescription(String newVal){ + description = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Rights.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Rights.java new file mode 100644 index 0000000000..b94a463150 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Rights.java @@ -0,0 +1,98 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import org.apache.log4j.Logger; + +/** + * Typically, rights information includes a statement about various property + * rights associated with the resource, including intellectual property rights. + * http://purl.org/dc/elements/1.1/rights + * + * http://dublincore.org/documents/dcmi-terms/ + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:15 + */ +public class Rights extends VersionableEntity { + static Logger logger = Logger.getLogger(Rights.class); + + //external location of copyright text + @Description("external location of copyright text") + private String uri; + @Description("") + private String statement; + @Description("") + private String abbreviatedStatement; + private RightsTerm type; + private Language language; + + public RightsTerm getType(){ + return type; + } + + /** + * + * @param newVal + */ + public void setType(RightsTerm newVal){ + type = newVal; + } + + public Language getLanguage(){ + return language; + } + + /** + * + * @param newVal + */ + public void setLanguage(Language newVal){ + language = newVal; + } + + public String getUri(){ + return uri; + } + + /** + * + * @param newVal + */ + public void setUri(String newVal){ + uri = newVal; + } + + public String getStatement(){ + return statement; + } + + /** + * + * @param newVal + */ + public void setStatement(String newVal){ + statement = newVal; + } + + public String getAbbreviatedStatement(){ + return abbreviatedStatement; + } + + /** + * + * @param newVal + */ + public void setAbbreviatedStatement(String newVal){ + abbreviatedStatement = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/RightsTerm.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/RightsTerm.java new file mode 100644 index 0000000000..dffe2e3052 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/RightsTerm.java @@ -0,0 +1,38 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:15 + */ +public class RightsTerm extends DefinedTermBase { + static Logger logger = Logger.getLogger(RightsTerm.class); + + /** + * http://purl.org/dc/terms/accessRights + */ + public static final RightsTerm ACCESS_RIGHTS(){ + return null; + } + + public static final RightsTerm COPYRIGHT(){ + return null; + } + + public static final RightsTerm LICENSE(){ + return null; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/VersionableEntity.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/VersionableEntity.java index ef81291e20..5b2df15912 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/VersionableEntity.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/VersionableEntity.java @@ -1,149 +1,166 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.common; - - -import org.apache.log4j.Logger; - -import java.util.*; -import javax.persistence.*; - - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:18 - */ -@MappedSuperclass -public abstract class VersionableEntity extends CdmBase{ - static Logger logger = Logger.getLogger(VersionableEntity.class); - - - /*Default creator*/ - public static String createdWhoDefault = "test"; - - private Calendar createdWhen; - private String createdWho; - private int id; - private String notes; - private Calendar updatedWhen; - private String updatedWho; - //the globally unique identifier - private String uuid; - private ArrayList m_View; - - public Calendar getCreatedWhen(){ - if (createdWhen == null){ - createdWhen = Calendar.getInstance(); - } - return createdWhen; - } - - public String getCreatedWho(){ - if (createdWho == null){ - createdWho = createdWhoDefault; - } - return createdWho; - } - - @Id @GeneratedValue(generator="system-increment") - public int getId(){ - return id; - } - - public ArrayList getM_View(){ - return m_View; - } - - public String getNotes(){ - return notes; - } - - public Calendar getUpdatedWhen(){ - return updatedWhen; - } - - public String getUpdatedWho(){ - return updatedWho; - } - - public String getUuid(){ - if (uuid == null){ - uuid = UUID.randomUUID().toString(); - } - return uuid; - } - - /** - * - * @param newVal - */ - public void setCreatedWhen(Calendar newVal){ - createdWhen = newVal; - } - - /** - * - * @param newVal - */ - public void setCreatedWho(String newVal){ - createdWho = newVal; - } - - /** - * - * @param newVal - */ - public void setId(int newVal){ - id = newVal; - } - - /** - * - * @param newVal - */ - public void setM_View(ArrayList newVal){ - m_View = newVal; - } - - /** - * - * @param newVal - */ - public void setNotes(String newVal){ - notes = newVal; - } - - /** - * - * @param newVal - */ - public void setUpdatedWhen(Calendar newVal){ - updatedWhen = newVal; - } - - /** - * - * @param newVal - */ - public void setUpdatedWho(String newVal){ - updatedWho = newVal; - } - - /** - * - * @param newVal - */ - public void setUuid(String newVal){ - uuid = newVal; - } - - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.common; + + +import etaxonomy.cdm.model.agent.Person; +import etaxonomy.cdm.model.view.View; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:25 + */ +@MappedSuperclass +public abstract class VersionableEntity { + static Logger logger = Logger.getLogger(VersionableEntity.class); + + @Description("") + private int id; + //the globally unique identifier + @Description("the globally unique identifier") + private String uuid; + @Description("") + private Calendar created; + //time of last update for this object + @Description("time of last update for this object") + private Calendar updated; + private ArrayList m_View; + private VersionableEntity nextVersion; + private VersionableEntity previousVersion; + private Person updatedBy; + private Person createdBy; + + public ArrayList getM_View(){ + return m_View; + } + + /** + * + * @param newVal + */ + public void setM_View(ArrayList newVal){ + m_View = newVal; + } + + public VersionableEntity getNextVersion(){ + return nextVersion; + } + + /** + * + * @param newVal + */ + public void setNextVersion(VersionableEntity newVal){ + nextVersion = newVal; + } + + public VersionableEntity getPreviousVersion(){ + return previousVersion; + } + + /** + * + * @param newVal + */ + public void setPreviousVersion(VersionableEntity newVal){ + previousVersion = newVal; + } + + public Person getUpdatedBy(){ + return updatedBy; + } + + /** + * + * @param newVal + */ + public void setUpdatedBy(Person newVal){ + updatedBy = newVal; + } + + public Person getCreatedBy(){ + return createdBy; + } + + /** + * + * @param newVal + */ + public void setCreatedBy(Person newVal){ + createdBy = newVal; + } + + public int getId(){ + return id; + } + + /** + * + * @param newVal + */ + public void setId(int newVal){ + id = newVal; + } + + public String getUuid(){ + return uuid; + } + + /** + * + * @param newVal + */ + public void setUuid(String newVal){ + uuid = newVal; + } + + public Calendar getCreated(){ + return created; + } + + /** + * + * @param newVal + */ + public void setCreated(Calendar newVal){ + created = newVal; + } + + public Calendar getUpdated(){ + return updated; + } + + /** + * + * @param newVal + */ + public void setUpdated(Calendar newVal){ + updated = newVal; + } + + /** + * based on created + */ + @Transient + public Calendar getValidFrom(){ + return null; + } + + /** + * based on updated + */ + @Transient + public Calendar getValidTo(){ + return null; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/AbsenceTerm.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/AbsenceTerm.java new file mode 100644 index 0000000000..3466395a0c --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/AbsenceTerm.java @@ -0,0 +1,23 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:33 + */ +public class AbsenceTerm extends PresenceAbsenceTermBase { + static Logger logger = Logger.getLogger(AbsenceTerm.class); + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/CategoricalData.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/CategoricalData.java new file mode 100644 index 0000000000..8b0caf62bf --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/CategoricalData.java @@ -0,0 +1,52 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:39 + */ +public class CategoricalData extends FeatureBase { + static Logger logger = Logger.getLogger(CategoricalData.class); + + //whether the sequence of ordered states is important + @Description("whether the sequence of ordered states is important") + private boolean orderRelevant; + private java.util.ArrayList states; + + public java.util.ArrayList getStates(){ + return states; + } + + /** + * + * @param newVal + */ + public void setStates(java.util.ArrayList newVal){ + states = newVal; + } + + public boolean getOrderRelevant(){ + return orderRelevant; + } + + /** + * + * @param newVal + */ + public void setOrderRelevant(boolean newVal){ + orderRelevant = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/CharacterTree.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/CharacterTree.java new file mode 100644 index 0000000000..7c9dad8380 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/CharacterTree.java @@ -0,0 +1,40 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import etaxonomy.cdm.model.common.VersionableEntity; +import org.apache.log4j.Logger; + +/** + * Character trees arrange concepts and characters. They may also be used to + * define flat char. subsets for filtering purposes. + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:40 + */ +public class CharacterTree extends VersionableEntity { + static Logger logger = Logger.getLogger(CharacterTree.class); + + private ArrayList characters; + + public ArrayList getCharacters(){ + return characters; + } + + /** + * + * @param newVal + */ + public void setCharacters(ArrayList newVal){ + characters = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Source.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/CommonTaxonName.java similarity index 51% rename from cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Source.java rename to cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/CommonTaxonName.java index ea92bc4144..c674afa474 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Source.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/CommonTaxonName.java @@ -1,53 +1,53 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.common; - - -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:12 - */ -@Entity -public class Source extends VersionableEntity { - static Logger logger = Logger.getLogger(Source.class); - - private String name; - private String version; - - public String getName(){ - return name; - } - - public String getVersion(){ - return version; - } - - /** - * - * @param newVal - */ - public void setName(String newVal){ - name = newVal; - } - - /** - * - * @param newVal - */ - public void setVersion(String newVal){ - version = newVal; - } - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import etaxonomy.cdm.model.common.Language; +import org.apache.log4j.Logger; + +/** + * only valid for Taxa, not specimen/occurrences. Check DescriptionBase relation. + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:40 + */ +public class CommonTaxonName extends FeatureBase { + static Logger logger = Logger.getLogger(CommonTaxonName.class); + + @Description("") + private String name; + private Language language; + + public Language getLanguage(){ + return language; + } + + /** + * + * @param newVal + */ + public void setLanguage(Language newVal){ + language = newVal; + } + + public String getName(){ + return name; + } + + /** + * + * @param newVal + */ + public void setName(String newVal){ + name = newVal; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/Description.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/Description.java new file mode 100644 index 0000000000..b024240109 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/Description.java @@ -0,0 +1,93 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import etaxonomy.cdm.model.location.NamedArea; +import etaxonomy.cdm.model.common.IdentifiableEntity; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:44 + */ +public class Description extends IdentifiableEntity { + static Logger logger = Logger.getLogger(Description.class); + + //in 95% of all cases this will be the taxon name. getLabel() should return the taxon name in case label is null. + @Description("in 95% of all cases this will be the taxon name. getLabel() should return the taxon name in case label is null.") + private String label; + private ArrayList sources; + private ArrayList geoScopes; + private ArrayList scopes; + private ArrayList features; + + public ArrayList getSources(){ + return sources; + } + + /** + * + * @param newVal + */ + public void setSources(ArrayList newVal){ + sources = newVal; + } + + public ArrayList getGeoScopes(){ + return geoScopes; + } + + /** + * + * @param newVal + */ + public void setGeoScopes(ArrayList newVal){ + geoScopes = newVal; + } + + public ArrayList getScopes(){ + return scopes; + } + + /** + * + * @param newVal + */ + public void setScopes(ArrayList newVal){ + scopes = newVal; + } + + public ArrayList getFeatures(){ + return features; + } + + /** + * + * @param newVal + */ + public void setFeatures(ArrayList newVal){ + features = newVal; + } + + public String getLabel(){ + return label; + } + + /** + * + * @param newVal + */ + public void setLabel(String newVal){ + label = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/DescriptionInSource.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/DescriptionInSource.java new file mode 100644 index 0000000000..5ab369d569 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/DescriptionInSource.java @@ -0,0 +1,24 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import etaxonomy.cdm.model.common.EntityInSourceBase; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:44 + */ +public class DescriptionInSource extends EntityInSourceBase { + static Logger logger = Logger.getLogger(DescriptionInSource.class); + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/DescriptiveConcept.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/DescriptiveConcept.java new file mode 100644 index 0000000000..bea414615c --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/DescriptiveConcept.java @@ -0,0 +1,28 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import etaxonomy.cdm.model.common.VersionableEntity; +import org.apache.log4j.Logger; + +/** + * Descriptive concepts (properties, object parts, observation methods, etc.) + * define an optional ontology for descriptions. In contrast to characters, + * concepts can not be scored in descriptions. - Reusable states and char. + * dependencies are expressed here as well. + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:45 + */ +public class DescriptiveConcept extends VersionableEntity { + static Logger logger = Logger.getLogger(DescriptiveConcept.class); + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/Distribution.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/Distribution.java new file mode 100644 index 0000000000..9de16304bc --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/Distribution.java @@ -0,0 +1,57 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import etaxonomy.cdm.model.location.NamedArea; +import org.apache.log4j.Logger; + +/** + * fact attribute contains the concrete occurrence term like "Extinct" + * This allows all terms to enter the database and classify them basically + * according to class hierarchy of distribution. + * + * {validInRegion mandatory} + * {type is "distribution"} + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:45 + */ +public class Distribution extends FeatureBase { + static Logger logger = Logger.getLogger(Distribution.class); + + private NamedArea area; + private PresenceAbsenceTermBase status; + + public NamedArea getArea(){ + return area; + } + + /** + * + * @param newVal + */ + public void setArea(NamedArea newVal){ + area = newVal; + } + + public PresenceAbsenceTermBase getStatus(){ + return status; + } + + /** + * + * @param newVal + */ + public void setStatus(PresenceAbsenceTermBase newVal){ + status = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/DiurnalTerm.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/DiurnalTerm.java new file mode 100644 index 0000000000..3e3925ae2e --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/DiurnalTerm.java @@ -0,0 +1,23 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:46 + */ +public class DiurnalTerm extends Scope { + static Logger logger = Logger.getLogger(DiurnalTerm.class); + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/FeatureBase.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/FeatureBase.java new file mode 100644 index 0000000000..2dffdfd562 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/FeatureBase.java @@ -0,0 +1,94 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import etaxonomy.cdm.model.reference.StrictReferenceBase; +import etaxonomy.cdm.model.common.Media; +import etaxonomy.cdm.model.common.IReferencedEntity; +import etaxonomy.cdm.model.common.AnnotatableEntity; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:48 + */ +public abstract class FeatureBase extends AnnotatableEntity implements IReferencedEntity { + static Logger logger = Logger.getLogger(FeatureBase.class); + + @Description("") + private String modifyingText; + private ArrayList media; + /** + * type, category of information. In structured descriptions characters + */ + private FeatureType type; + private ArrayList modifiers; + + public ArrayList getMedia(){ + return media; + } + + /** + * + * @param newVal + */ + public void setMedia(ArrayList newVal){ + media = newVal; + } + + public FeatureType getType(){ + return type; + } + + /** + * + * @param newVal + */ + public void setType(FeatureType newVal){ + type = newVal; + } + + public ArrayList getModifiers(){ + return modifiers; + } + + /** + * + * @param newVal + */ + public void setModifiers(ArrayList newVal){ + modifiers = newVal; + } + + public String getModifyingText(){ + return modifyingText; + } + + /** + * + * @param newVal + */ + public void setModifyingText(String newVal){ + modifyingText = newVal; + } + + @Transient + public String getCitation(){ + return ""; + } + + @Transient + public StrictReferenceBase getCitation(){ + return null; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/FeatureType.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/FeatureType.java new file mode 100644 index 0000000000..d6d7574f13 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/FeatureType.java @@ -0,0 +1,167 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import etaxonomy.cdm.model.common.DefinedTermBase; +import etaxonomy.cdm.model.common.Enumeration; +import org.apache.log4j.Logger; + +/** + * NEEDS TO BE COMPLEMENTED + * SPM / TDWG + * http://rs.tdwg.org/ontology/voc/SpeciesProfileModel + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:49 + */ +public class FeatureType extends DefinedTermBase { + static Logger logger = Logger.getLogger(FeatureType.class); + + @Description("") + private boolean supportsQuantitativeData; + @Description("") + private boolean supportsTextData; + @Description("") + private boolean supportsDistribution; + @Description("") + private boolean supportsIndividualAssociation; + @Description("") + private boolean supportsTaxonInteraction; + @Description("") + private boolean supportsCommonTaxonName; + private ArrayList recommendedModifierEnumeration; + private ArrayList recommendedStatisticalMeasures; + private ArrayList supportedCategoricalEnumerations; + + public ArrayList getRecommendedModifierEnumeration(){ + return recommendedModifierEnumeration; + } + + /** + * + * @param newVal + */ + public void setRecommendedModifierEnumeration(ArrayList newVal){ + recommendedModifierEnumeration = newVal; + } + + public ArrayList getRecommendedStatisticalMeasures(){ + return recommendedStatisticalMeasures; + } + + /** + * + * @param newVal + */ + public void setRecommendedStatisticalMeasures(ArrayList newVal){ + recommendedStatisticalMeasures = newVal; + } + + public ArrayList getSupportedCategoricalEnumerations(){ + return supportedCategoricalEnumerations; + } + + /** + * + * @param newVal + */ + public void setSupportedCategoricalEnumerations(ArrayList newVal){ + supportedCategoricalEnumerations = newVal; + } + + public boolean getSupportsQuantitativeData(){ + return supportsQuantitativeData; + } + + /** + * + * @param newVal + */ + public void setSupportsQuantitativeData(boolean newVal){ + supportsQuantitativeData = newVal; + } + + public boolean getSupportsTextData(){ + return supportsTextData; + } + + /** + * + * @param newVal + */ + public void setSupportsTextData(boolean newVal){ + supportsTextData = newVal; + } + + public boolean getSupportsDistribution(){ + return supportsDistribution; + } + + /** + * + * @param newVal + */ + public void setSupportsDistribution(boolean newVal){ + supportsDistribution = newVal; + } + + public boolean getSupportsIndividualAssociation(){ + return supportsIndividualAssociation; + } + + /** + * + * @param newVal + */ + public void setSupportsIndividualAssociation(boolean newVal){ + supportsIndividualAssociation = newVal; + } + + public boolean getSupportsTaxonInteraction(){ + return supportsTaxonInteraction; + } + + /** + * + * @param newVal + */ + public void setSupportsTaxonInteraction(boolean newVal){ + supportsTaxonInteraction = newVal; + } + + public boolean getSupportsCommonTaxonName(){ + return supportsCommonTaxonName; + } + + /** + * + * @param newVal + */ + public void setSupportsCommonTaxonName(boolean newVal){ + supportsCommonTaxonName = newVal; + } + + public static final FeatureType DISTRIBUTION(){ + return null; + } + + /** + * special kind of OrganismInteraction + */ + public static final FeatureType HYBRID_PARENT(){ + return null; + } + + public static final FeatureType COMMON_NAME(){ + return null; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/IdentificationKey.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/IdentificationKey.java new file mode 100644 index 0000000000..bcdcb32010 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/IdentificationKey.java @@ -0,0 +1,42 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import etaxonomy.cdm.model.taxon.Taxon; +import etaxonomy.cdm.model.common.Media; +import etaxonomy.cdm.model.common.VersionableEntity; +import org.apache.log4j.Logger; + +/** + * Dichotomous or multifurcating + * authored keys (incl. legacy data) + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:52 + */ +public class IdentificationKey extends Media VersionableEntity { + static Logger logger = Logger.getLogger(IdentificationKey.class); + + private ArrayList coveredTaxa; + + public ArrayList getCoveredTaxa(){ + return coveredTaxa; + } + + /** + * + * @param newVal + */ + public void setCoveredTaxa(ArrayList newVal){ + coveredTaxa = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/IndividualsAssociation.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/IndividualsAssociation.java new file mode 100644 index 0000000000..525f951c92 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/IndividualsAssociation.java @@ -0,0 +1,54 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import etaxonomy.cdm.model.common.MultilanguageString; +import etaxonomy.cdm.model.occurrence.ObservationalUnit; +import org.apache.log4j.Logger; + +/** + * {type is "host" or "hybrid_parent"} + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:53 + */ +public class IndividualsAssociation extends FeatureBase { + static Logger logger = Logger.getLogger(IndividualsAssociation.class); + + @Description("") + private MultilanguageString description; + private ObservationalUnit observationalUnit2; + + public ObservationalUnit getObservationalUnit2(){ + return observationalUnit2; + } + + /** + * + * @param newVal + */ + public void setObservationalUnit2(ObservationalUnit newVal){ + observationalUnit2 = newVal; + } + + public MultilanguageString getDescription(){ + return description; + } + + /** + * + * @param newVal + */ + public void setDescription(MultilanguageString newVal){ + description = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/MeasurementUnit.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/MeasurementUnit.java new file mode 100644 index 0000000000..256f50a473 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/MeasurementUnit.java @@ -0,0 +1,26 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import etaxonomy.cdm.model.common.EnumeratedTermBase; +import org.apache.log4j.Logger; + +/** + * This class contains the measurement units such as "centimeter" or "degree + * Celsius" + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:59 + */ +public class MeasurementUnit extends EnumeratedTermBase { + static Logger logger = Logger.getLogger(MeasurementUnit.class); + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/Modifier.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/Modifier.java new file mode 100644 index 0000000000..8d9e1dcef1 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/Modifier.java @@ -0,0 +1,26 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import etaxonomy.cdm.model.common.EnumeratedTermBase; +import org.apache.log4j.Logger; + +/** + * This class contains possible modulations for the InfoItems such as "variance", + * "maximum", "often", "probably" + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:00 + */ +public class Modifier extends EnumeratedTermBase { + static Logger logger = Logger.getLogger(Modifier.class); + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/Paragraph.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/Paragraph.java new file mode 100644 index 0000000000..ab40756c41 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/Paragraph.java @@ -0,0 +1,52 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import etaxonomy.cdm.model.common.VersionableEntity; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:06 + */ +public class Paragraph extends VersionableEntity { + static Logger logger = Logger.getLogger(Paragraph.class); + + @Description("") + private String content; + private TextFormat format; + + public TextFormat getFormat(){ + return format; + } + + /** + * + * @param newVal + */ + public void setFormat(TextFormat newVal){ + format = newVal; + } + + public String getContent(){ + return content; + } + + /** + * + * @param newVal + */ + public void setContent(String newVal){ + content = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/PresenceAbsenceTermBase.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/PresenceAbsenceTermBase.java new file mode 100644 index 0000000000..414c6867dc --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/PresenceAbsenceTermBase.java @@ -0,0 +1,24 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import etaxonomy.cdm.model.common.EnumeratedTermBase; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:09 + */ +public abstract class PresenceAbsenceTermBase extends EnumeratedTermBase { + static Logger logger = Logger.getLogger(PresenceAbsenceTermBase.class); + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/PresenceTerm.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/PresenceTerm.java new file mode 100644 index 0000000000..fb1e1a5629 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/PresenceTerm.java @@ -0,0 +1,23 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:09 + */ +public class PresenceTerm extends PresenceAbsenceTermBase { + static Logger logger = Logger.getLogger(PresenceTerm.class); + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/QuantitativeData.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/QuantitativeData.java new file mode 100644 index 0000000000..395888bff5 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/QuantitativeData.java @@ -0,0 +1,70 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:11 + */ +public class QuantitativeData extends FeatureBase { + static Logger logger = Logger.getLogger(QuantitativeData.class); + + private MeasurementUnit unit; + private ArrayList statisticalValues; + + public ArrayList getStatisticalValues(){ + return statisticalValues; + } + + /** + * + * @param newVal + */ + public void setStatisticalValues(ArrayList newVal){ + statisticalValues = newVal; + } + + public MeasurementUnit getUnit(){ + return unit; + } + + /** + * + * @param newVal + */ + public void setUnit(MeasurementUnit newVal){ + unit = newVal; + } + + @Transient + public float getMin(){ + return null; + } + + @Transient + public float getMax(){ + return null; + } + + @Transient + public float getTypicalLowerBoundary(){ + return null; + } + + @Transient + public float getTypicalUpperBoundary(){ + return null; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/Scope.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/Scope.java new file mode 100644 index 0000000000..2f24aef645 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/Scope.java @@ -0,0 +1,23 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:15 + */ +public class Scope extends Modifier { + static Logger logger = Logger.getLogger(Scope.class); + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/SeasonalTerm.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/SeasonalTerm.java new file mode 100644 index 0000000000..735fe01bfb --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/SeasonalTerm.java @@ -0,0 +1,23 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:15 + */ +public class SeasonalTerm extends Scope { + static Logger logger = Logger.getLogger(SeasonalTerm.class); + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/NomenclaturalReference.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/Sex.java similarity index 64% rename from cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/NomenclaturalReference.java rename to cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/Sex.java index 6c68b71229..ca4d6465af 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/NomenclaturalReference.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/Sex.java @@ -1,22 +1,23 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.publication; - - -import org.apache.log4j.Logger; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:10 - */ -public interface NomenclaturalReference { - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:17 + */ +public class Sex extends Scope { + static Logger logger = Logger.getLogger(Sex.class); + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/Stage.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/Stage.java new file mode 100644 index 0000000000..d012b3282f --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/Stage.java @@ -0,0 +1,23 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:18 + */ +public class Stage extends Scope { + static Logger logger = Logger.getLogger(Stage.class); + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NameFactType.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/State.java similarity index 56% rename from cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NameFactType.java rename to cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/State.java index 99901fdafe..87daf0c708 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NameFactType.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/State.java @@ -1,24 +1,24 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.name; - - -import org.apache.log4j.Logger; - -/** - * The list should be extensible at runtime through configuration. This needs to - * be investigated. - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:08 - */ -public enum NameFactType { - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import etaxonomy.cdm.model.common.EnumeratedTermBase; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:18 + */ +public class State extends EnumeratedTermBase { + static Logger logger = Logger.getLogger(State.class); + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/StateData.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/StateData.java new file mode 100644 index 0000000000..a21666d517 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/StateData.java @@ -0,0 +1,65 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import etaxonomy.cdm.model.common.VersionableEntity; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:18 + */ +public class StateData extends VersionableEntity { + static Logger logger = Logger.getLogger(StateData.class); + + @Description("") + private String modifyingText; + private State state; + private ArrayList modifiers; + + public State getState(){ + return state; + } + + /** + * + * @param newVal + */ + public void setState(State newVal){ + state = newVal; + } + + public ArrayList getModifiers(){ + return modifiers; + } + + /** + * + * @param newVal + */ + public void setModifiers(ArrayList newVal){ + modifiers = newVal; + } + + public String getModifyingText(){ + return modifyingText; + } + + /** + * + * @param newVal + */ + public void setModifyingText(String newVal){ + modifyingText = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/StatisticalMeasure.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/StatisticalMeasure.java new file mode 100644 index 0000000000..87ced1419f --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/StatisticalMeasure.java @@ -0,0 +1,52 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import etaxonomy.cdm.model.common.DefinedTermBase; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:19 + */ +public class StatisticalMeasure extends DefinedTermBase { + static Logger logger = Logger.getLogger(StatisticalMeasure.class); + + public static final StatisticalMeasure MIN(){ + return null; + } + + public static final StatisticalMeasure MAX(){ + return null; + } + + public static final StatisticalMeasure AVERAGE(){ + return null; + } + + public static final StatisticalMeasure SAMPLE_SIZE(){ + return null; + } + + public static final StatisticalMeasure VARIANCE(){ + return null; + } + + public static final StatisticalMeasure TYPICAL_LOWER_BOUNDARY(){ + return null; + } + + public static final StatisticalMeasure TYPICAL_UPPER_BOUNDARY(){ + return null; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/StatisticalMeasurementValue.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/StatisticalMeasurementValue.java new file mode 100644 index 0000000000..d5a8349579 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/StatisticalMeasurementValue.java @@ -0,0 +1,65 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import etaxonomy.cdm.model.common.VersionableEntity; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:19 + */ +public class StatisticalMeasurementValue extends VersionableEntity { + static Logger logger = Logger.getLogger(StatisticalMeasurementValue.class); + + @Description("") + private float value; + private StatisticalMeasure type; + private ArrayList modifiers; + + public StatisticalMeasure getType(){ + return type; + } + + /** + * + * @param newVal + */ + public void setType(StatisticalMeasure newVal){ + type = newVal; + } + + public ArrayList getModifiers(){ + return modifiers; + } + + /** + * + * @param newVal + */ + public void setModifiers(ArrayList newVal){ + modifiers = newVal; + } + + public float getValue(){ + return value; + } + + /** + * + * @param newVal + */ + public void setValue(float newVal){ + value = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/TaxonInteraction.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/TaxonInteraction.java new file mode 100644 index 0000000000..d8ea6fda29 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/TaxonInteraction.java @@ -0,0 +1,54 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import etaxonomy.cdm.model.common.MultilanguageString; +import etaxonomy.cdm.model.taxon.TaxonBase; +import org.apache.log4j.Logger; + +/** + * FIXME + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:21 + */ +public class TaxonInteraction extends FeatureBase { + static Logger logger = Logger.getLogger(TaxonInteraction.class); + + @Description("") + private MultilanguageString description; + private TaxonBase taxon2; + + public TaxonBase getTaxon2(){ + return taxon2; + } + + /** + * + * @param newVal + */ + public void setTaxon2(TaxonBase newVal){ + taxon2 = newVal; + } + + public MultilanguageString getDescription(){ + return description; + } + + /** + * + * @param newVal + */ + public void setDescription(MultilanguageString newVal){ + description = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/TextData.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/TextData.java new file mode 100644 index 0000000000..a285594bfb --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/TextData.java @@ -0,0 +1,51 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import etaxonomy.cdm.model.common.Language; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:23 + */ +public class TextData extends FeatureBase { + static Logger logger = Logger.getLogger(TextData.class); + + private Language language; + private java.util.ArrayList m_Paragraph; + + public java.util.ArrayList getM_Paragraph(){ + return m_Paragraph; + } + + /** + * + * @param newVal + */ + public void setM_Paragraph(java.util.ArrayList newVal){ + m_Paragraph = newVal; + } + + public Language getLanguage(){ + return language; + } + + /** + * + * @param newVal + */ + public void setLanguage(Language newVal){ + language = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/TextFormat.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/TextFormat.java new file mode 100644 index 0000000000..4f5db205b4 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/description/TextFormat.java @@ -0,0 +1,26 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.description; + + +import etaxonomy.cdm.model.common.DefinedTermBase; +import org.apache.log4j.Logger; + +/** + * kind of format used for structuring text. E.g. xml schema namespace, rdf, or + * any other format + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:24 + */ +public class TextFormat extends DefinedTermBase { + static Logger logger = Logger.getLogger(TextFormat.class); + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/location/Continent.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/location/Continent.java new file mode 100644 index 0000000000..1120e3898d --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/location/Continent.java @@ -0,0 +1,52 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.location; + + +import etaxonomy.cdm.model.common.DefinedTermBase; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:42 + */ +public class Continent extends DefinedTermBase { + static Logger logger = Logger.getLogger(Continent.class); + + public static final Continent EUROPE(){ + return null; + } + + public static final Continent AFRICA(){ + return null; + } + + public static final Continent ASIA(){ + return null; + } + + public static final Continent NORTH_AMERICA(){ + return null; + } + + public static final Continent ANTARCTICA(){ + return null; + } + + public static final Continent SOUTH_AMERICA(){ + return null; + } + + public static final Continent OCEANIA(){ + return null; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/location/NamedArea.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/location/NamedArea.java new file mode 100644 index 0000000000..c2e36a59f9 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/location/NamedArea.java @@ -0,0 +1,122 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.location; + + +import etaxonomy.cdm.model.common.EnumeratedTermBase; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:01 + */ +public class NamedArea extends EnumeratedTermBase { + static Logger logger = Logger.getLogger(NamedArea.class); + + //description of this area + @Description("description of this area") + private String description; + //description of time valid context of this area. e.g. year range + @Description("description of time valid context of this area. e.g. year range") + private TimePeriod validPeriod; + //Binary shape definition for user's defined area as polygon + @Description("Binary shape definition for user's defined area as polygon") + private Binary shapeFile; + private NamedAreaInSource source; + private ArrayList countriesOrWaterbodies; + private NamedAreaType type; + private NamedAreaLevel level; + + public NamedAreaInSource getSource(){ + return source; + } + + /** + * + * @param newVal + */ + public void setSource(NamedAreaInSource newVal){ + source = newVal; + } + + public ArrayList getCountriesOrWaterbodies(){ + return countriesOrWaterbodies; + } + + /** + * + * @param newVal + */ + public void setCountriesOrWaterbodies(ArrayList newVal){ + countriesOrWaterbodies = newVal; + } + + public NamedAreaType getType(){ + return type; + } + + /** + * + * @param newVal + */ + public void setType(NamedAreaType newVal){ + type = newVal; + } + + public NamedAreaLevel getLevel(){ + return level; + } + + /** + * + * @param newVal + */ + public void setLevel(NamedAreaLevel newVal){ + level = newVal; + } + + public String getDescription(){ + return description; + } + + /** + * + * @param newVal + */ + public void setDescription(String newVal){ + description = newVal; + } + + public TimePeriod getValidPeriod(){ + return validPeriod; + } + + /** + * + * @param newVal + */ + public void setValidPeriod(TimePeriod newVal){ + validPeriod = newVal; + } + + public Binary getShapeFile(){ + return shapeFile; + } + + /** + * + * @param newVal + */ + public void setShapeFile(Binary newVal){ + shapeFile = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/location/NamedAreaInSource.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/location/NamedAreaInSource.java new file mode 100644 index 0000000000..5f71dd69a3 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/location/NamedAreaInSource.java @@ -0,0 +1,24 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.location; + + +import etaxonomy.cdm.model.common.EntityInSourceBase; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:02 + */ +public class NamedAreaInSource extends EntityInSourceBase { + static Logger logger = Logger.getLogger(NamedAreaInSource.class); + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/location/NamedAreaLevel.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/location/NamedAreaLevel.java new file mode 100644 index 0000000000..deef8247dc --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/location/NamedAreaLevel.java @@ -0,0 +1,67 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.location; + + +import etaxonomy.cdm.model.common.EnumeratedTermBase; +import org.apache.log4j.Logger; + +/** + * Controlled vocabulary to diferenctiate levels of areas such as province, state, + * etc. + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:02 + */ +public class NamedAreaLevel extends EnumeratedTermBase { + static Logger logger = Logger.getLogger(NamedAreaLevel.class); + + /** + * continents + */ + public static final NamedAreaLevel TDWG_LEVEL1(){ + return null; + } + + /** + * larger regions + */ + public static final NamedAreaLevel TDWG_LEVEL2(){ + return null; + } + + /** + * mostly countries + */ + public static final NamedAreaLevel TDWG_LEVEL3(){ + return null; + } + + public static final NamedAreaLevel TDWG_LEVEL4(){ + return null; + } + + public static final NamedAreaLevel NATURE_RESERVE(){ + return null; + } + + public static final NamedAreaLevel STATE(){ + return null; + } + + public static final NamedAreaLevel PROVINCE(){ + return null; + } + + public static final NamedAreaLevel TOWN(){ + return null; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/location/NamedAreaType.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/location/NamedAreaType.java new file mode 100644 index 0000000000..782c9dbf5a --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/location/NamedAreaType.java @@ -0,0 +1,39 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.location; + + +import etaxonomy.cdm.model.common.DefinedTermBase; +import org.apache.log4j.Logger; + +/** + * Controlled vocabulary to diferenctiate categories of areas + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:02 + */ +public class NamedAreaType extends DefinedTermBase { + static Logger logger = Logger.getLogger(NamedAreaType.class); + + /** + * The boundaries are given by natural factors (mountains, valleys, climate, etc.) + */ + public static final NamedAreaType NATURAL_AREA(){ + return null; + } + + /** + * The boundaries depend on administration (county, state, reserve, etc.) + */ + public static final NamedAreaType ADMINISTRATION_AREA(){ + return null; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/location/Point.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/location/Point.java new file mode 100644 index 0000000000..a4cbb10060 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/location/Point.java @@ -0,0 +1,81 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.location; + + +import etaxonomy.cdm.model.common.VersionableEntity; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:08 + */ +public class Point extends VersionableEntity { + static Logger logger = Logger.getLogger(Point.class); + + @Description("") + private float longitude; + @Description("") + private float latitude; + //in Meters + @Description("in Meters") + private int errorRadius; + private ReferenceSystem referenceSystem; + + public ReferenceSystem getReferenceSystem(){ + return referenceSystem; + } + + /** + * + * @param newVal + */ + public void setReferenceSystem(ReferenceSystem newVal){ + referenceSystem = newVal; + } + + public float getLongitude(){ + return longitude; + } + + /** + * + * @param newVal + */ + public void setLongitude(float newVal){ + longitude = newVal; + } + + public float getLatitude(){ + return latitude; + } + + /** + * + * @param newVal + */ + public void setLatitude(float newVal){ + latitude = newVal; + } + + public int getErrorRadius(){ + return errorRadius; + } + + /** + * + * @param newVal + */ + public void setErrorRadius(int newVal){ + errorRadius = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonFactType.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/location/ReferenceSystem.java similarity index 50% rename from cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonFactType.java rename to cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/location/ReferenceSystem.java index 8e7227c03e..70954bd89c 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonFactType.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/location/ReferenceSystem.java @@ -1,24 +1,32 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.taxon; - - -import org.apache.log4j.Logger; - -/** - * The list should be extensible at runtime through configuration. This needs to - * be investigated. - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:15 - */ -public enum TaxonFactType { - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.location; + + +import etaxonomy.cdm.model.common.DefinedTermBase; +import org.apache.log4j.Logger; + +/** + * Reference systems for coordinates also according to OGC (Open Geographical + * Consosrtium) + * The list should be extensible at runtime through configuration. This needs to + * be investigated. + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:14 + */ +public class ReferenceSystem extends DefinedTermBase { + static Logger logger = Logger.getLogger(ReferenceSystem.class); + + public static final ReferenceSystem WGS84(){ + return null; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/location/WaterbodyOrCountry.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/location/WaterbodyOrCountry.java new file mode 100644 index 0000000000..e7cc2a5925 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/location/WaterbodyOrCountry.java @@ -0,0 +1,107 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.location; + + +import etaxonomy.cdm.model.common.DefinedTermBase; +import org.apache.log4j.Logger; + +/** + * +/- current ISO codes. year given with each entry + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:27 + */ +public class WaterbodyOrCountry extends DefinedTermBase { + static Logger logger = Logger.getLogger(WaterbodyOrCountry.class); + + @Description("") + private String iso2code; + @Description("") + private TimePeriod validPeriod; + private ArrayList continents; + + public ArrayList getContinents(){ + return continents; + } + + /** + * + * @param newVal + */ + public void setContinents(ArrayList newVal){ + continents = newVal; + } + + public String getIso2code(){ + return iso2code; + } + + /** + * + * @param newVal + */ + public void setIso2code(String newVal){ + iso2code = newVal; + } + + public TimePeriod getValidPeriod(){ + return validPeriod; + } + + /** + * + * @param newVal + */ + public void setValidPeriod(TimePeriod newVal){ + validPeriod = newVal; + } + + public static final WaterbodyOrCountry ARCTIC_OCEAN(){ + return null; + } + + public static final WaterbodyOrCountry ATLANTIC_OCEAN(){ + return null; + } + + public static final WaterbodyOrCountry PACIFIC_OCEAN(){ + return null; + } + + public static final WaterbodyOrCountry INDIAN_OCEAN(){ + return null; + } + + public static final WaterbodyOrCountry SOUTHERN_OCEAN(){ + return null; + } + + public static final WaterbodyOrCountry MEDITERRANEAN_SEA(){ + return null; + } + + public static final WaterbodyOrCountry BLACK_SEA(){ + return null; + } + + public static final WaterbodyOrCountry CASPIAN_SEA(){ + return null; + } + + public static final WaterbodyOrCountry RED_SEA(){ + return null; + } + + public static final WaterbodyOrCountry PERSIAN_GULF(){ + return null; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/molecular/DnaSample.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/molecular/DnaSample.java new file mode 100644 index 0000000000..17e93d9f72 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/molecular/DnaSample.java @@ -0,0 +1,112 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.molecular; + + +import etaxonomy.cdm.model.occurrence.Collection; +import etaxonomy.cdm.model.common.IdentifiableEntity; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:46 + */ +public class DnaSample extends IdentifiableEntity { + static Logger logger = Logger.getLogger(DnaSample.class); + + @Description("") + private String bankNumber; + //Notes on extraction, purification or amplification process + @Description("Notes on extraction, purification or amplification process") + private String productionNotes; + @Description("") + private Calendar dateProduced; + private ArrayList sequences; + private TissueSample extractedFrom; + private Collection storedAt; + + public ArrayList getSequences(){ + return sequences; + } + + /** + * + * @param newVal + */ + public void setSequences(ArrayList newVal){ + sequences = newVal; + } + + public Collection getStoredAt(){ + return storedAt; + } + + /** + * + * @param newVal + */ + public void setStoredAt(Collection newVal){ + storedAt = newVal; + } + + public TissueSample getExtractedFrom(){ + return extractedFrom; + } + + /** + * + * @param newVal + */ + public void setExtractedFrom(TissueSample newVal){ + extractedFrom = newVal; + } + + public String getBankNumber(){ + return bankNumber; + } + + /** + * + * @param newVal + */ + public void setBankNumber(String newVal){ + bankNumber = newVal; + } + + public String getProductionNotes(){ + return productionNotes; + } + + /** + * + * @param newVal + */ + public void setProductionNotes(String newVal){ + productionNotes = newVal; + } + + public Calendar getDateProduced(){ + return dateProduced; + } + + /** + * + * @param newVal + */ + public void setDateProduced(Calendar newVal){ + dateProduced = newVal; + } + + public String generateTitle(){ + return ""; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/molecular/GenBankAccession.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/molecular/GenBankAccession.java new file mode 100644 index 0000000000..4d30738765 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/molecular/GenBankAccession.java @@ -0,0 +1,53 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.molecular; + + +import etaxonomy.cdm.model.common.VersionableEntity; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:50 + */ +public class GenBankAccession extends VersionableEntity { + static Logger logger = Logger.getLogger(GenBankAccession.class); + + @Description("") + private String accessionNumber; + @Description("") + private String uri; + + public String getAccessionNumber(){ + return accessionNumber; + } + + /** + * + * @param newVal + */ + public void setAccessionNumber(String newVal){ + accessionNumber = newVal; + } + + public String getUri(){ + return uri; + } + + /** + * + * @param newVal + */ + public void setUri(String newVal){ + uri = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/view/Group.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/molecular/Locus.java similarity index 55% rename from cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/view/Group.java rename to cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/molecular/Locus.java index 8cdd33b6a2..e5d9b1823d 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/view/Group.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/molecular/Locus.java @@ -1,53 +1,54 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.view; - - -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:04 - */ -@Entity -public class Group { - static Logger logger = Logger.getLogger(Group.class); - - private String description; - private String location; - - public String getDescription(){ - return description; - } - - public String getLocation(){ - return location; - } - - /** - * - * @param newVal - */ - public void setDescription(String newVal){ - description = newVal; - } - - /** - * - * @param newVal - */ - public void setLocation(String newVal){ - location = newVal; - } - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.molecular; + + +import etaxonomy.cdm.model.common.VersionableEntity; +import org.apache.log4j.Logger; + +/** + * The region name of a DNA string. E.g. 18S, COX, etc. + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:58 + */ +public class Locus extends VersionableEntity { + static Logger logger = Logger.getLogger(Locus.class); + + @Description("") + private String name; + @Description("") + private String description; + + public String getName(){ + return name; + } + + /** + * + * @param newVal + */ + public void setName(String newVal){ + name = newVal; + } + + public String getDescription(){ + return description; + } + + /** + * + * @param newVal + */ + public void setDescription(String newVal){ + description = newVal; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/molecular/PhylogeneticTree.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/molecular/PhylogeneticTree.java new file mode 100644 index 0000000000..35e6c0e1c8 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/molecular/PhylogeneticTree.java @@ -0,0 +1,38 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.molecular; + + +import etaxonomy.cdm.model.common.ReferencedMedia; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:08 + */ +public class PhylogeneticTree extends ReferencedMedia { + static Logger logger = Logger.getLogger(PhylogeneticTree.class); + + private ArrayList usedSequences; + + public ArrayList getUsedSequences(){ + return usedSequences; + } + + /** + * + * @param newVal + */ + public void setUsedSequences(ArrayList newVal){ + usedSequences = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/molecular/Sequence.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/molecular/Sequence.java new file mode 100644 index 0000000000..618c1e83c0 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/molecular/Sequence.java @@ -0,0 +1,183 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.molecular; + + +import etaxonomy.cdm.model.reference.ReferenceBase; +import etaxonomy.cdm.model.reference.StrictReferenceBase; +import etaxonomy.cdm.model.common.IdentifiableEntity; +import etaxonomy.cdm.model.common.Media; +import etaxonomy.cdm.model.common.IReferencedEntity; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:16 + */ +public class Sequence extends IdentifiableEntity implements IReferencedEntity { + static Logger logger = Logger.getLogger(Sequence.class); + + //the sequence as a string of base pairs. 5'->3' + @Description("the sequence as a string of base pairs. 5'->3'") + private String sequence; + //should be calculated in case sequence is set + @Description("should be calculated in case sequence is set") + private int length; + //should be calculated in case sequence is set + @Description("should be calculated in case sequence is set") + private Calendar dateSequenced; + //should be calculated in case sequence is set + @Description("should be calculated in case sequence is set") + private boolean isBarcode; + //the sequence as a string of base pairs. 5'->3' + @Description("the sequence as a string of base pairs. 5'->3'") + private String citationMicroReference; + private ReferenceBase publishedIn; + private ArrayList citations; + private ArrayList chromatograms; + private ArrayList genBankAccession; + private Locus locus; + + public Locus getLocus(){ + return locus; + } + + /** + * + * @param newVal + */ + public void setLocus(Locus newVal){ + locus = newVal; + } + + public ReferenceBase getPublishedIn(){ + return publishedIn; + } + + /** + * + * @param newVal + */ + public void setPublishedIn(ReferenceBase newVal){ + publishedIn = newVal; + } + + public ArrayList getChromatograms(){ + return chromatograms; + } + + /** + * + * @param newVal + */ + public void setChromatograms(ArrayList newVal){ + chromatograms = newVal; + } + + public ArrayList getCitations(){ + return citations; + } + + /** + * + * @param newVal + */ + public void setCitations(ArrayList newVal){ + citations = newVal; + } + + public ArrayList getGenBankAccession(){ + return genBankAccession; + } + + /** + * + * @param newVal + */ + public void setGenBankAccession(ArrayList newVal){ + genBankAccession = newVal; + } + + public String getSequence(){ + return sequence; + } + + /** + * + * @param newVal + */ + public void setSequence(String newVal){ + sequence = newVal; + } + + public int getLength(){ + return length; + } + + /** + * + * @param newVal + */ + public void setLength(int newVal){ + length = newVal; + } + + public Calendar getDateSequenced(){ + return dateSequenced; + } + + /** + * + * @param newVal + */ + public void setDateSequenced(Calendar newVal){ + dateSequenced = newVal; + } + + public boolean isBarcode(){ + return isBarcode; + } + + /** + * + * @param newVal + */ + public void setBarcode(boolean newVal){ + isBarcode = newVal; + } + + public String getCitationMicroReference(){ + return citationMicroReference; + } + + /** + * + * @param newVal + */ + public void setCitationMicroReference(String newVal){ + citationMicroReference = newVal; + } + + @Transient + public StrictReferenceBase getCitation(){ + return null; + } + + @Transient + public String getCitation(){ + return ""; + } + + public String generateTitle(){ + return ""; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/molecular/TissueSample.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/molecular/TissueSample.java new file mode 100644 index 0000000000..07c7a79169 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/molecular/TissueSample.java @@ -0,0 +1,67 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.molecular; + + +import etaxonomy.cdm.model.occurrence.ObservationalUnit; +import etaxonomy.cdm.model.common.VersionableEntity; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:24 + */ +public class TissueSample extends VersionableEntity { + static Logger logger = Logger.getLogger(TissueSample.class); + + @Description("") + private String description; + @Description("") + private Calendar samplingDate; + private ObservationalUnit sampledFrom; + + public ObservationalUnit getSampledFrom(){ + return sampledFrom; + } + + /** + * + * @param newVal + */ + public void setSampledFrom(ObservationalUnit newVal){ + sampledFrom = newVal; + } + + public String getDescription(){ + return description; + } + + /** + * + * @param newVal + */ + public void setDescription(String newVal){ + description = newVal; + } + + public Calendar getSamplingDate(){ + return samplingDate; + } + + /** + * + * @param newVal + */ + public void setSamplingDate(Calendar newVal){ + samplingDate = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/BacterialName.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/BacterialName.java new file mode 100644 index 0000000000..dde065b555 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/BacterialName.java @@ -0,0 +1,55 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.name; + + +import org.apache.log4j.Logger; + +/** + * Taxon name class for bacteria + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:35 + */ +public class BacterialName extends NonViralName { + static Logger logger = Logger.getLogger(BacterialName.class); + + //Author team and year of the subgenus name + @Description("Author team and year of the subgenus name") + private String subGenusAuthorship; + //Approbation of name according to approved list, validation list,or validly published, paper in IJSB after 1980 + @Description("Approbation of name according to approved list, validation list,or validly published, paper in IJSB after 1980") + private String nameApprobation; + + public String getSubGenusAuthorship(){ + return subGenusAuthorship; + } + + /** + * + * @param newVal + */ + public void setSubGenusAuthorship(String newVal){ + subGenusAuthorship = newVal; + } + + public String getNameApprobation(){ + return nameApprobation; + } + + /** + * + * @param newVal + */ + public void setNameApprobation(String newVal){ + nameApprobation = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/BotanicalName.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/BotanicalName.java new file mode 100644 index 0000000000..1a73a8ea20 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/BotanicalName.java @@ -0,0 +1,124 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.name; + + +import org.apache.log4j.Logger; + +/** + * Taxon name class for plants + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:39 + */ +public class BotanicalName extends NonViralName { + static Logger logger = Logger.getLogger(BotanicalName.class); + + //if set: this name is a hybrid formula (a hybrid that does not have an own name) and no other hybrid flags may be set. A + //hybrid name may not have either an authorteam nor other name components. + @Description("if set: this name is a hybrid formula (a hybrid that does not have an own name) and no other hybrid flags may be set. A hybrid name may not have either an authorteam nor other name components. ") + private boolean isHybridFormula = False; + @Description("") + private boolean isMonomHybrid = False; + @Description("") + private boolean isBinomHybrid = False; + @Description("") + private boolean isTrinomHybrid = False; + //Only for fungi: to indicate that the type of the name is asexual or not + @Description("Only for fungi: to indicate that the type of the name is asexual or not") + private boolean isAnamorphic; + private ArrayList parentRelationships; + private ArrayList childRelationships; + + public ArrayList getParentRelationships(){ + return parentRelationships; + } + + /** + * + * @param newVal + */ + public void setParentRelationships(ArrayList newVal){ + parentRelationships = newVal; + } + + public ArrayList getChildRelationships(){ + return childRelationships; + } + + /** + * + * @param newVal + */ + public void setChildRelationships(ArrayList newVal){ + childRelationships = newVal; + } + + public boolean isHybridFormula(){ + return isHybridFormula; + } + + /** + * + * @param newVal + */ + public void setHybridFormula(boolean newVal){ + isHybridFormula = newVal; + } + + public boolean isMonomHybrid(){ + return isMonomHybrid; + } + + /** + * + * @param newVal + */ + public void setMonomHybrid(boolean newVal){ + isMonomHybrid = newVal; + } + + public boolean isBinomHybrid(){ + return isBinomHybrid; + } + + /** + * + * @param newVal + */ + public void setBinomHybrid(boolean newVal){ + isBinomHybrid = newVal; + } + + public boolean isTrinomHybrid(){ + return isTrinomHybrid; + } + + /** + * + * @param newVal + */ + public void setTrinomHybrid(boolean newVal){ + isTrinomHybrid = newVal; + } + + public boolean isAnamorphic(){ + return isAnamorphic; + } + + /** + * + * @param newVal + */ + public void setAnamorphic(boolean newVal){ + isAnamorphic = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/CultivarPlantName.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/CultivarPlantName.java new file mode 100644 index 0000000000..67a2a52b0f --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/CultivarPlantName.java @@ -0,0 +1,42 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.name; + + +import org.apache.log4j.Logger; + +/** + * Taxon name class for cultivars. + * {only possible for CULTIVAR, GREX, CONVAR, CULTIVAR_GROUP, GRAFT_CHIMAERA and + * DENOMINATION_CLASS ranks} + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:42 + */ +public class CultivarPlantName extends BotanicalName { + static Logger logger = Logger.getLogger(CultivarPlantName.class); + + //the caracteristical name of the cultivar + @Description("the caracteristical name of the cultivar") + private String cultivarName; + + public String getCultivarName(){ + return cultivarName; + } + + /** + * + * @param newVal + */ + public void setCultivarName(String newVal){ + cultivarName = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/HybridRelationship.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/HybridRelationship.java new file mode 100644 index 0000000000..f4ebea03c8 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/HybridRelationship.java @@ -0,0 +1,81 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.name; + + +import etaxonomy.cdm.model.common.ReferencedEntityBase; +import org.apache.log4j.Logger; + +/** + * http://rs.tdwg.org/ontology/voc/TaxonName.rdf#NomenclaturalNote + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:51 + */ +public class HybridRelationship extends ReferencedEntityBase { + static Logger logger = Logger.getLogger(HybridRelationship.class); + + //The nomenclatural code rule considered. The article/note/recommendation in the code in question that is commented on in + //the note property. + @Description("The nomenclatural code rule considered. The article/note/recommendation in the code in question that is commented on in the note property.") + private String ruleConsidered; + private BotanicalName parentName; + private BotanicalName hybridName; + private HybridRelationshipType type; + + public HybridRelationshipType getType(){ + return type; + } + + /** + * + * @param newVal + */ + public void setType(HybridRelationshipType newVal){ + type = newVal; + } + + public BotanicalName getParentName(){ + return parentName; + } + + /** + * + * @param newVal + */ + public void setParentName(BotanicalName newVal){ + parentName = newVal; + } + + public BotanicalName getHybridName(){ + return hybridName; + } + + /** + * + * @param newVal + */ + public void setHybridName(BotanicalName newVal){ + hybridName = newVal; + } + + public String getRuleConsidered(){ + return ruleConsidered; + } + + /** + * + * @param newVal + */ + public void setRuleConsidered(String newVal){ + ruleConsidered = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/HybridRelationshipType.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/HybridRelationshipType.java new file mode 100644 index 0000000000..fd37e813b0 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/HybridRelationshipType.java @@ -0,0 +1,43 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.name; + + +import etaxonomy.cdm.model.common.EnumeratedTermBase; +import org.apache.log4j.Logger; + +/** + * The list should be extensible at runtime through configuration. This needs to + * be investigated. + * + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:51 + */ +public class HybridRelationshipType extends EnumeratedTermBase { + static Logger logger = Logger.getLogger(HybridRelationshipType.class); + + public static final HybridRelationshipType FIRST_PARENT(){ + return null; + } + + public static final HybridRelationshipType SECOND_PARENT(){ + return null; + } + + public static final HybridRelationshipType FEMALE_PARENT(){ + return null; + } + + public static final HybridRelationshipType MALE_PARENT(){ + return null; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Fact.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/ITypeDesignation.java similarity index 69% rename from cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Fact.java rename to cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/ITypeDesignation.java index 12004aad6b..b0f68948d1 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/common/Fact.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/ITypeDesignation.java @@ -1,22 +1,22 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.common; - - -import org.apache.log4j.Logger; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:03 - */ -public interface Fact { - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.name; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:55 + */ +public interface ITypeDesignation { + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NameFact.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NameFact.java deleted file mode 100644 index 6cb31540a1..0000000000 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NameFact.java +++ /dev/null @@ -1,69 +0,0 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.name; - -import eu.etaxonomy.cdm.model.publication.PublicationBase; -import eu.etaxonomy.cdm.model.common.Fact; -import eu.etaxonomy.cdm.model.common.Media; -import eu.etaxonomy.cdm.model.common.FactBase; -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:08 - */ -@Entity -public class NameFact extends FactBase implements Fact { - static Logger logger = Logger.getLogger(NameFact.class); - - private ArrayList medias; - private PublicationBase citation; - private NameFactType type; - - public PublicationBase getCitation(){ - return citation; - } - - public ArrayList getMedias(){ - return medias; - } - - public NameFactType getType(){ - return type; - } - - /** - * - * @param newVal - */ - public void setCitation(PublicationBase newVal){ - citation = newVal; - } - - /** - * - * @param newVal - */ - public void setMedias(ArrayList newVal){ - medias = newVal; - } - - /** - * - * @param newVal - */ - public void setType(NameFactType newVal){ - type = newVal; - } - -} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NameInSource.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NameInSource.java new file mode 100644 index 0000000000..a5b38c11ea --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NameInSource.java @@ -0,0 +1,24 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.name; + + +import etaxonomy.cdm.model.common.EntityInSourceBase; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:03 + */ +public class NameInSource extends EntityInSourceBase { + static Logger logger = Logger.getLogger(NameInSource.class); + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NameRelationship.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NameRelationship.java index bb58312d3e..1129cc91ef 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NameRelationship.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NameRelationship.java @@ -1,110 +1,81 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.name; - - -import eu.etaxonomy.cdm.model.publication.PublicationBase; -import eu.etaxonomy.cdm.model.common.VersionableEntity; -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:08 - */ -@Entity -public class NameRelationship extends VersionableEntity { - static Logger logger = Logger.getLogger(NameRelationship.class); - - private String citationMicroReference; - private String ruleConsidered; - private PublicationBase citation; - private NameRelationshipType type; - private TaxonName toName; - private TaxonName fromName; - - @Transient - public PublicationBase getCitation(){ - return citation; - } - - public String getCitationMicroReference(){ - return citationMicroReference; - } - - @ManyToOne( cascade = {CascadeType.PERSIST, CascadeType.MERGE} ) - public TaxonName getFromName(){ - return fromName; - } - - public String getRuleConsidered(){ - return ruleConsidered; - } - - @ManyToOne( cascade = {CascadeType.PERSIST, CascadeType.MERGE} ) - public TaxonName getToName(){ - return toName; - } - - public NameRelationshipType getType(){ - return type; - } - - /** - * - * @param newVal - */ - public void setCitation(PublicationBase newVal){ - citation = newVal; - } - - /** - * - * @param newVal - */ - public void setCitationMicroReference(String newVal){ - citationMicroReference = newVal; - } - - /** - * - * @param newVal - */ - public void setFromName(TaxonName newVal){ - fromName = newVal; - } - - /** - * - * @param newVal - */ - public void setRuleConsidered(String newVal){ - ruleConsidered = newVal; - } - - /** - * - * @param newVal - */ - public void setToName(TaxonName newVal){ - toName = newVal; - } - - /** - * - * @param newVal - */ - public void setType(NameRelationshipType newVal){ - type = newVal; - } - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.name; + + +import etaxonomy.cdm.model.common.ReferencedEntityBase; +import org.apache.log4j.Logger; + +/** + * http://rs.tdwg.org/ontology/voc/TaxonName.rdf#NomenclaturalNote + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:03 + */ +public class NameRelationship extends ReferencedEntityBase { + static Logger logger = Logger.getLogger(NameRelationship.class); + + //The nomenclatural code rule considered. The article/note/recommendation in the code in question that is commented on in + //the note property. + @Description("The nomenclatural code rule considered. The article/note/recommendation in the code in question that is commented on in the note property.") + private String ruleConsidered; + private TaxonNameBase fromName; + private NameRelationshipType type; + private TaxonNameBase toName; + + public TaxonNameBase getFromName(){ + return fromName; + } + + /** + * + * @param newVal + */ + public void setFromName(TaxonNameBase newVal){ + fromName = newVal; + } + + public NameRelationshipType getType(){ + return type; + } + + /** + * + * @param newVal + */ + public void setType(NameRelationshipType newVal){ + type = newVal; + } + + public TaxonNameBase getToName(){ + return toName; + } + + /** + * + * @param newVal + */ + public void setToName(TaxonNameBase newVal){ + toName = newVal; + } + + public String getRuleConsidered(){ + return ruleConsidered; + } + + /** + * + * @param newVal + */ + public void setRuleConsidered(String newVal){ + ruleConsidered = newVal; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NameRelationshipType.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NameRelationshipType.java index 39067e9708..849c46d47f 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NameRelationshipType.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NameRelationshipType.java @@ -1,143 +1,148 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.name; - - -import org.apache.log4j.Logger; - -/** - * Nomenclatural status are also included. - * - * The list should be extensible at runtime through configuration. This needs to - * be investigated. - * - * - * Subgroups are: - * ================ - * - * Typification: - * ------------------- - * Type - * ConservedType - * RejectedType - * SameType - * LectoType - * NeoType - * - * - * Hyprid: - * ----------------------- - * FirstParent - * SecondParent - * FemaleParent - * MaleParent - * - * - * Illegitimate: - * ------------------------ - * Illegitimate, - * Superfluous, - * LaterHomonym, - * TreatedAsLaterHomonym, - * RejectedInFavour, - * Rejected, - * UtiqueRejected, - * ConservedProp, - * OrthographyConservedProp - * - * Legitimate: - * ------------------------ - * Legitimate, - * Basionym, - * ReplacedSynonym, - * Novum, - * AlternativeName, - * Alternativ, - * ConservedAgainst, - * Conserved, - * OrthographyConserved, - * RejectedProp, - * UtiqueRejectedProp - * - * Invalid: - * ----------------------------------- - * Invalid, - * Nudum, - * Provisional, - * CombinationInvalid, - * ValidatedByName, - * LaterValidatedByName - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:09 - */ -public enum NameRelationshipType { - ORTHOGRAPHIC_VARIANT, - AMBIGUOUS, - DOUBTFUL, - CONFUSUM, - TYPE, - CONSERVED_TYPE, - REJECTED_TYPE, - SAME_TYPE, - LECTOTYPE, - NEOTYPE, - FIRST_PARENT, - SECOND_PARENT, - FEMALE_PARENT, - MALE_PARENT, - ILLEGITIMATE, - LATER_HOMONYM, - SUPERFLUOUS, - REJECTED_IN_FAVOR, - TREATED_AS_LATER_HOMONYM, - REJECTED, - UTIQUE_REJECTED, - CONSERVED_PROP, - ORTHOGRAPHY_CONSERVED_PROP, - LEGITIMATE, - ALTERNATIVE, - UTIQUE_REJECTED_PROP, - ORTHOGRAPHY_CONSERVED, - REJECTED_PROP, - CONSERVED, - CONSERVED_AGAINST, - ALTERNATIVE_NAME, - BASIONYM, - NOVUM, - REPLACED_SYNONYM, - SANCTIONED, - INVALID, - NUDUM, - COMBINATION_INVALID, - PROVISIONAL, - VALIDATED_BY_NAME, - LATER_VALIDATED_BY_NAME; - - public boolean isHybridType(){ - return false; - } - - public boolean isInvalidType(){ - return false; - } - - public boolean isLegitimateType(){ - return false; - } - - public boolean isTypificationType(){ - return false; - } - - public boolean isIllegitimateType(){ - return false; - } +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.name; + + +import etaxonomy.cdm.model.common.EnumeratedTermBase; +import org.apache.log4j.Logger; + +/** + * The list should be extensible at runtime through configuration. This needs to + * be investigated. + * + * + * Subgroups are: + * ================ + * + * + * Illegitimate: + * ------------------------ + * LaterHomonym, + * TreatedAsLaterHomonym, + * RejectedInFavour + * + * Legitimate: + * ------------------------ + * ReplacedSynonym, + * AlternativeName, + * ConservedAgainst, + * OrthographyConserved + * + * Invalid: + * ----------------------------------- + * ValidatedByName, + * LaterValidatedByName + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:03 + */ +public class NameRelationshipType extends EnumeratedTermBase { + static Logger logger = Logger.getLogger(NameRelationshipType.class); + + @Description("") + private static final int initializationClassUri = http://rs.tdwg.org/ontology/voc/TaxonName.rdf#NomenclaturalNoteTypeTerm; + + public getInitializationClassUri(){ + return initializationClassUri; + } + + /** + * + * @param newVal + */ + public void setInitializationClassUri(newVal){ + initializationClassUri = newVal; + } + + public boolean isInvalidType(){ + //True, if enum is of type: + //Invalid, + //Nudum, + //Provisional, + //CombinationInvalid, + //ValidatedByName, + //LaterValidatedByName + + return false; + } + + public boolean isLegitimateType(){ + //True, if enum is of type: + //Legitimate, + //Basionym, + //ReplacedSynonym, + //Novum, + //AlternativeName, + //Alternativ, + //ConservedAgainst, + //Conserved, + //OrthographyConserved, + //RejectedProp, + //UtiqueRejectedProp + + return false; + } + + public boolean isIllegitimateType(){ + //True, if enum is of type: + //Illegitimate, + //Superfluous, + //LaterHomonym, + //TreatedAsLaterHomonym, + //RejectedInFavour, + //Rejected, + //UtiqueRejected, + //ConservedProp, + //OrthographyConservedProp + + return false; + } + + public static final NameRelationshipType ORTHOGRAPHIC_VARIANT(){ + return null; + } + + public static final NameRelationshipType REJECTED_IN_FAVOUR(){ + return null; + } + + public static final NameRelationshipType LATER_HOMONYM(){ + return null; + } + + public static final NameRelationshipType TREATED_AS_LATER_HOMONYM(){ + return null; + } + + public static final NameRelationshipType ALTERNATIVE_NAME(){ + return null; + } + + public static final NameRelationshipType BASIONYM(){ + return null; + } + + public static final NameRelationshipType REPLACED_SYNONYM(){ + return null; + } + + public static final NameRelationshipType CONSERVED_AGAINST(){ + return null; + } + + public static final NameRelationshipType VALIDATED_BY_NAME(){ + return null; + } + + public static final NameRelationshipType LATER_VALIDATED_BY_NAME(){ + return null; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NameTypeDesignation.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NameTypeDesignation.java new file mode 100644 index 0000000000..7379f6d5ac --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NameTypeDesignation.java @@ -0,0 +1,68 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.name; + + +import etaxonomy.cdm.model.common.ReferencedEntityBase; +import org.apache.log4j.Logger; + +/** + * {only for typified names which have a rank above "species", in this case the + * type has to be a "species" name} + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:04 + */ +public class NameTypeDesignation extends ReferencedEntityBase implements ITypeDesignation { + static Logger logger = Logger.getLogger(NameTypeDesignation.class); + + @Description("") + private boolean isRejectedType; + @Description("") + private boolean isConservedType; + private TaxonNameBase typeSpecies; + + public TaxonNameBase getTypeSpecies(){ + return typeSpecies; + } + + /** + * + * @param newVal + */ + public void setTypeSpecies(TaxonNameBase newVal){ + typeSpecies = newVal; + } + + public boolean isRejectedType(){ + return isRejectedType; + } + + /** + * + * @param newVal + */ + public void setRejectedType(boolean newVal){ + isRejectedType = newVal; + } + + public boolean isConservedType(){ + return isConservedType; + } + + /** + * + * @param newVal + */ + public void setConservedType(boolean newVal){ + isConservedType = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NomenclaturalCode.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NomenclaturalCode.java deleted file mode 100644 index aa65a86657..0000000000 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NomenclaturalCode.java +++ /dev/null @@ -1,40 +0,0 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.name; - - -import org.apache.log4j.Logger; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:09 - */ -public enum NomenclaturalCode { - ICBN, - ICZN, - BACTERIOLOGICAL, - ICNCP, - VIRAL; - -// private ArrayList m_TaxonName; -// -// public ArrayList getM_TaxonName(){ -// return m_TaxonName; -// } -// -// /** -// * -// * @param newVal -// */ -// public void setM_TaxonName(ArrayList newVal){ -// m_TaxonName = newVal; -// } -} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NomenclaturalStatus.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NomenclaturalStatus.java new file mode 100644 index 0000000000..5aba1c887f --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NomenclaturalStatus.java @@ -0,0 +1,55 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.name; + + +import etaxonomy.cdm.model.common.ReferencedEntityBase; +import org.apache.log4j.Logger; + +/** + * http://rs.tdwg.org/ontology/voc/TaxonName.rdf#PublicationStatus + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:04 + */ +public class NomenclaturalStatus extends ReferencedEntityBase { + static Logger logger = Logger.getLogger(NomenclaturalStatus.class); + + //The nomenclatural code rule considered. The article/note/recommendation in the code in question that is commented on in + //the note property. + @Description("The nomenclatural code rule considered. The article/note/recommendation in the code in question that is commented on in the note property.") + private String ruleConsidered; + private NomenclaturalStatusType type; + + public NomenclaturalStatusType getType(){ + return type; + } + + /** + * + * @param newVal + */ + public void setType(NomenclaturalStatusType newVal){ + type = newVal; + } + + public String getRuleConsidered(){ + return ruleConsidered; + } + + /** + * + * @param newVal + */ + public void setRuleConsidered(String newVal){ + ruleConsidered = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NomenclaturalStatusType.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NomenclaturalStatusType.java new file mode 100644 index 0000000000..2ecdd52039 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NomenclaturalStatusType.java @@ -0,0 +1,200 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.name; + + +import etaxonomy.cdm.model.common.EnumeratedTermBase; +import org.apache.log4j.Logger; + +/** + * The list should be extensible at runtime through configuration. This needs to + * be investigated. + * + * http://rs.tdwg.org/ontology/voc/TaxonName.rdf#NomenclaturalNoteTypeTerm + * + * Subgroups are: + * ================ + * + * Illegitimate: + * ------------------------ + * Illegitimate, + * Superfluous, + * Rejected, + * UtiqueRejected, + * ConservedProp, + * OrthographyConservedProp + * + * Legitimate: + * ------------------------ + * Legitimate, + * Novum, + * Alternativ, + * Conserved, + * OrthographyConserved, + * RejectedProp, + * UtiqueRejectedProp + * + * Invalid: + * ----------------------------------- + * Invalid, + * Nudum, + * Provisional, + * CombinationInvalid + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:05 + */ +public class NomenclaturalStatusType extends EnumeratedTermBase { + static Logger logger = Logger.getLogger(NomenclaturalStatusType.class); + + @Description("") + private static final int ontologyClassUri = http://rs.tdwg.org/ontology/voc/TaxonName.rdf#PublicationStatus; + + public getOntologyClassUri(){ + return ontologyClassUri; + } + + /** + * + * @param newVal + */ + public void setOntologyClassUri(newVal){ + ontologyClassUri = newVal; + } + + public boolean isInvalidType(){ + //True, if enum is of type: + //Invalid, + //Nudum, + //Provisional, + //CombinationInvalid, + //ValidatedByName, + //LaterValidatedByName + + return false; + } + + public boolean isLegitimateType(){ + //True, if enum is of type: + //Legitimate, + //Basionym, + //ReplacedSynonym, + //Novum, + //AlternativeName, + //Alternativ, + //ConservedAgainst, + //Conserved, + //OrthographyConserved, + //RejectedProp, + //UtiqueRejectedProp + + return false; + } + + public boolean isIllegitimateType(){ + //True, if enum is of type: + //Illegitimate, + //Superfluous, + //LaterHomonym, + //TreatedAsLaterHomonym, + //RejectedInFavour, + //Rejected, + //UtiqueRejected, + //ConservedProp, + //OrthographyConservedProp + + return false; + } + + public static final NomenclaturalStatusType AMBIGUOUS(){ + return null; + } + + public static final NomenclaturalStatusType DOUBTFUL(){ + return null; + } + + public static final NomenclaturalStatusType CONFUSUM(){ + return null; + } + + public static final NomenclaturalStatusType ILLEGITIMATE(){ + return null; + } + + public static final NomenclaturalStatusType SUPERFLUOUS(){ + return null; + } + + public static final NomenclaturalStatusType REJECTED(){ + return null; + } + + public static final NomenclaturalStatusType UTIQUE_REJECTED(){ + return null; + } + + public static final NomenclaturalStatusType CONSERVED_PROP(){ + return null; + } + + public static final NomenclaturalStatusType ORTHOGRAPHY_CONSERVED_PROP(){ + return null; + } + + public static final NomenclaturalStatusType LEGITIMATE(){ + return null; + } + + public static final NomenclaturalStatusType ALTERNATIVE(){ + return null; + } + + public static final NomenclaturalStatusType NOVUM(){ + return null; + } + + public static final NomenclaturalStatusType UTIQUE_REJECTED_PROP(){ + return null; + } + + public static final NomenclaturalStatusType ORTHOGRAPHY_CONSERVED(){ + return null; + } + + public static final NomenclaturalStatusType REJECTED_PROP(){ + return null; + } + + public static final NomenclaturalStatusType CONSERVED(){ + return null; + } + + public static final NomenclaturalStatusType SANCTIONED(){ + return null; + } + + public static final NomenclaturalStatusType INVALID(){ + return null; + } + + public static final NomenclaturalStatusType NUDUM(){ + return null; + } + + public static final NomenclaturalStatusType COMBINATION_INVALID(){ + return null; + } + + public static final NomenclaturalStatusType PROVISIONAL(){ + return null; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NonViralName.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NonViralName.java new file mode 100644 index 0000000000..931119d10f --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/NonViralName.java @@ -0,0 +1,128 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.name; + + +import etaxonomy.cdm.model.agent.Team; +import org.apache.log4j.Logger; + +/** + * Taxon name class for all non viral taxa. + * Parentetical authorship is derived from basionym relationship. + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:05 + */ +public class NonViralName extends TaxonNameBase { + static Logger logger = Logger.getLogger(NonViralName.class); + + //The suprageneric or the genus name + @Description("The suprageneric or the genus name") + private String uninomial; + //Genus subdivision epithet + @Description("Genus subdivision epithet") + private String infraGenericEpithet; + //species epithet + @Description("species epithet") + private String specificEpithet; + //Species subdivision epithet + @Description("Species subdivision epithet") + private String infraSpecificEpithet; + /** + * Author team that published the present combination + */ + private Team combinationAuthorTeam; + /** + * Author team that contributed to the publication of the present combination + */ + private Team exCombinationAuthorTeam; + + public Team getCombinationAuthorTeam(){ + return combinationAuthorTeam; + } + + /** + * + * @param newVal + */ + public void setCombinationAuthorTeam(Team newVal){ + combinationAuthorTeam = newVal; + } + + public Team getExCombinationAuthorTeam(){ + return exCombinationAuthorTeam; + } + + /** + * + * @param newVal + */ + public void setExCombinationAuthorTeam(Team newVal){ + exCombinationAuthorTeam = newVal; + } + + public String getUninomial(){ + return uninomial; + } + + /** + * + * @param newVal + */ + public void setUninomial(String newVal){ + uninomial = newVal; + } + + public String getInfraGenericEpithet(){ + return infraGenericEpithet; + } + + /** + * + * @param newVal + */ + public void setInfraGenericEpithet(String newVal){ + infraGenericEpithet = newVal; + } + + public String getSpecificEpithet(){ + return specificEpithet; + } + + /** + * + * @param newVal + */ + public void setSpecificEpithet(String newVal){ + specificEpithet = newVal; + } + + public String getInfraSpecificEpithet(){ + return infraSpecificEpithet; + } + + /** + * + * @param newVal + */ + public void setInfraSpecificEpithet(String newVal){ + infraSpecificEpithet = newVal; + } + + /** + * returns concatenated und formated authorteams including basionym and + * combination authors + */ + @Transient + public String getFullAuthorship(){ + return ""; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/Rank.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/Rank.java index 5627379a01..6019c51457 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/Rank.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/Rank.java @@ -1,98 +1,299 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.name; - - -import org.apache.log4j.Logger; - -/** - * The list should be extensible at runtime through configuration. This needs to - * be investigated. - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:11 - */ -public enum Rank { - EMPIRE, - DOMAIN, - SUPER_KINGDOM, - KINGDOM, - SUBKINGDOM, - INFRAKINGDOM, - SUPERPHYLUM, - PHYLUM, - SUBPHYLUM, - INFRAPHYLUM, - SUPERDIVISION, - DIVISION, - SUBDIVISION, - INFRADIVISION, - SUPERCLASS, - CLASS, - SUBCLASS, - INFRACLASS, - SUPERORDER, - ORDER, - SUBORDER, - INFRAORDER, - SUPERFAMILY, - FAMILY, - SUBFAMILY, - INFRAFAMILY, - SUPERTRIBE, - TRIBE, - SUBTRIBE, - INFRATRIBE, - SUPRAGENERIC_TAXON, - GENUS, - SUBGENUS, - INFRAGENUS, - SECTION, - SUBSECTION, - SERIES, - SUBSERIES, - SPECIES_AGGREGATE, - INFRAGENERIC_TAXON, - SPECIES, - SUBSPECIFIC_AGGREGATE, - SUBSPECIES, - INFRASPECIES, - VARIETY, - BIO_VARIETY, - PATHO_VARIETY, - SUB_VARIETY, - SUB_SUB_VARIETY, - FORM, - SPECIAL_FORM, - SUBFORM, - SUBSUBFORM, - INFRASPECIFIC_TAXON, - CANDIDATE, - DENOMINATION_CLASS, - GRAFT_CHIMAERA, - CULTIVAR_GROUP, - GREX, - CONVAR, - CULTIVAR; - -// private ArrayList m_TaxonName; -// -// public ArrayList getM_TaxonName(){ -// return m_TaxonName; -// } -// -// /** -// * -// * @param newVal -// */ -// public void setM_TaxonName(ArrayList newVal){ -// m_TaxonName = newVal; -// } +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.name; + + +import etaxonomy.cdm.model.common.EnumeratedTermBase; +import org.apache.log4j.Logger; + +/** + * This list should be extensible at runtime through configuration. This needs to + * be investigated. + * http://rs.tdwg.org/ontology/voc/TaxonRank + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:12 + */ +public class Rank extends EnumeratedTermBase { + static Logger logger = Logger.getLogger(Rank.class); + + @Description("") + private static final int ontologyClassUri = http://rs.tdwg.org/ontology/voc/TaxonRank#TaxonRankTerm; + private ArrayList m_TaxonNameBase; + + public ArrayList getM_TaxonNameBase(){ + return m_TaxonNameBase; + } + + /** + * + * @param newVal + */ + public void setM_TaxonNameBase(ArrayList newVal){ + m_TaxonNameBase = newVal; + } + + public getOntologyClassUri(){ + return ontologyClassUri; + } + + /** + * + * @param newVal + */ + public void setOntologyClassUri(newVal){ + ontologyClassUri = newVal; + } + + public static final Rank EMPIRE(){ + return null; + } + + public static final Rank DOMAIN(){ + return null; + } + + public static final Rank SUPER_KINGDOM(){ + return null; + } + + public static final Rank KINGDOM(){ + return null; + } + + public static final Rank SUBKINGDOM(){ + return null; + } + + public static final Rank INFRAKINGDOM(){ + return null; + } + + public static final Rank SUPERPHYLUM(){ + return null; + } + + public static final Rank PHYLUM(){ + return null; + } + + public static final Rank SUBPHYLUM(){ + return null; + } + + public static final Rank INFRAPHYLUM(){ + return null; + } + + public static final Rank SUPERDIVISION(){ + return null; + } + + public static final Rank DIVISION(){ + return null; + } + + public static final Rank SUBDIVISION(){ + return null; + } + + public static final Rank INFRADIVISION(){ + return null; + } + + public static final Rank SUPERCLASS(){ + return null; + } + + public static final Rank CLASS(){ + return null; + } + + public static final Rank SUBCLASS(){ + return null; + } + + public static final Rank INFRACLASS(){ + return null; + } + + public static final Rank SUPERORDER(){ + return null; + } + + public static final Rank ORDER(){ + return null; + } + + public static final Rank SUBORDER(){ + return null; + } + + public static final Rank INFRAORDER(){ + return null; + } + + public static final Rank SUPERFAMILY(){ + return null; + } + + public static final Rank FAMILY(){ + return null; + } + + public static final Rank SUBFAMILY(){ + return null; + } + + public static final Rank INFRAFAMILY(){ + return null; + } + + public static final Rank SUPERTRIBE(){ + return null; + } + + public static final Rank TRIBE(){ + return null; + } + + public static final Rank SUBTRIBE(){ + return null; + } + + public static final Rank INFRATRIBE(){ + return null; + } + + public static final Rank SUPRAGENERIC_TAXON(){ + return null; + } + + public static final Rank GENUS(){ + return null; + } + + public static final Rank SUBGENUS(){ + return null; + } + + public static final Rank INFRAGENUS(){ + return null; + } + + public static final Rank SECTION(){ + return null; + } + + public static final Rank SUBSECTION(){ + return null; + } + + public static final Rank SERIES(){ + return null; + } + + public static final Rank SUBSERIES(){ + return null; + } + + public static final Rank SPECIES_AGGREGATE(){ + return null; + } + + public static final Rank INFRAGENERIC_TAXON(){ + return null; + } + + public static final Rank SPECIES(){ + return null; + } + + public static final Rank SUBSPECIFIC_AGGREGATE(){ + return null; + } + + public static final Rank SUBSPECIES(){ + return null; + } + + public static final Rank INFRASPECIES(){ + return null; + } + + public static final Rank VARIETY(){ + return null; + } + + public static final Rank BIO_VARIETY(){ + return null; + } + + public static final Rank PATHO_VARIETY(){ + return null; + } + + public static final Rank SUBVARIETY(){ + return null; + } + + public static final Rank SUBSUBVARIETY(){ + return null; + } + + public static final Rank CONVAR(){ + return null; + } + + public static final Rank FORM(){ + return null; + } + + public static final Rank SPECIAL_FORM(){ + return null; + } + + public static final Rank SUBFORM(){ + return null; + } + + public static final Rank SUBSUBFORM(){ + return null; + } + + public static final Rank INFRASPECIFIC_TAXON(){ + return null; + } + + public static final Rank CANDIDATE(){ + return null; + } + + public static final Rank DENOMINATION_CLASS(){ + return null; + } + + public static final Rank GREX(){ + return null; + } + + public static final Rank GRAFT_CHIMAERA(){ + return null; + } + + public static final Rank CULTIVAR_GROUP(){ + return null; + } + + public static final Rank CULTIVAR(){ + return null; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/TypeDesignation.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/SpecimenTypeDesignation.java similarity index 52% rename from cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/TypeDesignation.java rename to cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/SpecimenTypeDesignation.java index 994d519c6e..6773a46b84 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/TypeDesignation.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/SpecimenTypeDesignation.java @@ -1,55 +1,53 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.name; - - -import eu.etaxonomy.cdm.model.specimen.Specimen; -import eu.etaxonomy.cdm.model.common.VersionableEntity; -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:17 - */ -@Entity -public class TypeDesignation extends VersionableEntity { - static Logger logger = Logger.getLogger(TypeDesignation.class); - - private Specimen typeSpecimen; - private TypeDesignationStatus typeStatus; - - public Specimen getTypeSpecimen(){ - return typeSpecimen; - } - - public TypeDesignationStatus getTypeStatus(){ - return typeStatus; - } - - /** - * - * @param newVal - */ - public void setTypeSpecimen(Specimen newVal){ - typeSpecimen = newVal; - } - - /** - * - * @param newVal - */ - public void setTypeStatus(TypeDesignationStatus newVal){ - typeStatus = newVal; - } - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.name; + + +import etaxonomy.cdm.model.occurrence.ObservationalUnit; +import etaxonomy.cdm.model.common.ReferencedEntityBase; +import org.apache.log4j.Logger; + +/** + * {only for typified names which have the "species" rank or below} + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:17 + */ +public class SpecimenTypeDesignation extends ReferencedEntityBase implements ITypeDesignation { + static Logger logger = Logger.getLogger(SpecimenTypeDesignation.class); + + private ObservationalUnit typeSpecimen; + private TypeDesignationStatus typeStatus; + + public ObservationalUnit getTypeSpecimen(){ + return typeSpecimen; + } + + /** + * + * @param newVal + */ + public void setTypeSpecimen(ObservationalUnit newVal){ + typeSpecimen = newVal; + } + + public TypeDesignationStatus getTypeStatus(){ + return typeStatus; + } + + /** + * + * @param newVal + */ + public void setTypeStatus(TypeDesignationStatus newVal){ + typeStatus = newVal; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/TaxonName.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/TaxonName.java deleted file mode 100644 index de8f2665fa..0000000000 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/TaxonName.java +++ /dev/null @@ -1,516 +0,0 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.name; - - -import java.util.ArrayList; - -import javax.persistence.CascadeType; -import javax.persistence.Entity; -import javax.persistence.ManyToOne; -import javax.persistence.Transient; - -import org.apache.log4j.Logger; - -import eu.etaxonomy.cdm.model.agent.Team; -import eu.etaxonomy.cdm.model.common.IdentifiableEntity; -import eu.etaxonomy.cdm.model.common.Source; -import eu.etaxonomy.cdm.model.publication.NomenclaturalReference; -import eu.etaxonomy.cdm.strategy.INameCacheStrategy; - -import javax.xml.bind.annotation.XmlElement; -import javax.xml.bind.annotation.XmlRootElement; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:15 - */ -@XmlRootElement //JAXP test dummy -@Entity -public class TaxonName extends IdentifiableEntity { - static Logger logger = Logger.getLogger(TaxonName.class); - - private INameCacheStrategy cacheStrategy; - private String year; - - //TODO make private but then the Aspect class has problems !! - public TaxonName(){ - - } - - public TaxonName(INameCacheStrategy cacheStrategy){ - setCacheStrategy(cacheStrategy); - } - - //TODO inserted for PROTOTYPE - public String getYear(){ - return this.year; - } - public void setYear(String strYear){ - this.year = strYear; - } - - //TODO for PROTOTYPE - @Transient - public INameCacheStrategy getCacheStrategy() { - return cacheStrategy; - } - public void setCacheStrategy(INameCacheStrategy cacheStrategy) { - this.cacheStrategy = cacheStrategy; - } - - - //The complete author string and maybe year - private String authorship; - private String cultivarName; - //The full name including author strings and maybe year - private String fullName; - //Genus part of a name - private String genus; - private boolean hasProblem; - private String idInSource; - //Genus subdivision epithet - private String infragenericEpithet; - private String infraSpecificEpithet; - private boolean isAnamorphic; - //alternative naming: useFullName - //when not set this flag protects the detailed parsed attributes from being overwritten - private boolean isAtomised; - private boolean isBinomHybrid; - private boolean isCultivarGroup; - //if set: this name is a hybrid formula (a hybrid that does not have an own name) and no other hybrid flags may be set. A - //hybrid name may not have either an authorteam nor other name components. - private boolean isHybridFormula; - private boolean isMonomHybrid; - private boolean isTrinomHybrid; - //The name without author strings and year - private String name; - private String nameInSource; - private String nomenclaturalMicroReference; - //The species epithet - private String specificEpithet; - //Name of taxon when rank is above genus - private String uninomial; - //Non-atomised addition to a name - private String unnamedNamePhrase; - private Rank rank; - private ArrayList inverseNameRelation; - private NomenclaturalCode nomenclaturalCode; - private ArrayList facts; - private ArrayList nameRelation; - private ArrayList typeDesignations; - private NomenclaturalReference nomenclaturalReference; - private Source source; - private Team authorTeam; - private Team exAuthorTeam; - - public String getAuthorship(){ - return authorship; - } - - @ManyToOne(cascade = {CascadeType.PERSIST, CascadeType.MERGE} ) - public Team getAuthorTeam(){ - return authorTeam; - } - - @XmlElement - public String getCultivarName(){ - return cultivarName; - } - - @ManyToOne( cascade = {CascadeType.PERSIST, CascadeType.MERGE} ) - public Team getExAuthorTeam(){ - return exAuthorTeam; - } - - public ArrayList getFacts(){ - return facts; - } - - public String getFullName(){ - if (name == null){ - return cacheStrategy.getFullNameCache(this); - }else{ - return fullName; - } - } - - public String getGenus(){ - return genus; - } - - public boolean getHasProblem(){ - return hasProblem; - } - - public String getIdInSource(){ - return idInSource; - } - - public String getInfragenericEpithet(){ - return infragenericEpithet; - } - - public String getInfraSpecificEpithet(){ - return infraSpecificEpithet; - } - - public ArrayList getInverseNameRelation(){ - return inverseNameRelation; - } - - public String getName(){ - if (name == null){ - return cacheStrategy.getNameCache(this); - }else{ - return name; - } - } - - public String getNameInSource(){ - return nameInSource; - } - - public ArrayList getNameRelation(){ - return nameRelation; - } - - public NomenclaturalCode getNomenclaturalCode(){ - return nomenclaturalCode; - } - - public String getNomenclaturalMicroReference(){ - return nomenclaturalMicroReference; - } - - @Transient - public NomenclaturalReference getNomenclaturalReference(){ - return nomenclaturalReference; - } - - @Transient - public String[] getProblems(){ - return null; - } - - public Rank getRank(){ - return rank; - } - - @Transient - public Source getSource(){ - return source; - } - - public String getSpecificEpithet(){ - return specificEpithet; - } - - public ArrayList getTypeDesignations(){ - return typeDesignations; - } - - public String getUninomial(){ - return uninomial; - } - - public String getUnnamedNamePhrase(){ - return unnamedNamePhrase; - } - - - public boolean isAnamorphic(){ - return isAnamorphic; - } - - public boolean isAtomised(){ - return isAtomised; - } - - public boolean isBinomHybrid(){ - return isBinomHybrid; - } - - public boolean isCultivarGroup(){ - return isCultivarGroup; - } - - public boolean isHybridFormula(){ - return isHybridFormula; - } - - public boolean isMonomHybrid(){ - return isMonomHybrid; - } - - public boolean isTrinomHybrid(){ - return isTrinomHybrid; - } - - /** - * - * @param fullname - */ - public boolean parseName(String fullname){ - return false; - } - - /** - * - * @param newVal - */ - public void setAnamorphic(boolean newVal){ - isAnamorphic = newVal; - - } - - /** - * - * @param newVal - */ - public void setAtomised(boolean newVal){ - isAtomised = newVal; - } - - /** - * - * @param newVal - */ - public void setAuthorship(String newVal){ - authorship = newVal; - } - - /** - * - * @param newVal - */ - public void setAuthorTeam(Team newVal){ - authorTeam = newVal; - } - - /** - * - * @param newVal - */ - public void setBinomHybrid(boolean newVal){ - isBinomHybrid = newVal; - } - - /** - * - * @param newVal - */ - public void setCultivarGroup(boolean newVal){ - isCultivarGroup = newVal; - } - - /** - * - * @param newVal - */ - public void setCultivarName(String newVal){ - cultivarName = newVal; - } - - /** - * - * @param newVal - */ - public void setExAuthorTeam(Team newVal){ - exAuthorTeam = newVal; - } - - /** - * - * @param newVal - */ - public void setFacts(ArrayList newVal){ - facts = newVal; - } - - /** - * - * @param newVal - */ - public void setFullName(String newVal){ - fullName = newVal; - } - - /** - * - * @param newVal - */ - public void setGenus(String newVal){ - genus = newVal; - } - - /** - * - * @param newVal - */ - public void setHasProblem(boolean newVal){ - hasProblem = newVal; - } - - /** - * - * @param newVal - */ - public void setHybridFormula(boolean newVal){ - isHybridFormula = newVal; - } - - /** - * - * @param newVal - */ - public void setIdInSource(String newVal){ - idInSource = newVal; - } - - /** - * - * @param newVal - */ - public void setInfragenericEpithet(String newVal){ - infragenericEpithet = newVal; - } - - /** - * - * @param newVal - */ - public void setInfraSpecificEpithet(String newVal){ - infraSpecificEpithet = newVal; - } - - /** - * - * @param newVal - */ - public void setInverseNameRelation(ArrayList newVal){ - inverseNameRelation = newVal; - } - - /** - * - * @param newVal - */ - public void setMonomHybrid(boolean newVal){ - isMonomHybrid = newVal; - } - - /** - * - * @param newVal - */ - public void setName(String newVal){ - name = newVal; - } - - /** - * - * @param newVal - */ - public void setNameInSource(String newVal){ - nameInSource = newVal; - } - - /** - * - * @param newVal - */ - public void setNameRelation(ArrayList newVal){ - nameRelation = newVal; - } - - /** - * - * @param newVal - */ - public void setNomenclaturalCode(NomenclaturalCode newVal){ - nomenclaturalCode = newVal; - } - - /** - * - * @param newVal - */ - public void setNomenclaturalMicroReference(String newVal){ - nomenclaturalMicroReference = newVal; - } - - /** - * - * @param newVal - */ - public void setNomenclaturalReference(NomenclaturalReference newVal){ - nomenclaturalReference = newVal; - } - - /** - * - * @param newVal - */ - public void setRank(Rank newVal){ - rank = newVal; - } - - /** - * - * @param newVal - */ - public void setSource(Source newVal){ - source = newVal; - } - - /** - * - * @param newVal - */ - public void setSpecificEpithet(String newVal){ - specificEpithet = newVal; - } - - /** - * - * @param newVal - */ - public void setTrinomHybrid(boolean newVal){ - isTrinomHybrid = newVal; - } - - /** - * - * @param newVal - */ - public void setTypeDesignations(ArrayList newVal){ - //super.changeSupport.firePropertyChange("typeDesignations", typeDesignations, newVal); - typeDesignations = newVal; - } - - /** - * - * @param newVal - */ - public void setUninomial(String newVal){ - uninomial = newVal; - } - - /** - * - * @param newVal - */ - public void setUnnamedNamePhrase(String newVal){ - unnamedNamePhrase = newVal; - } - -} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/TaxonNameBase.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/TaxonNameBase.java new file mode 100644 index 0000000000..95950dff9a --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/TaxonNameBase.java @@ -0,0 +1,246 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.name; + + +import etaxonomy.cdm.model.reference.INomenclaturalReference; +import etaxonomy.cdm.model.reference.StrictReferenceBase; +import etaxonomy.cdm.model.common.IReferencedEntity; +import etaxonomy.cdm.model.common.IdentifiableEntity; +import org.apache.log4j.Logger; + +/** + * The upmost (abstract) class for scientific taxon names regardless of the any + * particular nomenclatural code. The scientific name including author strings and + * maybe year is stored in IdentifiableEntity.titleCache + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:22 + */ +public abstract class TaxonNameBase extends IdentifiableEntity implements IReferencedEntity { + static Logger logger = Logger.getLogger(TaxonNameBase.class); + + //The scientific name without author strings and year + @Description("The scientific name without author strings and year") + private String name; + //Non-atomised addition to a name not ruled by a nomenclatural code + @Description("Non-atomised addition to a name not ruled by a nomenclatural code") + private String appendedPhrase; + //Details of the nomenclatural reference (protologue). These are mostly (implicitly) pages but can also be figures or + //tables or any other element of a publication. + //{only if a nomenclatural reference exists} + @Description("Details of the nomenclatural reference (protologue). These are mostly (implicitly) pages but can also be figures or tables or any other element of a publication. + {only if a nomenclatural reference exists}") + private String nomenclaturalMicroReference; + //this flag will be set to true if the parseName method was unable to successfully parse the name + @Description("this flag will be set to true if the parseName method was unable to successfully parse the name") + private boolean hasProblem = False; + private Rank rank; + private ArrayList newCombinations; + private TaxonNameBase basionym; + /** + * if set, the Reference.isNomenclaturallyRelevant flag should be set to true! + */ + private INomenclaturalReference nomenclaturalReference; + private ArrayList typeDesignations; + private ArrayList nameInSource; + private ArrayList nameRelations; + private ArrayList inverseNameRelations; + private ArrayList status; + + public Rank getRank(){ + return rank; + } + + /** + * + * @param newVal + */ + public void setRank(Rank newVal){ + rank = newVal; + } + + public ArrayList getNameRelations(){ + return nameRelations; + } + + /** + * + * @param newVal + */ + public void setNameRelations(ArrayList newVal){ + nameRelations = newVal; + } + + public ArrayList getInverseNameRelations(){ + return inverseNameRelations; + } + + /** + * + * @param newVal + */ + public void setInverseNameRelations(ArrayList newVal){ + inverseNameRelations = newVal; + } + + public ArrayList getTypeDesignations(){ + return typeDesignations; + } + + /** + * + * @param newVal + */ + public void setTypeDesignations(ArrayList newVal){ + typeDesignations = newVal; + } + + public ArrayList getStatus(){ + return status; + } + + /** + * + * @param newVal + */ + public void setStatus(ArrayList newVal){ + status = newVal; + } + + public INomenclaturalReference getNomenclaturalReference(){ + return nomenclaturalReference; + } + + /** + * + * @param newVal + */ + public void setNomenclaturalReference(INomenclaturalReference newVal){ + nomenclaturalReference = newVal; + } + + public ArrayList getNameInSource(){ + return nameInSource; + } + + /** + * + * @param newVal + */ + public void setNameInSource(ArrayList newVal){ + nameInSource = newVal; + } + + public ArrayList getNewCombinations(){ + return newCombinations; + } + + /** + * + * @param newVal + */ + public void setNewCombinations(ArrayList newVal){ + newCombinations = newVal; + } + + public TaxonNameBase getBasionym(){ + return basionym; + } + + /** + * + * @param newVal + */ + public void setBasionym(TaxonNameBase newVal){ + basionym = newVal; + } + + public String getName(){ + return name; + } + + /** + * + * @param newVal + */ + public void setName(String newVal){ + name = newVal; + } + + public String getAppendedPhrase(){ + return appendedPhrase; + } + + /** + * + * @param newVal + */ + public void setAppendedPhrase(String newVal){ + appendedPhrase = newVal; + } + + public String getNomenclaturalMicroReference(){ + return nomenclaturalMicroReference; + } + + /** + * + * @param newVal + */ + public void setNomenclaturalMicroReference(String newVal){ + nomenclaturalMicroReference = newVal; + } + + public boolean getHasProblem(){ + return hasProblem; + } + + /** + * + * @param newVal + */ + public void setHasProblem(boolean newVal){ + hasProblem = newVal; + } + + @Transient + public StrictReferenceBase getCitation(){ + return null; + } + + @Transient + public String getCitationString(){ + return ""; + } + + @Transient + public String[] getProblems(){ + return ""; + } + + /** + * returns year of according nomenclatural reference, null if nomenclatural + * reference does not exist + */ + @Transient + public String getYear(){ + return ""; + } + + /** + * + * @param fullname + */ + public boolean parseName(String fullname){ + return false; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/TypeDesignationStatus.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/TypeDesignationStatus.java index 59ff507b4b..6f07300098 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/TypeDesignationStatus.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/TypeDesignationStatus.java @@ -1,39 +1,105 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.name; - - -import org.apache.log4j.Logger; - -/** - * The list should be extensible at runtime through configuration. This needs to - * be investigated. - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:17 - */ -public enum TypeDesignationStatus { - HOLOTYPE, - LECTOTYPE, - NEOTYPE, - EPITYPE, - ISOLECTOTYPE, - ISONEOTYPE, - ISOTYPE, - PARANEOTYPE, - PARATYPE, - SECOND_STEP_LECTOTYPE, - SECOND_STEP_NEOTYPE, - SYNTYPE, - PARALECTOTYPE, - ISOEPITYPE, - ICONOTYPE, - PHOTOTYPE +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.name; + + +import etaxonomy.cdm.model.common.EnumeratedTermBase; +import org.apache.log4j.Logger; + +/** + * The list should be extensible at runtime through configuration. This needs to + * be investigated. + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:25 + */ +public class TypeDesignationStatus extends EnumeratedTermBase { + static Logger logger = Logger.getLogger(TypeDesignationStatus.class); + + @Description("") + private static final int initializationClassUri = http://rs.tdwg.org/ontology/voc/TaxonName#NomencalturalTypeTypeTerm; + + public getInitializationClassUri(){ + return initializationClassUri; + } + + /** + * + * @param newVal + */ + public void setInitializationClassUri(newVal){ + initializationClassUri = newVal; + } + + public static final TypeDesignationStatus HOLOTYPE(){ + return null; + } + + public static final TypeDesignationStatus LECTOTYPE(){ + return null; + } + + public static final TypeDesignationStatus NEOTYPE(){ + return null; + } + + public static final TypeDesignationStatus EPITYPE(){ + return null; + } + + public static final TypeDesignationStatus ISOLECTOTYPE(){ + return null; + } + + public static final TypeDesignationStatus ISONEOTYPE(){ + return null; + } + + public static final TypeDesignationStatus ISOTYPE(){ + return null; + } + + public static final TypeDesignationStatus PARANEOTYPE(){ + return null; + } + + public static final TypeDesignationStatus PARATYPE(){ + return null; + } + + public static final TypeDesignationStatus SECOND_STEP_LECTOTYPE(){ + return null; + } + + public static final TypeDesignationStatus SECOND_STEP_NEOTYPE(){ + return null; + } + + public static final TypeDesignationStatus SYNTYPE(){ + return null; + } + + public static final TypeDesignationStatus PARALECTOTYPE(){ + return null; + } + + public static final TypeDesignationStatus ISOEPITYPE(){ + return null; + } + + public static final TypeDesignationStatus ICONOTYPE(){ + return null; + } + + public static final TypeDesignationStatus PHOTOTYPE(){ + return null; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/ViralName.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/ViralName.java new file mode 100644 index 0000000000..362a1ed716 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/ViralName.java @@ -0,0 +1,43 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.name; + + +import org.apache.log4j.Logger; + +/** + * use name attribute for the entire virus name! + * + * examples see ICTVdb: + * http://www.ncbi.nlm.nih.gov/ICTVdb/Ictv/vn_indxA.htm + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:26 + */ +public class ViralName extends TaxonNameBase { + static Logger logger = Logger.getLogger(ViralName.class); + + //The accepted acronym for the Virus, e.g. PCV for Peanut Clump Virus + @Description("The accepted acronym for the Virus, e.g. PCV for Peanut Clump Virus") + private String acronym; + + public String getAcronym(){ + return acronym; + } + + /** + * + * @param newVal + */ + public void setAcronym(String newVal){ + acronym = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/ZoologicalName.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/ZoologicalName.java new file mode 100644 index 0000000000..23f9c9659d --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/name/ZoologicalName.java @@ -0,0 +1,45 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.name; + + +import org.apache.log4j.Logger; + +/** + * Taxon name class for animals + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:27 + */ +public class ZoologicalName extends NonViralName { + static Logger logger = Logger.getLogger(ZoologicalName.class); + + //Name of the breed of an animal + @Description("Name of the breed of an animal") + private String breed; + + public String getBreed(){ + return breed; + } + + /** + * + * @param newVal + */ + public void setBreed(String newVal){ + breed = newVal; + } + + @Transient + public String getFullAuthorship(){ + return ""; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/specimen/Collection.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/Collection.java similarity index 77% rename from cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/specimen/Collection.java rename to cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/Collection.java index c88fad18e8..2c36b5d9c9 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/specimen/Collection.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/Collection.java @@ -1,93 +1,99 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.specimen; - - -import eu.etaxonomy.cdm.model.common.VersionableEntity; -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:01 - */ -@Entity -public class Collection extends VersionableEntity { - static Logger logger = Logger.getLogger(Collection.class); - - private String code; - private String codeStandard; - private String name; - private String townOrLocation; - private Institution institute; - - public String getCode(){ - return code; - } - - public String getCodeStandard(){ - return codeStandard; - } - - public Institution getInstitute(){ - return institute; - } - - public String getName(){ - return name; - } - - public String getTownOrLocation(){ - return townOrLocation; - } - - /** - * - * @param newVal - */ - public void setCode(String newVal){ - code = newVal; - } - - /** - * - * @param newVal - */ - public void setCodeStandard(String newVal){ - codeStandard = newVal; - } - - /** - * - * @param newVal - */ - public void setInstitute(Institution newVal){ - institute = newVal; - } - - /** - * - * @param newVal - */ - public void setName(String newVal){ - name = newVal; - } - - /** - * - * @param newVal - */ - public void setTownOrLocation(String newVal){ - townOrLocation = newVal; - } - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.occurrence; + + +import etaxonomy.cdm.model.agent.Institution; +import etaxonomy.cdm.model.common.IdentifiableEntity; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:40 + */ +public class Collection extends IdentifiableEntity { + static Logger logger = Logger.getLogger(Collection.class); + + @Description("") + private String code; + @Description("") + private String codeStandard; + @Description("") + private String name; + @Description("") + private String townOrLocation; + private Institution institute; + + public Institution getInstitute(){ + return institute; + } + + /** + * + * @param newVal + */ + public void setInstitute(Institution newVal){ + institute = newVal; + } + + public String getCode(){ + return code; + } + + /** + * + * @param newVal + */ + public void setCode(String newVal){ + code = newVal; + } + + public String getCodeStandard(){ + return codeStandard; + } + + /** + * + * @param newVal + */ + public void setCodeStandard(String newVal){ + codeStandard = newVal; + } + + public String getName(){ + return name; + } + + /** + * + * @param newVal + */ + public void setName(String newVal){ + name = newVal; + } + + public String getTownOrLocation(){ + return townOrLocation; + } + + /** + * + * @param newVal + */ + public void setTownOrLocation(String newVal){ + townOrLocation = newVal; + } + + public String generateTitle(){ + return ""; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/Determination.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/Determination.java new file mode 100644 index 0000000000..fa9eaeb0ed --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/Determination.java @@ -0,0 +1,67 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.occurrence; + + +import etaxonomy.cdm.model.taxon.Taxon; +import etaxonomy.cdm.model.agent.Team; +import etaxonomy.cdm.model.common.AnnotatableEntity; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:45 + */ +public class Determination extends AnnotatableEntity { + static Logger logger = Logger.getLogger(Determination.class); + + @Description("") + private Calendar identificationDate; + private Taxon taxon; + private Team identifierTeam; + + public Taxon getTaxon(){ + return taxon; + } + + /** + * + * @param newVal + */ + public void setTaxon(Taxon newVal){ + taxon = newVal; + } + + public Team getIdentifierTeam(){ + return identifierTeam; + } + + /** + * + * @param newVal + */ + public void setIdentifierTeam(Team newVal){ + identifierTeam = newVal; + } + + public Calendar getIdentificationDate(){ + return identificationDate; + } + + /** + * + * @param newVal + */ + public void setIdentificationDate(Calendar newVal){ + identificationDate = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/Fossil.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/Fossil.java new file mode 100644 index 0000000000..6f6a228536 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/Fossil.java @@ -0,0 +1,23 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.occurrence; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:49 + */ +public class Fossil extends Specimen { + static Logger logger = Logger.getLogger(Fossil.class); + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/LivingIndividual.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/LivingIndividual.java new file mode 100644 index 0000000000..7d17001b3e --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/LivingIndividual.java @@ -0,0 +1,50 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.occurrence; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:57 + */ +public class LivingIndividual extends Occurrence { + static Logger logger = Logger.getLogger(LivingIndividual.class); + + private ArrayList parents; + private ArrayList offspring; + + public ArrayList getParents(){ + return parents; + } + + /** + * + * @param newVal + */ + public void setParents(ArrayList newVal){ + parents = newVal; + } + + public ArrayList getOffspring(){ + return offspring; + } + + /** + * + * @param newVal + */ + public void setOffspring(ArrayList newVal){ + offspring = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/Observation.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/Observation.java new file mode 100644 index 0000000000..e5ff3034d9 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/Observation.java @@ -0,0 +1,23 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.occurrence; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:05 + */ +public class Observation extends Occurrence { + static Logger logger = Logger.getLogger(Observation.class); + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/ObservationalUnit.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/ObservationalUnit.java new file mode 100644 index 0000000000..9275360bd1 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/ObservationalUnit.java @@ -0,0 +1,82 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.occurrence; + + +import etaxonomy.cdm.model.common.MultilanguageString; +import etaxonomy.cdm.model.description.Description; +import etaxonomy.cdm.model.common.IdentifiableEntity; +import org.apache.log4j.Logger; + +/** + * part of a specimen or observation that is being described or determined. + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:06 + */ +public class ObservationalUnit extends IdentifiableEntity { + static Logger logger = Logger.getLogger(ObservationalUnit.class); + + //Description defining the Observational unit in the context of the original Occurrence + @Description("Description defining the Observational unit in the context of the original Occurrence") + private MultilanguageString definition; + private ArrayList descriptions; + private ArrayList determinations; + private Occurrence occurence; + + public ArrayList getDeterminations(){ + return determinations; + } + + /** + * + * @param newVal + */ + public void setDeterminations(ArrayList newVal){ + determinations = newVal; + } + + public Occurrence getOccurence(){ + return occurence; + } + + /** + * + * @param newVal + */ + public void setOccurence(Occurrence newVal){ + occurence = newVal; + } + + public ArrayList getDescriptions(){ + return descriptions; + } + + /** + * + * @param newVal + */ + public void setDescriptions(ArrayList newVal){ + descriptions = newVal; + } + + public MultilanguageString getDefinition(){ + return definition; + } + + /** + * + * @param newVal + */ + public void setDefinition(MultilanguageString newVal){ + definition = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/Occurrence.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/Occurrence.java new file mode 100644 index 0000000000..0a728cb16a --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/Occurrence.java @@ -0,0 +1,129 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.occurrence; + + +import etaxonomy.cdm.model.location.Point; +import etaxonomy.cdm.model.agent.Team; +import etaxonomy.cdm.model.location.NamedArea; +import etaxonomy.cdm.model.common.IdentifiableEntity; +import etaxonomy.cdm.model.common.Media; +import org.apache.log4j.Logger; + +/** + * type figures are observations with at least a figure object in media + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:06 + */ +public class Occurrence extends IdentifiableEntity { + static Logger logger = Logger.getLogger(Occurrence.class); + + //Locality name (as free text) where this occurrence happened + @Description("Locality name (as free text) where this occurrence happened ") + private String locality; + //Date on which this occurrence happened + @Description("Date on which this occurrence happened ") + private Calendar eventDate; + private ArrayList media; + private Collection collection; + private Point exactLocation; + private NamedArea namedArea; + private Team collector; + + public Collection getCollection(){ + return collection; + } + + /** + * + * @param newVal + */ + public void setCollection(Collection newVal){ + collection = newVal; + } + + public Point getExactLocation(){ + return exactLocation; + } + + /** + * + * @param newVal + */ + public void setExactLocation(Point newVal){ + exactLocation = newVal; + } + + public ArrayList getMedia(){ + return media; + } + + /** + * + * @param newVal + */ + public void setMedia(ArrayList newVal){ + media = newVal; + } + + public Team getCollector(){ + return collector; + } + + /** + * + * @param newVal + */ + public void setCollector(Team newVal){ + collector = newVal; + } + + public NamedArea getNamedArea(){ + return namedArea; + } + + /** + * + * @param newVal + */ + public void setNamedArea(NamedArea newVal){ + namedArea = newVal; + } + + public String getLocality(){ + return locality; + } + + /** + * + * @param newVal + */ + public void setLocality(String newVal){ + locality = newVal; + } + + public Calendar getEventDate(){ + return eventDate; + } + + /** + * + * @param newVal + */ + public void setEventDate(Calendar newVal){ + eventDate = newVal; + } + + public String generateTitle(){ + return ""; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/PreservationMethod.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/PreservationMethod.java new file mode 100644 index 0000000000..b9e42599bd --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/PreservationMethod.java @@ -0,0 +1,39 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.occurrence; + + +import etaxonomy.cdm.model.common.DefinedTermBase; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:09 + */ +public class PreservationMethod extends DefinedTermBase { + static Logger logger = Logger.getLogger(PreservationMethod.class); + + @Description("") + private static final int initializationClassUri = http://rs.tdwg.org/ontology/voc/Collection.rdf#SpecimenPreservationMethodTypeTerm; + + public getInitializationClassUri(){ + return initializationClassUri; + } + + /** + * + * @param newVal + */ + public void setInitializationClassUri(newVal){ + initializationClassUri = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/Specimen.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/Specimen.java new file mode 100644 index 0000000000..90a329b34f --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/occurrence/Specimen.java @@ -0,0 +1,50 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.occurrence; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:17 + */ +public class Specimen extends Occurrence { + static Logger logger = Logger.getLogger(Specimen.class); + + private PreservationMethod preservation; + private Specimen derivedFrom; + + public PreservationMethod getPreservation(){ + return preservation; + } + + /** + * + * @param newVal + */ + public void setPreservation(PreservationMethod newVal){ + preservation = newVal; + } + + public Specimen getDerivedFrom(){ + return derivedFrom; + } + + /** + * + * @param newVal + */ + public void setDerivedFrom(Specimen newVal){ + derivedFrom = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/BookSection.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/BookSection.java deleted file mode 100644 index 88dd5bb34c..0000000000 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/BookSection.java +++ /dev/null @@ -1,40 +0,0 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.publication; - - -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:00 - */ -@Entity -public class BookSection extends PublicationBase implements NomenclaturalReference { - static Logger logger = Logger.getLogger(BookSection.class); - - private Book inBook; - - public Book getInBook(){ - return inBook; - } - - /** - * - * @param newVal - */ - public void setInBook(Book newVal){ - inBook = newVal; - } - -} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/PublicationBase.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/PublicationBase.java deleted file mode 100644 index 43a984f187..0000000000 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/PublicationBase.java +++ /dev/null @@ -1,158 +0,0 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.publication; - - -import eu.etaxonomy.cdm.model.agent.Team; -import eu.etaxonomy.cdm.model.common.NameAlias; -import eu.etaxonomy.cdm.model.common.IdentifiableEntity; -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * A year() method is required to get the year of publication out of the - * datePublished field - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:11 - */ -@Entity -public abstract class PublicationBase extends IdentifiableEntity { - static Logger logger = Logger.getLogger(PublicationBase.class); - - private String datePublished; - private String doi; - private String pages; - private String placePublished; - private String publisher; - private String title; - private String url; - private ArrayList otherTitles; - private Team authorship; - - public Team getAuthorship(){ - return authorship; - } - - public String getDatePublished(){ - return datePublished; - } - - public String getDoi(){ - return doi; - } - - public ArrayList getOtherTitles(){ - return otherTitles; - } - - public String getPages(){ - return pages; - } - - public String getPlacePublished(){ - return placePublished; - } - - public String getPublisher(){ - return publisher; - } - - public String getTitle(){ - return title; - } - - public String getUrl(){ - return url; - } - - /** - * - * @param datePublished - */ - @Transient - public int getYear(String datePublished){ - return 0; - } - - /** - * - * @param newVal - */ - public void setAuthorship(Team newVal){ - authorship = newVal; - } - - /** - * - * @param newVal - */ - public void setDatePublished(String newVal){ - datePublished = newVal; - } - - /** - * - * @param newVal - */ - public void setDoi(String newVal){ - doi = newVal; - } - - /** - * - * @param newVal - */ - public void setOtherTitles(ArrayList newVal){ - otherTitles = newVal; - } - - /** - * - * @param newVal - */ - public void setPages(String newVal){ - pages = newVal; - } - - /** - * - * @param newVal - */ - public void setPlacePublished(String newVal){ - placePublished = newVal; - } - - /** - * - * @param newVal - */ - public void setPublisher(String newVal){ - publisher = newVal; - } - - /** - * - * @param newVal - */ - public void setTitle(String newVal){ - title = newVal; - } - - /** - * - * @param newVal - */ - public void setUrl(String newVal){ - url = newVal; - } - -} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Unpublished.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Unpublished.java deleted file mode 100644 index 254702fb84..0000000000 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Unpublished.java +++ /dev/null @@ -1,23 +0,0 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.publication; - - -import org.apache.log4j.Logger; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:17 - */ -public class Unpublished extends PublicationBase { - static Logger logger = Logger.getLogger(Unpublished.class); - -} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Article.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Article.java similarity index 52% rename from cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Article.java rename to cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Article.java index 16df815cdd..b41550f18c 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Article.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Article.java @@ -1,66 +1,102 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.publication; - - -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:35:59 - */ -@Entity -public class Article extends PublicationBase implements NomenclaturalReference { - static Logger logger = Logger.getLogger(Article.class); - - private String series; - private String volume; - private Journal inJournal; - - public Journal getInJournal(){ - return inJournal; - } - - public String getSeries(){ - return series; - } - - public String getVolume(){ - return volume; - } - - /** - * - * @param newVal - */ - public void setInJournal(Journal newVal){ - inJournal = newVal; - } - - /** - * - * @param newVal - */ - public void setSeries(String newVal){ - series = newVal; - } - - /** - * - * @param newVal - */ - public void setVolume(String newVal){ - volume = newVal; - } - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:35 + */ +public class Article extends StrictReferenceBase implements INomenclaturalReference { + static Logger logger = Logger.getLogger(Article.class); + + @Description("") + private String series; + @Description("") + private String volume; + @Description("") + private String pages; + private Journal inJournal; + + public Journal getInJournal(){ + return inJournal; + } + + /** + * + * @param newVal + */ + public void setInJournal(Journal newVal){ + inJournal = newVal; + } + + public String getSeries(){ + return series; + } + + /** + * + * @param newVal + */ + public void setSeries(String newVal){ + series = newVal; + } + + public String getVolume(){ + return volume; + } + + /** + * + * @param newVal + */ + public void setVolume(String newVal){ + volume = newVal; + } + + public String getPages(){ + return pages; + } + + /** + * + * @param newVal + */ + public void setPages(String newVal){ + pages = newVal; + } + + /** + * returns a formatted string containing the entire reference citation including + * authors + */ + @Transient + public String getCitation(){ + return ""; + } + + /** + * returns a formatted string containing the reference citation excluding authors + * as used in a taxon name + */ + @Transient + public String getNomenclaturalCitation(){ + return ""; + } + + @Transient + public String getYear(){ + return ""; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/BibtexEntryType.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/BibtexEntryType.java new file mode 100644 index 0000000000..ba7c996eaf --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/BibtexEntryType.java @@ -0,0 +1,154 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import etaxonomy.cdm.model.common.EnumeratedTermBase; +import org.apache.log4j.Logger; + +/** + * Bibtex bibliography entries are split by types + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:36 + */ +public class BibtexEntryType extends EnumeratedTermBase { + static Logger logger = Logger.getLogger(BibtexEntryType.class); + + /** + * An article from a journal or magazine. + * Required fields: author, title, journal, year + * Optional fields: volume, number, pages, month, note + */ + public static final BibtexEntryType ARTICLE(){ + return null; + } + + /** + * A book with an explicit publisher. + * Required fields: author/editor, title, publisher, year + * Optional fields: volume, series, address, edition, month, note + */ + public static final BibtexEntryType BOOK(){ + return null; + } + + /** + * A work that is printed and bound, but without a named publisher or sponsoring + * institution. + * Required fields: title + * Optional fields: author, howpublished, address, month, year, note + */ + public static final BibtexEntryType BOOKLET(){ + return null; + } + + /** + * A part of a book, which may be a chapter (or section or whatever) and/or a + * range of pages. + * Required fields: author/editor, title, chapter/pages, publisher, year + * Optional fields: volume, series, address, edition, month, note + */ + public static final BibtexEntryType INBOOK(){ + return null; + } + + /** + * A part of a book having its own title. + * Required fields: author, title, booktitle, year + * Optional fields: editor, pages, organization, publisher, address, month, note + */ + public static final BibtexEntryType INCOLLECTION(){ + return null; + } + + /** + * The proceedings of a conference. + * Required fields: title, year + * Optional fields: editor, publisher, organization, address, month, note + */ + public static final BibtexEntryType PROCEEDINGS(){ + return null; + } + + /** + * An article in a conference proceedings. + * Required fields: author, title, booktitle, year + * Optional fields: editor, pages, organization, publisher, address, month, note + */ + public static final BibtexEntryType INPROCEEDINGS(){ + return null; + } + + /** + * The same as inproceedings. + * Required fields: author, title, booktitle, year + * Optional fields: editor, pages, organization, publisher, address, month, note + */ + public static final BibtexEntryType CONFERENCE(){ + return null; + } + + /** + * Technical documentation. + * Required fields: title + * Optional fields: author, organization, address, edition, month, year, note + */ + public static final BibtexEntryType MANUAL(){ + return null; + } + + /** + * A Master's thesis. + * Required fields: author, title, school, year + * Optional fields: address, month, note + */ + public static final BibtexEntryType MASTERTHESIS(){ + return null; + } + + /** + * A Ph.D. thesis. + * Required fields: author, title, school, year + * Optional fields: address, month, note + */ + public static final BibtexEntryType PHDTHESIS(){ + return null; + } + + /** + * A report published by a school or other institution, usually numbered within a + * series. + * Required fields: author, title, institution, year + * Optional fields: type, number, address, month, note + */ + public static final BibtexEntryType TECHREPORT(){ + return null; + } + + /** + * A document having an author and title, but not formally published. + * Required fields: author, title, note + * Optional fields: month, year + */ + public static final BibtexEntryType UNPUBLISHED(){ + return null; + } + + /** + * For use when nothing else fits. + * Required fields: none + * Optional fields: author, title, howpublished, month, year, note + */ + public static final BibtexEntryType MISC(){ + return null; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/BibtexReference.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/BibtexReference.java new file mode 100644 index 0000000000..75dd3987b5 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/BibtexReference.java @@ -0,0 +1,453 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:36 + */ +public class BibtexReference extends ReferenceBase implements INomenclaturalReference { + static Logger logger = Logger.getLogger(BibtexReference.class); + + //The name(s) of the author(s) (in the case of more than one author, separated by and) + @Description("The name(s) of the author(s) (in the case of more than one author, separated by and)") + private String author; + //The journal or magazine the work was published in + + @Description("The journal or magazine the work was published in + ") + private String journal; + //The title of the book, if only part of it is being cited + @Description("The title of the book, if only part of it is being cited") + private String booktitle; + //The chapter number + @Description("The chapter number") + private String chapter; + //The title of the work + + @Description("The title of the work + ") + private String title; + //The series of books the book was published in (e.g. "The Hardy Boys") + + @Description("The series of books the book was published in (e.g. "The Hardy Boys") + ") + private String series; + //The edition of a book, long form (such as "first" or "second") + @Description("The edition of a book, long form (such as "first" or "second")") + private String edition; + //The volume of a journal or multi-volume book + + @Description("The volume of a journal or multi-volume book + ") + private String volume; + //The "number" of a journal, magazine, or tech-report, if applicable. (Most publications have a "volume", but no "number" + //field.) + // + + @Description("The "number" of a journal, magazine, or tech-report, if applicable. (Most publications have a "volume", but no "number" field.) + + ") + private String number; + //Page numbers, separated either by commas or double-hyphens + + @Description("Page numbers, separated either by commas or double-hyphens + ") + private String pages; + //An annotation for annotated bibliography styles (not typical) + @Description("An annotation for annotated bibliography styles (not typical)") + private String annote; + //The name(s) of the editor(s) + + @Description("The name(s) of the editor(s) + ") + private String editor; + //The institution that was involved in the publishing, but not necessarily the publisher + + @Description("The institution that was involved in the publishing, but not necessarily the publisher + ") + private String institution; + //The school where the thesis was written + @Description("The school where the thesis was written ") + private String school; + //The conference sponsor + + @Description("The conference sponsor + ") + private String organization; + //The publisher's name + // + + @Description("The publisher's name + + ") + private String publisher; + //Publisher's address (usually just the city, but can be the full address for lesser-known publishers) + @Description("Publisher's address (usually just the city, but can be the full address for lesser-known publishers)") + private String address; + //How it was published, if the publishing method is nonstandard + + @Description("How it was published, if the publishing method is nonstandard + ") + private String howpublished; + //The type of tech-report, for example, "Research Note" + // + + @Description("The type of tech-report, for example, "Research Note" + + ") + private String type; + //The month of publication (or, if unpublished, the month of creation) + // + + @Description("The month of publication (or, if unpublished, the month of creation) + + ") + private String month; + //The year of publication (or, if unpublished, the year of creation) + + @Description("The year of publication (or, if unpublished, the year of creation) + ") + private String year; + //A specification of an electronic publication, often a preprint or a technical report + + @Description("A specification of an electronic publication, often a preprint or a technical report + ") + private String eprint; + //Miscellaneous extra information + // + + @Description("Miscellaneous extra information + + ") + private String note; + private BibtexReference crossref; + + public BibtexReference getCrossref(){ + return crossref; + } + + /** + * + * @param newVal + */ + public void setCrossref(BibtexReference newVal){ + crossref = newVal; + } + + public String getAuthor(){ + return author; + } + + /** + * + * @param newVal + */ + public void setAuthor(String newVal){ + author = newVal; + } + + public String getJournal(){ + return journal; + } + + /** + * + * @param newVal + */ + public void setJournal(String newVal){ + journal = newVal; + } + + public String getBooktitle(){ + return booktitle; + } + + /** + * + * @param newVal + */ + public void setBooktitle(String newVal){ + booktitle = newVal; + } + + public String getChapter(){ + return chapter; + } + + /** + * + * @param newVal + */ + public void setChapter(String newVal){ + chapter = newVal; + } + + public String getTitle(){ + return title; + } + + /** + * + * @param newVal + */ + public void setTitle(String newVal){ + title = newVal; + } + + public String getSeries(){ + return series; + } + + /** + * + * @param newVal + */ + public void setSeries(String newVal){ + series = newVal; + } + + public String getEdition(){ + return edition; + } + + /** + * + * @param newVal + */ + public void setEdition(String newVal){ + edition = newVal; + } + + public String getVolume(){ + return volume; + } + + /** + * + * @param newVal + */ + public void setVolume(String newVal){ + volume = newVal; + } + + public String getNumber(){ + return number; + } + + /** + * + * @param newVal + */ + public void setNumber(String newVal){ + number = newVal; + } + + public String getPages(){ + return pages; + } + + /** + * + * @param newVal + */ + public void setPages(String newVal){ + pages = newVal; + } + + public String getAnnote(){ + return annote; + } + + /** + * + * @param newVal + */ + public void setAnnote(String newVal){ + annote = newVal; + } + + public String getEditor(){ + return editor; + } + + /** + * + * @param newVal + */ + public void setEditor(String newVal){ + editor = newVal; + } + + public String getInstitution(){ + return institution; + } + + /** + * + * @param newVal + */ + public void setInstitution(String newVal){ + institution = newVal; + } + + public String getSchool(){ + return school; + } + + /** + * + * @param newVal + */ + public void setSchool(String newVal){ + school = newVal; + } + + public String getOrganization(){ + return organization; + } + + /** + * + * @param newVal + */ + public void setOrganization(String newVal){ + organization = newVal; + } + + public String getPublisher(){ + return publisher; + } + + /** + * + * @param newVal + */ + public void setPublisher(String newVal){ + publisher = newVal; + } + + public String getAddress(){ + return address; + } + + /** + * + * @param newVal + */ + public void setAddress(String newVal){ + address = newVal; + } + + public String getHowpublished(){ + return howpublished; + } + + /** + * + * @param newVal + */ + public void setHowpublished(String newVal){ + howpublished = newVal; + } + + public String getType(){ + return type; + } + + /** + * + * @param newVal + */ + public void setType(String newVal){ + type = newVal; + } + + public String getMonth(){ + return month; + } + + /** + * + * @param newVal + */ + public void setMonth(String newVal){ + month = newVal; + } + + public String getYear(){ + return year; + } + + /** + * + * @param newVal + */ + public void setYear(String newVal){ + year = newVal; + } + + public String getEprint(){ + return eprint; + } + + /** + * + * @param newVal + */ + public void setEprint(String newVal){ + eprint = newVal; + } + + public String getNote(){ + return note; + } + + /** + * + * @param newVal + */ + public void setNote(String newVal){ + note = newVal; + } + + /** + * returns a formatted string containing the entire reference citation including + * authors + */ + @Transient + public String getCitation(){ + return ""; + } + + /** + * returns a formatted string containing the reference citation excluding authors + * as used in a taxon name + */ + @Transient + public String getNomenclaturalCitation(){ + return ""; + } + + @Transient + public int getYear(){ + return 0; + } + + @Transient + public String getYear(){ + return ""; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Book.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Book.java similarity index 53% rename from cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Book.java rename to cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Book.java index 52d31eb4f5..b2d30ac95f 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Book.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Book.java @@ -1,79 +1,75 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.publication; - - -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:00 - */ -@Entity -public class Book extends PublicationBase implements NomenclaturalReference { - static Logger logger = Logger.getLogger(Book.class); - - private String edition; - private String editor; - private String isbn; - private BookSeries inSeries; - - public String getEdition(){ - return edition; - } - - public String getEditor(){ - return editor; - } - - public BookSeries getInSeries(){ - return inSeries; - } - - public String getIsbn(){ - return isbn; - } - - /** - * - * @param newVal - */ - public void setEdition(String newVal){ - edition = newVal; - } - - /** - * - * @param newVal - */ - public void setEditor(String newVal){ - editor = newVal; - } - - /** - * - * @param newVal - */ - public void setInSeries(BookSeries newVal){ - inSeries = newVal; - } - - /** - * - * @param newVal - */ - public void setIsbn(String newVal){ - isbn = newVal; - } - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:37 + */ +public class Book extends PrintedUnitBase implements INomenclaturalReference { + static Logger logger = Logger.getLogger(Book.class); + + @Description("") + private String edition; + @Description("") + private String isbn; + + public String getEdition(){ + return edition; + } + + /** + * + * @param newVal + */ + public void setEdition(String newVal){ + edition = newVal; + } + + public String getIsbn(){ + return isbn; + } + + /** + * + * @param newVal + */ + public void setIsbn(String newVal){ + isbn = newVal; + } + + /** + * returns a formatted string containing the entire reference citation including + * authors + */ + @Transient + public String getCitation(){ + return ""; + } + + /** + * returns a formatted string containing the reference citation excluding authors + * as used in a taxon name + */ + @Transient + public String getNomenclaturalCitation(){ + return ""; + } + + @Transient + public String getYear(){ + return ""; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/BookSection.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/BookSection.java new file mode 100644 index 0000000000..8946a225e2 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/BookSection.java @@ -0,0 +1,60 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:38 + */ +public class BookSection extends SectionBase implements INomenclaturalReference { + static Logger logger = Logger.getLogger(BookSection.class); + + private Book inBook; + + public Book getInBook(){ + return inBook; + } + + /** + * + * @param newVal + */ + public void setInBook(Book newVal){ + inBook = newVal; + } + + /** + * returns a formatted string containing the entire reference citation including + * authors + */ + @Transient + public String getCitation(){ + return ""; + } + + /** + * returns a formatted string containing the reference citation excluding authors + * as used in a taxon name + */ + @Transient + public String getNomenclaturalCitation(){ + return ""; + } + + @Transient + public String getYear(){ + return ""; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/CdDvd.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/CdDvd.java similarity index 76% rename from cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/CdDvd.java rename to cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/CdDvd.java index 004ddda978..1f749573d2 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/CdDvd.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/CdDvd.java @@ -1,23 +1,23 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.publication; - - -import org.apache.log4j.Logger; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:01 - */ -public class CdDvd extends PublicationBase { - static Logger logger = Logger.getLogger(CdDvd.class); - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:39 + */ +public class CdDvd extends PublicationBase { + static Logger logger = Logger.getLogger(CdDvd.class); + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/ConferenceProceedings.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/ConferenceProceedings.java similarity index 67% rename from cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/ConferenceProceedings.java rename to cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/ConferenceProceedings.java index 924cf06958..a13a63ada5 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/ConferenceProceedings.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/ConferenceProceedings.java @@ -1,23 +1,23 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.publication; - - -import org.apache.log4j.Logger; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:02 - */ -public class ConferenceProceedings extends PublicationBase { - static Logger logger = Logger.getLogger(ConferenceProceedings.class); - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:41 + */ +public class ConferenceProceedings extends StrictReferenceBase { + static Logger logger = Logger.getLogger(ConferenceProceedings.class); + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Database.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Database.java similarity index 77% rename from cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Database.java rename to cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Database.java index 9e832ae376..f2a5ba175a 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Database.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Database.java @@ -1,23 +1,23 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.publication; - - -import org.apache.log4j.Logger; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:03 - */ -public class Database extends PublicationBase { - static Logger logger = Logger.getLogger(Database.class); - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:43 + */ +public class Database extends PublicationBase { + static Logger logger = Logger.getLogger(Database.class); + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Generic.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Generic.java new file mode 100644 index 0000000000..24e824e847 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Generic.java @@ -0,0 +1,134 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import org.apache.log4j.Logger; + +/** + * This class is to represent all references which cannot be clearly assigned to a + * specific reference type. Therefore attributes which are only used by a unique + * reference type are not necessary here. + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:50 + */ +public class Generic extends StrictReferenceBase implements INomenclaturalReference { + static Logger logger = Logger.getLogger(Generic.class); + + @Description("") + private String publisher; + @Description("") + private String placePublished; + @Description("") + private String editor; + @Description("") + private String series; + @Description("") + private String volume; + @Description("") + private String pages; + + public String getPublisher(){ + return publisher; + } + + /** + * + * @param newVal + */ + public void setPublisher(String newVal){ + publisher = newVal; + } + + public String getPlacePublished(){ + return placePublished; + } + + /** + * + * @param newVal + */ + public void setPlacePublished(String newVal){ + placePublished = newVal; + } + + public String getEditor(){ + return editor; + } + + /** + * + * @param newVal + */ + public void setEditor(String newVal){ + editor = newVal; + } + + public String getSeries(){ + return series; + } + + /** + * + * @param newVal + */ + public void setSeries(String newVal){ + series = newVal; + } + + public String getVolume(){ + return volume; + } + + /** + * + * @param newVal + */ + public void setVolume(String newVal){ + volume = newVal; + } + + public String getPages(){ + return pages; + } + + /** + * + * @param newVal + */ + public void setPages(String newVal){ + pages = newVal; + } + + /** + * returns a formatted string containing the entire reference citation including + * authors + */ + @Transient + public String getCitation(){ + return ""; + } + + /** + * returns a formatted string containing the reference citation excluding authors + * as used in a taxon name + */ + @Transient + public String getNomenclaturalCitation(){ + return ""; + } + + @Transient + public String getYear(){ + return ""; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/INomenclaturalReference.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/INomenclaturalReference.java new file mode 100644 index 0000000000..57f6c82f44 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/INomenclaturalReference.java @@ -0,0 +1,32 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:54 + */ +public interface INomenclaturalReference { + + /** + * returns a formatted string containing the reference citation excluding authors + * as used in a taxon name + */ + @Transient + public String getNomenclaturalCitation(); + + @Transient + public String getYear(); + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/InProceedings.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/InProceedings.java new file mode 100644 index 0000000000..2ce994f8f5 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/InProceedings.java @@ -0,0 +1,37 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:54 + */ +public class InProceedings extends SectionBase { + static Logger logger = Logger.getLogger(InProceedings.class); + + private Proceedings inProceedings; + + public Proceedings getInProceedings(){ + return inProceedings; + } + + /** + * + * @param newVal + */ + public void setInProceedings(Proceedings newVal){ + inProceedings = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Journal.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Journal.java similarity index 80% rename from cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Journal.java rename to cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Journal.java index 17579143f2..e167de3c5c 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Journal.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Journal.java @@ -1,37 +1,38 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.publication; - - -import org.apache.log4j.Logger; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:05 - */ -public class Journal extends PublicationBase { - static Logger logger = Logger.getLogger(Journal.class); - - private String issn; - - public String getIssn(){ - return issn; - } - - /** - * - * @param newVal - */ - public void setIssn(String newVal){ - issn = newVal; - } - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:56 + */ +public class Journal extends PublicationBase { + static Logger logger = Logger.getLogger(Journal.class); + + @Description("") + private String issn; + + public String getIssn(){ + return issn; + } + + /** + * + * @param newVal + */ + public void setIssn(String newVal){ + issn = newVal; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Map.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Map.java similarity index 76% rename from cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Map.java rename to cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Map.java index 770aa261eb..8057dd9d46 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Map.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Map.java @@ -1,23 +1,23 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.publication; - - -import org.apache.log4j.Logger; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:06 - */ -public class Map extends PublicationBase { - static Logger logger = Logger.getLogger(Map.class); - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:58 + */ +public class Map extends PublicationBase { + static Logger logger = Logger.getLogger(Map.class); + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Patent.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Patent.java similarity index 68% rename from cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Patent.java rename to cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Patent.java index c1b493b6a9..0d10eed726 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Patent.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Patent.java @@ -1,23 +1,23 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.publication; - - -import org.apache.log4j.Logger; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:10 - */ -public class Patent extends PublicationBase { - static Logger logger = Logger.getLogger(Patent.class); - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:07 + */ +public class Patent extends StrictReferenceBase { + static Logger logger = Logger.getLogger(Patent.class); + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/PersonalCommunication.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/PersonalCommunication.java similarity index 67% rename from cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/PersonalCommunication.java rename to cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/PersonalCommunication.java index db1ddc5414..e36ae52924 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/PersonalCommunication.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/PersonalCommunication.java @@ -1,23 +1,23 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.publication; - - -import org.apache.log4j.Logger; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:10 - */ -public class PersonalCommunication extends PublicationBase { - static Logger logger = Logger.getLogger(PersonalCommunication.class); - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:07 + */ +public class PersonalCommunication extends StrictReferenceBase { + static Logger logger = Logger.getLogger(PersonalCommunication.class); + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/BookSeries.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/PrintSeries.java similarity index 61% rename from cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/BookSeries.java rename to cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/PrintSeries.java index 149543c14f..7c45c5d351 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/BookSeries.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/PrintSeries.java @@ -1,40 +1,38 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.publication; - - -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:01 - */ -@Entity -public class BookSeries extends PublicationBase { - static Logger logger = Logger.getLogger(BookSeries.class); - - private String series; - - public String getSeries(){ - return series; - } - - /** - * - * @param newVal - */ - public void setSeries(String newVal){ - series = newVal; - } - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:10 + */ +public class PrintSeries extends PublicationBase { + static Logger logger = Logger.getLogger(PrintSeries.class); + + @Description("") + private String series; + + public String getSeries(){ + return series; + } + + /** + * + * @param newVal + */ + public void setSeries(String newVal){ + series = newVal; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/PrintedUnitBase.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/PrintedUnitBase.java new file mode 100644 index 0000000000..a4a6976935 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/PrintedUnitBase.java @@ -0,0 +1,79 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:10 + */ +public abstract class PrintedUnitBase extends PublicationBase { + static Logger logger = Logger.getLogger(PrintedUnitBase.class); + + @Description("") + private String editor; + @Description("") + private String volume; + @Description("") + private String pages; + private PrintSeries inSeries; + + public PrintSeries getInSeries(){ + return inSeries; + } + + /** + * + * @param newVal + */ + public void setInSeries(PrintSeries newVal){ + inSeries = newVal; + } + + public String getEditor(){ + return editor; + } + + /** + * + * @param newVal + */ + public void setEditor(String newVal){ + editor = newVal; + } + + public String getVolume(){ + return volume; + } + + /** + * + * @param newVal + */ + public void setVolume(String newVal){ + volume = newVal; + } + + public String getPages(){ + return pages; + } + + /** + * + * @param newVal + */ + public void setPages(String newVal){ + pages = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Proceedings.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Proceedings.java new file mode 100644 index 0000000000..ebd2ab79f6 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Proceedings.java @@ -0,0 +1,39 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:10 + */ +public class Proceedings extends PrintedUnitBase { + static Logger logger = Logger.getLogger(Proceedings.class); + + //The conference sponsor + @Description("The conference sponsor") + private String organization; + + public String getOrganization(){ + return organization; + } + + /** + * + * @param newVal + */ + public void setOrganization(String newVal){ + organization = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/PublicationBase.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/PublicationBase.java new file mode 100644 index 0000000000..f16f74026e --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/PublicationBase.java @@ -0,0 +1,52 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:11 + */ +public abstract class PublicationBase extends StrictReferenceBase { + static Logger logger = Logger.getLogger(PublicationBase.class); + + @Description("") + private String publisher; + @Description("") + private String placePublished; + + public String getPublisher(){ + return publisher; + } + + /** + * + * @param newVal + */ + public void setPublisher(String newVal){ + publisher = newVal; + } + + public String getPlacePublished(){ + return placePublished; + } + + /** + * + * @param newVal + */ + public void setPlacePublished(String newVal){ + placePublished = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/ReferenceBase.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/ReferenceBase.java new file mode 100644 index 0000000000..2524231041 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/ReferenceBase.java @@ -0,0 +1,94 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import etaxonomy.cdm.model.agent.Team; +import etaxonomy.cdm.model.common.IdentifiableEntity; +import org.apache.log4j.Logger; + +/** + * A year() method is required to get the year of publication out of the + * datePublished field + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:12 + */ +public abstract class ReferenceBase extends IdentifiableEntity { + static Logger logger = Logger.getLogger(ReferenceBase.class); + + //URIs like DOIs, LSIDs or Handles for this reference + @Description("URIs like DOIs, LSIDs or Handles for this reference ") + private String uri; + //flag to subselect only references that could be useful for nomenclatural citations. If a reference is used as a + //nomenclatural reference in a name this flag should be automatically set + @Description("flag to subselect only references that could be useful for nomenclatural citations. If a reference is used as a nomenclatural reference in a name this flag should be automatically set") + private boolean isNomenclaturallyRelevant; + private ArrayList referenceInSource; + private Team authorTeam; + + public ArrayList getReferenceInSource(){ + return referenceInSource; + } + + /** + * + * @param newVal + */ + public void setReferenceInSource(ArrayList newVal){ + referenceInSource = newVal; + } + + public Team getAuthorTeam(){ + return authorTeam; + } + + /** + * + * @param newVal + */ + public void setAuthorTeam(Team newVal){ + authorTeam = newVal; + } + + public String getUri(){ + return uri; + } + + /** + * + * @param newVal + */ + public void setUri(String newVal){ + uri = newVal; + } + + public boolean isNomenclaturallyRelevant(){ + return isNomenclaturallyRelevant; + } + + /** + * + * @param newVal + */ + public void setNomenclaturallyRelevant(boolean newVal){ + isNomenclaturallyRelevant = newVal; + } + + /** + * returns a formatted string containing the entire reference citation including + * authors + */ + @Transient + public String getCitation(){ + return ""; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/ReferenceInSource.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/ReferenceInSource.java new file mode 100644 index 0000000000..2ef5126e91 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/ReferenceInSource.java @@ -0,0 +1,24 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import etaxonomy.cdm.model.common.EntityInSourceBase; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:13 + */ +public class ReferenceInSource extends EntityInSourceBase { + static Logger logger = Logger.getLogger(ReferenceInSource.class); + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Report.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Report.java new file mode 100644 index 0000000000..caad63b291 --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Report.java @@ -0,0 +1,39 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import etaxonomy.cdm.model.agent.Institution; +import org.apache.log4j.Logger; + +/** + * publisher is "institution" in BibTex ??? + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:14 + */ +public class Report extends PublicationBase { + static Logger logger = Logger.getLogger(Report.class); + + private Institution institution; + + public Institution getInstitution(){ + return institution; + } + + /** + * + * @param newVal + */ + public void setInstitution(Institution newVal){ + institution = newVal; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/SectionBase.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/SectionBase.java new file mode 100644 index 0000000000..d13ac3511b --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/SectionBase.java @@ -0,0 +1,43 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:16 + */ +public abstract class SectionBase extends StrictReferenceBase { + static Logger logger = Logger.getLogger(SectionBase.class); + + @Description("") + private String pages; + + public String getPages(){ + return pages; + } + + /** + * + * @param newVal + */ + public void setPages(String newVal){ + pages = newVal; + } + + @Transient + public PrintedUnitBase getPrintedUnit(){ + return null; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/StrictReferenceBase.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/StrictReferenceBase.java new file mode 100644 index 0000000000..a576cf421c --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/StrictReferenceBase.java @@ -0,0 +1,72 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import org.apache.log4j.Logger; + +/** + * A year() method is required to get the year of publication out of the + * datePublished field + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:19 + */ +public abstract class StrictReferenceBase extends ReferenceBase { + static Logger logger = Logger.getLogger(StrictReferenceBase.class); + + //Title of the reference + @Description("Title of the reference") + private String title; + //The date range assigned to the reference. + //ISO Date range like. Flexible, year can be left out, etc + @Description("The date range assigned to the reference. + ISO Date range like. Flexible, year can be left out, etc") + private DateRange datePublished; + + public String getTitle(){ + return title; + } + + /** + * + * @param newVal + */ + public void setTitle(String newVal){ + title = newVal; + } + + public DateRange getDatePublished(){ + return datePublished; + } + + /** + * + * @param newVal + */ + public void setDatePublished(DateRange newVal){ + datePublished = newVal; + } + + /** + * returns a formatted string containing the entire reference citation including + * authors + */ + @Transient + public String getCitation(){ + return ""; + } + + @Transient + public int getYear(){ + return 0; + } + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Thesis.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Thesis.java similarity index 56% rename from cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Thesis.java rename to cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Thesis.java index 6a81eed8ab..76d694069e 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/Thesis.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/Thesis.java @@ -1,23 +1,38 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.publication; - - -import org.apache.log4j.Logger; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:16 - */ -public class Thesis extends PublicationBase { - static Logger logger = Logger.getLogger(Thesis.class); - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import etaxonomy.cdm.model.agent.Institution; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:24 + */ +public class Thesis extends PublicationBase { + static Logger logger = Logger.getLogger(Thesis.class); + + private Institution school; + + public Institution getSchool(){ + return school; + } + + /** + * + * @param newVal + */ + public void setSchool(Institution newVal){ + school = newVal; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/WebPage.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/WebPage.java similarity index 77% rename from cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/WebPage.java rename to cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/WebPage.java index cfcc5257e3..c6b15d87c6 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/publication/WebPage.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/reference/WebPage.java @@ -1,23 +1,23 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.publication; - - -import org.apache.log4j.Logger; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:19 - */ -public class WebPage extends PublicationBase { - static Logger logger = Logger.getLogger(WebPage.class); - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.reference; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:27 + */ +public class WebPage extends PublicationBase { + static Logger logger = Logger.getLogger(WebPage.class); + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/specimen/Country.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/specimen/Country.java deleted file mode 100644 index 391a125fea..0000000000 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/specimen/Country.java +++ /dev/null @@ -1,41 +0,0 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.specimen; - - -import eu.etaxonomy.cdm.model.common.VersionableEntity; -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:03 - */ -@Entity -public class Country extends VersionableEntity { - static Logger logger = Logger.getLogger(Country.class); - - private String name; - - public String getName(){ - return name; - } - - /** - * - * @param newVal - */ - public void setName(String newVal){ - name = newVal; - } - -} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/specimen/Institution.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/specimen/Institution.java deleted file mode 100644 index ba1e452cfa..0000000000 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/specimen/Institution.java +++ /dev/null @@ -1,67 +0,0 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.specimen; - - -import eu.etaxonomy.cdm.model.common.VersionableEntity; -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:05 - */ -@Entity -public class Institution extends VersionableEntity { - static Logger logger = Logger.getLogger(Institution.class); - - private String code; - private String name; - private String townOrLocation; - - public String getCode(){ - return code; - } - - public String getName(){ - return name; - } - - public String getTownOrLocation(){ - return townOrLocation; - } - - /** - * - * @param newVal - */ - public void setCode(String newVal){ - code = newVal; - } - - /** - * - * @param newVal - */ - public void setName(String newVal){ - name = newVal; - } - - /** - * - * @param newVal - */ - public void setTownOrLocation(String newVal){ - townOrLocation = newVal; - } - -} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/specimen/Locality.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/specimen/Locality.java deleted file mode 100644 index 501f410fca..0000000000 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/specimen/Locality.java +++ /dev/null @@ -1,54 +0,0 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.specimen; - - -import eu.etaxonomy.cdm.model.common.VersionableEntity; -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:06 - */ -@Entity -public class Locality extends VersionableEntity { - static Logger logger = Logger.getLogger(Locality.class); - - private String name; - private Region region; - - public String getName(){ - return name; - } - - public Region getRegion(){ - return region; - } - - /** - * - * @param newVal - */ - public void setName(String newVal){ - name = newVal; - } - - /** - * - * @param newVal - */ - public void setRegion(Region newVal){ - region = newVal; - } - -} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/specimen/MaterialCategory.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/specimen/MaterialCategory.java deleted file mode 100644 index 6d2dc3c80e..0000000000 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/specimen/MaterialCategory.java +++ /dev/null @@ -1,27 +0,0 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.specimen; - - -import org.apache.log4j.Logger; - -/** - * The list should be extensible at runtime through configuration. This needs to - * be investigated. - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:06 - */ -public enum MaterialCategory { - SPECIMEN, - CULTURE, - FOSSIL, - OBSERVATION -} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/specimen/Region.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/specimen/Region.java deleted file mode 100644 index aafffbbf5f..0000000000 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/specimen/Region.java +++ /dev/null @@ -1,54 +0,0 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.specimen; - - -import eu.etaxonomy.cdm.model.common.VersionableEntity; -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:12 - */ -@Entity -public class Region extends VersionableEntity { - static Logger logger = Logger.getLogger(Region.class); - - private String name; - private Country country; - - public Country getCountry(){ - return country; - } - - public String getName(){ - return name; - } - - /** - * - * @param newVal - */ - public void setCountry(Country newVal){ - country = newVal; - } - - /** - * - * @param newVal - */ - public void setName(String newVal){ - name = newVal; - } - -} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/specimen/Specimen.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/specimen/Specimen.java deleted file mode 100644 index 0f36d968e2..0000000000 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/specimen/Specimen.java +++ /dev/null @@ -1,160 +0,0 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.specimen; - - -import eu.etaxonomy.cdm.model.agent.Team; -import eu.etaxonomy.cdm.model.common.IdentifiableEntity; -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:13 - */ -@Entity -public class Specimen extends IdentifiableEntity { - static Logger logger = Logger.getLogger(Specimen.class); - - private String citation; - private Calendar collectingDate; - private String coordinates; - //Elevation in meter above sea level - private int elevation; - private float latitude; - private float longitude; - private Locality locality; - private MaterialCategory material; - private Team collector; - private Collection collection; - - public String getCitation(){ - return citation; - } - - public Calendar getCollectingDate(){ - return collectingDate; - } - - public Collection getCollection(){ - return collection; - } - - public Team getCollector(){ - return collector; - } - - public String getCoordinates(){ - return coordinates; - } - - public int getElevation(){ - return elevation; - } - - public float getLatitude(){ - return latitude; - } - - public Locality getLocality(){ - return locality; - } - - public float getLongitude(){ - return longitude; - } - - public MaterialCategory getMaterial(){ - return material; - } - - /** - * - * @param newVal - */ - public void setCitation(String newVal){ - citation = newVal; - } - - /** - * - * @param newVal - */ - public void setCollectingDate(Calendar newVal){ - collectingDate = newVal; - } - - /** - * - * @param newVal - */ - public void setCollection(Collection newVal){ - collection = newVal; - } - - /** - * - * @param newVal - */ - public void setCollector(Team newVal){ - collector = newVal; - } - - /** - * - * @param newVal - */ - public void setCoordinates(String newVal){ - coordinates = newVal; - } - - /** - * - * @param newVal - */ - public void setElevation(int newVal){ - elevation = newVal; - } - - /** - * - * @param newVal - */ - public void setLatitude(float newVal){ - latitude = newVal; - } - - /** - * - * @param newVal - */ - public void setLocality(Locality newVal){ - locality = newVal; - } - - /** - * - * @param newVal - */ - public void setLongitude(float newVal){ - longitude = newVal; - } - - /** - * - * @param newVal - */ - public void setMaterial(MaterialCategory newVal){ - material = newVal; - } - -} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/ConceptRelationshipType.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/ConceptRelationshipType.java index 9c37fc596e..4be60d05c9 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/ConceptRelationshipType.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/ConceptRelationshipType.java @@ -1,56 +1,179 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.taxon; - - -import org.apache.log4j.Logger; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:02 - */ -public enum ConceptRelationshipType { - TAXONOMICALLY_INCLUDED_IN, - MISAPPLIED_NAME_FOR, - INVALID_DESIGNATION_FOR, - CONTRADICTION, - CONGRUENT_TO, - INCLUDED_IN, - CONGRUENT_TO_OR_INCLUDED_IN, - INCLUDES, - CONGRUENT_TO_OR_INCLUDES, - INCLUDED_IN_OR_INCLUDES, - CONGRUENT_TO_OR_INCLUDED_IN_OR_INCLUDES, - OVERLAPS, - CONGRUENT_TO_OR_OVERLAPS, - INCLUDED_IN_OR_OVERLAPS, - CONGRUENT_TO_OR_INCLUDED_IN_OR_OVERLAPS, - INCLUDES_OR_OVERLAPS, - CONGRUENT_TO_OR_INCLUDES_OR_OVERLAPS, - INCLUDED_IN_OR_INCLUDES_OR_OVERLAPS, - DOES_NOT_EXCLUDE, - EXCLUDES, - CONGRUENT_TO_OR_EXCLUDES, - INCLUDED_IN_OR_EXCLUDES, - CONGRUENT_TO_OR_INCLUDED_IN_OR_EXCLUDES, - INCLUDES_OR_EXCLUDES, - CONGRUENT_TO_OR_INCLUDES_OR_EXCLUDES, - INCLUDED_IN_OR_INCLUDES_OR_EXCLUDES, - DOES_NOT_OVERLAP, - OVERLAPS_OR_EXCLUDES, - CONGRUENT_TO_OR_OVERLAPS_OR_EXCLUDES, - INCLUDED_IN_OR_OVERLAPS_OR_EXCLUDES, - DOES_NOT_INCLUDE, - INCLUDES_OR_OVERLAPS_OR_EXCLUDES, - NOT_INCLUDED_IN, - NOT_CONGRUENT_TO, - ALL_RELATIONSHIPS +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.taxon; + + +import etaxonomy.cdm.model.common.EnumeratedTermBase; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:14:41 + */ +public class ConceptRelationshipType extends EnumeratedTermBase { + static Logger logger = Logger.getLogger(ConceptRelationshipType.class); + + @Description("") + private static final int initializationClassUri = http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonRelationshipTerm; + + public getInitializationClassUri(){ + return initializationClassUri; + } + + /** + * + * @param newVal + */ + public void setInitializationClassUri(newVal){ + initializationClassUri = newVal; + } + + public static final ConceptRelationshipType TAXONOMICALLY_INCLUDED_IN(){ + return null; + } + + public static final ConceptRelationshipType MISAPPLIED_NAME_FOR(){ + return null; + } + + public static final ConceptRelationshipType INVALID_DESIGNATION_FOR(){ + return null; + } + + public static final ConceptRelationshipType CONTRADICTION(){ + return null; + } + + public static final ConceptRelationshipType CONGRUENT_TO(){ + return null; + } + + public static final ConceptRelationshipType INCLUDED_IN(){ + return null; + } + + public static final ConceptRelationshipType CONGRUENT_TO_OR_INCLUDED_IN(){ + return null; + } + + public static final ConceptRelationshipType INCLUDES(){ + return null; + } + + public static final ConceptRelationshipType CONGRUENT_TO_OR_INCLUDES(){ + return null; + } + + public static final ConceptRelationshipType INCLUDED_IN_OR_INCLUDES(){ + return null; + } + + public static final ConceptRelationshipType CONGRUENT_TO_OR_INCLUDED_IN_OR_INCLUDES(){ + return null; + } + + public static final ConceptRelationshipType OVERLAPS(){ + return null; + } + + public static final ConceptRelationshipType CONGRUENT_TO_OR_OVERLAPS(){ + return null; + } + + public static final ConceptRelationshipType INCLUDED_IN_OR_OVERLAPS(){ + return null; + } + + public static final ConceptRelationshipType CONGRUENT_TO_OR_INCLUDED_IN_OR_OVERLAPS(){ + return null; + } + + public static final ConceptRelationshipType INCLUDES_OR_OVERLAPS(){ + return null; + } + + public static final ConceptRelationshipType CONGRUENT_TO_OR_INCLUDES_OR_OVERLAPS(){ + return null; + } + + public static final ConceptRelationshipType INCLUDED_IN_OR_INCLUDES_OR_OVERLAPS(){ + return null; + } + + public static final ConceptRelationshipType DOES_NOT_EXCLUDE(){ + return null; + } + + public static final ConceptRelationshipType EXCLUDES(){ + return null; + } + + public static final ConceptRelationshipType CONGRUENT_TO_OR_EXCLUDES(){ + return null; + } + + public static final ConceptRelationshipType INCLUDED_IN_OR_EXCLUDES(){ + return null; + } + + public static final ConceptRelationshipType CONGRUENT_TO_OR_INCLUDED_IN_OR_EXCLUDES(){ + return null; + } + + public static final ConceptRelationshipType INCLUDES_OR_EXCLUDES(){ + return null; + } + + public static final ConceptRelationshipType CONGRUENT_TO_OR_INCLUDES_OR_EXCLUDES(){ + return null; + } + + public static final ConceptRelationshipType INCLUDED_IN_OR_INCLUDES_OR_EXCLUDES(){ + return null; + } + + public static final ConceptRelationshipType DOES_NOT_OVERLAP(){ + return null; + } + + public static final ConceptRelationshipType OVERLAPS_OR_EXCLUDES(){ + return null; + } + + public static final ConceptRelationshipType CONGRUENT_TO_OR_OVERLAPS_OR_EXCLUDES(){ + return null; + } + + public static final ConceptRelationshipType INCLUDED_IN_OR_OVERLAPS_OR_EXCLUDES(){ + return null; + } + + public static final ConceptRelationshipType DOES_NOT_INCLUDE(){ + return null; + } + + public static final ConceptRelationshipType INCLUDES_OR_OVERLAPS_OR_EXCLUDES(){ + return null; + } + + public static final ConceptRelationshipType NOT_INCLUDED_IN(){ + return null; + } + + public static final ConceptRelationshipType NOT_CONGRUENT_TO(){ + return null; + } + + public static final ConceptRelationshipType ALL_RELATIONSHIPS(){ + return null; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/SynonymTaxon.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/Synonym.java similarity index 64% rename from cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/SynonymTaxon.java rename to cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/Synonym.java index aab9149fab..47f2857fea 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/SynonymTaxon.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/Synonym.java @@ -1,40 +1,37 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.taxon; - - -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:14 - */ -@Entity -public class SynonymTaxon extends TaxonBase { - static Logger logger = Logger.getLogger(SynonymTaxon.class); - - private ArrayList synoynmRelations; - - public ArrayList getSynoynmRelations(){ - return synoynmRelations; - } - - /** - * - * @param newVal - */ - public void setSynoynmRelations(ArrayList newVal){ - synoynmRelations = newVal; - } - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.taxon; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:20 + */ +public class Synonym extends TaxonBase { + static Logger logger = Logger.getLogger(Synonym.class); + + private ArrayList synoynmRelations; + + public ArrayList getSynoynmRelations(){ + return synoynmRelations; + } + + /** + * + * @param newVal + */ + public void setSynoynmRelations(ArrayList newVal){ + synoynmRelations = newVal; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/SynonymRelationship.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/SynonymRelationship.java index bd124da04b..38f94beba6 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/SynonymRelationship.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/SynonymRelationship.java @@ -1,67 +1,64 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.taxon; - - -import eu.etaxonomy.cdm.model.common.VersionableEntity; -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:13 - */ -@Entity -public class SynonymRelationship extends VersionableEntity { - static Logger logger = Logger.getLogger(SynonymRelationship.class); - - private AcceptedTaxon acceptedTaxon; - private SynonymRelationshipType type; - private SynonymTaxon synoynm; - - public AcceptedTaxon getAcceptedTaxon(){ - return acceptedTaxon; - } - - public SynonymTaxon getSynoynm(){ - return synoynm; - } - - public SynonymRelationshipType getType(){ - return type; - } - - /** - * - * @param newVal - */ - public void setAcceptedTaxon(AcceptedTaxon newVal){ - acceptedTaxon = newVal; - } - - /** - * - * @param newVal - */ - public void setSynoynm(SynonymTaxon newVal){ - synoynm = newVal; - } - - /** - * - * @param newVal - */ - public void setType(SynonymRelationshipType newVal){ - type = newVal; - } - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.taxon; + + +import etaxonomy.cdm.model.common.ReferencedEntityBase; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:20 + */ +public class SynonymRelationship extends ReferencedEntityBase { + static Logger logger = Logger.getLogger(SynonymRelationship.class); + + private Synonym synoynm; + private Taxon acceptedTaxon; + private SynonymRelationshipType type; + + public Taxon getAcceptedTaxon(){ + return acceptedTaxon; + } + + /** + * + * @param newVal + */ + public void setAcceptedTaxon(Taxon newVal){ + acceptedTaxon = newVal; + } + + public SynonymRelationshipType getType(){ + return type; + } + + /** + * + * @param newVal + */ + public void setType(SynonymRelationshipType newVal){ + type = newVal; + } + + public Synonym getSynoynm(){ + return synoynm; + } + + /** + * + * @param newVal + */ + public void setSynoynm(Synonym newVal){ + synoynm = newVal; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/SynonymRelationshipType.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/SynonymRelationshipType.java index 8ac2a00512..e497ca2118 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/SynonymRelationshipType.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/SynonymRelationshipType.java @@ -1,30 +1,59 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.taxon; - - -import org.apache.log4j.Logger; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:13 - */ -public enum SynonymRelationshipType { - SYNONYM_OF, - PRO_PARTE_SYNONYM_OF, - PARTIAL_SYNONYM_OF, - HOMOTYPIC_SYNONYM_OF, - HETEROTYPIC_SYNONYM_OF, - PRO_PARTE_AND_HOMOTYPIC_SYNONYM_OF, - PRO_PARTE_AND_HETEROTYPIC_SYNONYM_OF, - PARTIAL_AND_HOMOTYPIC_SYNONYM_OF, - PARTIAL_AND_HETEROTYPIC_SYNONYM_OF +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.taxon; + + +import etaxonomy.cdm.model.common.EnumeratedTermBase; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:20 + */ +public class SynonymRelationshipType extends EnumeratedTermBase { + static Logger logger = Logger.getLogger(SynonymRelationshipType.class); + + @Description("") + private static final int initializationClassUri = http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonRelationshipTerm; + + public getInitializationClassUri(){ + return initializationClassUri; + } + + /** + * + * @param newVal + */ + public void setInitializationClassUri(newVal){ + initializationClassUri = newVal; + } + + public static final SynonymRelationshipType SYNONYM_OF(){ + return null; + } + + public static final SynonymRelationshipType PRO_PARTE_SYNONYM_OF(){ + return null; + } + + public static final SynonymRelationshipType PARTIAL_SYNONYM_OF(){ + return null; + } + + public static final SynonymRelationshipType HOMOTYPIC_SYNONYM_OF(){ + return null; + } + + public static final SynonymRelationshipType HETEROTYPIC_SYNONYM_OF(){ + return null; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/AcceptedTaxon.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/Taxon.java similarity index 63% rename from cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/AcceptedTaxon.java rename to cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/Taxon.java index 29f74ec7f7..4d75fffe30 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/AcceptedTaxon.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/Taxon.java @@ -1,93 +1,90 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.taxon; - - -import eu.etaxonomy.cdm.model.common.Media; -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:35:59 - */ -@Entity -public class AcceptedTaxon extends TaxonBase { - static Logger logger = Logger.getLogger(AcceptedTaxon.class); - - private ArrayList facts; - private ArrayList inverseSynonymRelations; - private ArrayList medias; - private ArrayList taxonRelations; - private ArrayList inverseTaxonRelations; - - public ArrayList getFacts(){ - return facts; - } - - public ArrayList getInverseSynonymRelations(){ - return inverseSynonymRelations; - } - - public ArrayList getInverseTaxonRelations(){ - return inverseTaxonRelations; - } - - public ArrayList getMedias(){ - return medias; - } - - public ArrayList getTaxonRelations(){ - return taxonRelations; - } - - /** - * - * @param newVal - */ - public void setFacts(ArrayList newVal){ - facts = newVal; - } - - /** - * - * @param newVal - */ - public void setInverseSynonymRelations(ArrayList newVal){ - inverseSynonymRelations = newVal; - } - - /** - * - * @param newVal - */ - public void setInverseTaxonRelations(ArrayList newVal){ - inverseTaxonRelations = newVal; - } - - /** - * - * @param newVal - */ - public void setMedias(ArrayList newVal){ - medias = newVal; - } - - /** - * - * @param newVal - */ - public void setTaxonRelations(ArrayList newVal){ - taxonRelations = newVal; - } - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.taxon; + + +import etaxonomy.cdm.model.description.Description; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:20 + */ +public class Taxon extends TaxonBase { + static Logger logger = Logger.getLogger(Taxon.class); + + private ArrayList descriptions; + private ArrayList inverseSynonymRelations; + private ArrayList taxonInSource; + private ArrayList taxonRelations; + private ArrayList inverseTaxonRelations; + + public ArrayList getTaxonInSource(){ + return taxonInSource; + } + + /** + * + * @param newVal + */ + public void setTaxonInSource(ArrayList newVal){ + taxonInSource = newVal; + } + + public ArrayList getDescriptions(){ + return descriptions; + } + + /** + * + * @param newVal + */ + public void setDescriptions(ArrayList newVal){ + descriptions = newVal; + } + + public ArrayList getInverseSynonymRelations(){ + return inverseSynonymRelations; + } + + /** + * + * @param newVal + */ + public void setInverseSynonymRelations(ArrayList newVal){ + inverseSynonymRelations = newVal; + } + + public ArrayList getTaxonRelations(){ + return taxonRelations; + } + + /** + * + * @param newVal + */ + public void setTaxonRelations(ArrayList newVal){ + taxonRelations = newVal; + } + + public ArrayList getInverseTaxonRelations(){ + return inverseTaxonRelations; + } + + /** + * + * @param newVal + */ + public void setInverseTaxonRelations(ArrayList newVal){ + inverseTaxonRelations = newVal; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonBase.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonBase.java index 6f5833da79..67e04e69e4 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonBase.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonBase.java @@ -1,69 +1,55 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.taxon; - - -import eu.etaxonomy.cdm.model.name.TaxonName; -import eu.etaxonomy.cdm.model.publication.PublicationBase; -import eu.etaxonomy.cdm.model.common.IdentifiableEntity; -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:14 - */ -@Entity -public abstract class TaxonBase extends IdentifiableEntity { - static Logger logger = Logger.getLogger(TaxonBase.class); - - private boolean isDoubtful; - private PublicationBase sec; - private TaxonName name; - - public TaxonName getName(){ - return name; - } - - public PublicationBase getSec(){ - return sec; - } - - public boolean isDoubtful(){ - return isDoubtful; - } - - /** - * - * @param newVal - */ - public void setDoubtful(boolean newVal){ - isDoubtful = newVal; - } - - /** - * - * @param newVal - */ - public void setName(TaxonName newVal){ - name = newVal; - } - - /** - * - * @param newVal - */ - public void setSec(PublicationBase newVal){ - sec = newVal; - } - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.taxon; + + +import etaxonomy.cdm.model.name.TaxonNameBase; +import etaxonomy.cdm.model.common.IdentifiableEntity; +import org.apache.log4j.Logger; + +/** + * {unique name within view/treatment} + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:21 + */ +public abstract class TaxonBase extends IdentifiableEntity { + static Logger logger = Logger.getLogger(TaxonBase.class); + + //The assignement to the Taxon or to the Synonym class is not definitive + @Description("The assignement to the Taxon or to the Synonym class is not definitive") + private boolean isDoubtful; + private TaxonNameBase name; + + public TaxonNameBase getName(){ + return name; + } + + /** + * + * @param newVal + */ + public void setName(TaxonNameBase newVal){ + name = newVal; + } + + public boolean isDoubtful(){ + return isDoubtful; + } + + /** + * + * @param newVal + */ + public void setDoubtful(boolean newVal){ + isDoubtful = newVal; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonFact.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonFact.java deleted file mode 100644 index e5511a3c29..0000000000 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonFact.java +++ /dev/null @@ -1,70 +0,0 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.taxon; - - -import eu.etaxonomy.cdm.model.publication.PublicationBase; -import eu.etaxonomy.cdm.model.common.FactBase; -import eu.etaxonomy.cdm.model.common.Media; -import eu.etaxonomy.cdm.model.common.Fact; -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:14 - */ -@Entity -public class TaxonFact extends FactBase implements Fact { - static Logger logger = Logger.getLogger(TaxonFact.class); - - private TaxonFactType type; - private PublicationBase citation; - private ArrayList medias; - - public PublicationBase getCitation(){ - return citation; - } - - public ArrayList getMedias(){ - return medias; - } - - public TaxonFactType getType(){ - return type; - } - - /** - * - * @param newVal - */ - public void setCitation(PublicationBase newVal){ - citation = newVal; - } - - /** - * - * @param newVal - */ - public void setMedias(ArrayList newVal){ - medias = newVal; - } - - /** - * - * @param newVal - */ - public void setType(TaxonFactType newVal){ - type = newVal; - } - -} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonInSource.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonInSource.java new file mode 100644 index 0000000000..544729d10d --- /dev/null +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonInSource.java @@ -0,0 +1,24 @@ +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.taxon; + + +import etaxonomy.cdm.model.common.EntityInSourceBase; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:21 + */ +public class TaxonInSource extends EntityInSourceBase { + static Logger logger = Logger.getLogger(TaxonInSource.class); + +} \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonRelationship.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonRelationship.java index 3265778d2d..205f420109 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonRelationship.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonRelationship.java @@ -1,81 +1,64 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.taxon; - - -import eu.etaxonomy.cdm.model.publication.PublicationBase; -import eu.etaxonomy.cdm.model.common.VersionableEntity; -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:16 - */ -@Entity -public class TaxonRelationship extends VersionableEntity { - static Logger logger = Logger.getLogger(TaxonRelationship.class); - - private PublicationBase citation; - private AcceptedTaxon fromTaxon; - private AcceptedTaxon toTaxon; - private ConceptRelationshipType type; - - public PublicationBase getCitation(){ - return citation; - } - - public AcceptedTaxon getFromTaxon(){ - return fromTaxon; - } - - public AcceptedTaxon getToTaxon(){ - return toTaxon; - } - - public ConceptRelationshipType getType(){ - return type; - } - - /** - * - * @param newVal - */ - public void setCitation(PublicationBase newVal){ - citation = newVal; - } - - /** - * - * @param newVal - */ - public void setFromTaxon(AcceptedTaxon newVal){ - fromTaxon = newVal; - } - - /** - * - * @param newVal - */ - public void setToTaxon(AcceptedTaxon newVal){ - toTaxon = newVal; - } - - /** - * - * @param newVal - */ - public void setType(ConceptRelationshipType newVal){ - type = newVal; - } - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.taxon; + + +import etaxonomy.cdm.model.common.ReferencedEntityBase; +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:23 + */ +public class TaxonRelationship extends ReferencedEntityBase { + static Logger logger = Logger.getLogger(TaxonRelationship.class); + + private ConceptRelationshipType type; + private Taxon fromTaxon; + private Taxon toTaxon; + + public ConceptRelationshipType getType(){ + return type; + } + + /** + * + * @param newVal + */ + public void setType(ConceptRelationshipType newVal){ + type = newVal; + } + + public Taxon getFromTaxon(){ + return fromTaxon; + } + + /** + * + * @param newVal + */ + public void setFromTaxon(Taxon newVal){ + fromTaxon = newVal; + } + + public Taxon getToTaxon(){ + return toTaxon; + } + + /** + * + * @param newVal + */ + public void setToTaxon(Taxon newVal){ + toTaxon = newVal; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/view/User.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/view/User.java index 041b40e1c8..604af82bca 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/view/User.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/view/User.java @@ -1,92 +1,93 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.view; - - -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:18 - */ -@Entity -public class User { - static Logger logger = Logger.getLogger(User.class); - - private int created; - private String email; - private String name; - private String openID; - private ArrayList views; - - public int getCreated(){ - return created; - } - - public String getEmail(){ - return email; - } - - public String getName(){ - return name; - } - - public String getOpenID(){ - return openID; - } - - public ArrayList getViews(){ - return views; - } - - /** - * - * @param newVal - */ - public void setCreated(int newVal){ - created = newVal; - } - - /** - * - * @param newVal - */ - public void setEmail(String newVal){ - email = newVal; - } - - /** - * - * @param newVal - */ - public void setName(String newVal){ - name = newVal; - } - - /** - * - * @param newVal - */ - public void setOpenID(String newVal){ - openID = newVal; - } - - /** - * - * @param newVal - */ - public void setViews(ArrayList newVal){ - views = newVal; - } - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.view; + + +import org.apache.log4j.Logger; + +/** + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:25 + */ +public class User { + static Logger logger = Logger.getLogger(User.class); + + @Description("") + private String name; + @Description("") + private String email; + @Description("") + private String openID; + @Description("") + private Calendar created; + private ArrayList views; + + public ArrayList getViews(){ + return views; + } + + /** + * + * @param newVal + */ + public void setViews(ArrayList newVal){ + views = newVal; + } + + public String getName(){ + return name; + } + + /** + * + * @param newVal + */ + public void setName(String newVal){ + name = newVal; + } + + public String getEmail(){ + return email; + } + + /** + * + * @param newVal + */ + public void setEmail(String newVal){ + email = newVal; + } + + public String getOpenID(){ + return openID; + } + + /** + * + * @param newVal + */ + public void setOpenID(String newVal){ + openID = newVal; + } + + public Calendar getCreated(){ + return created; + } + + /** + * + * @param newVal + */ + public void setCreated(Calendar newVal){ + created = newVal; + } + } \ No newline at end of file diff --git a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/view/View.java b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/view/View.java index 67cbc7e142..cf61800426 100644 --- a/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/view/View.java +++ b/cdmlibrary/src/main/java/eu/etaxonomy/cdm/model/view/View.java @@ -1,81 +1,80 @@ -/** -* Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy -* http://www.e-taxonomy.eu -* -* The contents of this file are subject to the Mozilla Public License Version 1.1 -* See LICENSE.TXT at the top of this package for the full license terms. -*/ - -package eu.etaxonomy.cdm.model.view; - - -import org.apache.log4j.Logger; -import java.util.*; -import javax.persistence.*; - -/** - * use ARCHIVE view/dataset to maintain an archive. All members of that view will - * never be changed - * @author Andreas Mueller - * @version 1.0 - * @created 15-Aug-2007 18:36:19 - */ -@Entity -public class View { - static Logger logger = Logger.getLogger(View.class); - - private String description; - private String name; - private java.util.ArrayList superView; - private ArrayList users; - - public String getDescription(){ - return description; - } - - public String getName(){ - return name; - } - - public java.util.ArrayList getSuperView(){ - return superView; - } - - public ArrayList getUsers(){ - return users; - } - - /** - * - * @param newVal - */ - public void setDescription(String newVal){ - description = newVal; - } - - /** - * - * @param newVal - */ - public void setName(String newVal){ - name = newVal; - } - - /** - * - * @param newVal - */ - public void setSuperView(java.util.ArrayList newVal){ - superView = newVal; - } - - /** - * - * @param newVal - */ - public void setUsers(ArrayList newVal){ - users = newVal; - } - +/** +* Copyright (C) 2007 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ + +package etaxonomy.cdm.model.view; + + +import org.apache.log4j.Logger; + +/** + * use ARCHIVE view/dataset to maintain an archive. All members of that view will + * never be changed + * @author m.doering + * @version 1.0 + * @created 02-Nov-2007 18:15:26 + */ +public class View { + static Logger logger = Logger.getLogger(View.class); + + @Description("") + private String name; + @Description("") + private String description; + private ArrayList users; + private java.util.ArrayList superView; + + public java.util.ArrayList getSuperView(){ + return superView; + } + + /** + * + * @param newVal + */ + public void setSuperView(java.util.ArrayList newVal){ + superView = newVal; + } + + public ArrayList getUsers(){ + return users; + } + + /** + * + * @param newVal + */ + public void setUsers(ArrayList newVal){ + users = newVal; + } + + public String getName(){ + return name; + } + + /** + * + * @param newVal + */ + public void setName(String newVal){ + name = newVal; + } + + public String getDescription(){ + return description; + } + + /** + * + * @param newVal + */ + public void setDescription(String newVal){ + description = newVal; + } + } \ No newline at end of file