From: Patrick Plitzner Date: Wed, 7 Oct 2015 09:03:46 +0000 (+0200) Subject: Delete unused classes X-Git-Tag: 3.12.0^2~62^2~7^2~49 X-Git-Url: https://dev.e-taxonomy.eu/gitweb/taxeditor.git/commitdiff_plain/63c806cad1a630b94df19ba2efb85a2d06ced0e4 Delete unused classes --- diff --git a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/searchFilter/DerivateContentProvider.java b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/searchFilter/DerivateContentProvider.java deleted file mode 100644 index 20b65e29e..000000000 --- a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/searchFilter/DerivateContentProvider.java +++ /dev/null @@ -1,144 +0,0 @@ -package eu.etaxonomy.taxeditor.editor.view.derivate.searchFilter; - -import java.util.ArrayList; -import java.util.LinkedHashSet; -import java.util.List; -import java.util.Set; - -import org.eclipse.jface.viewers.ITreeContentProvider; -import org.eclipse.jface.viewers.TreeNode; -import org.eclipse.jface.viewers.Viewer; - -import eu.etaxonomy.cdm.model.molecular.DnaSample; -import eu.etaxonomy.cdm.model.molecular.Sequence; -import eu.etaxonomy.cdm.model.molecular.SingleRead; -import eu.etaxonomy.cdm.model.occurrence.DerivationEvent; -import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; -import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase; -import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType; - -public class DerivateContentProvider implements ITreeContentProvider { - - List rootNodes; - - @Override - public void dispose() { - // TODO Auto-generated method stub - - } - - public List getRootElements() { - List elements = new ArrayList(); - - if(rootNodes != null) { - for(TreeNode node : rootNodes) { - elements.add((SpecimenOrObservationBase)node.getValue()); - } - } - return elements; - } - - @Override - public void inputChanged(Viewer viewer, Object oldInput, Object newInput) { - } - - @Override - public Object[] getElements(Object inputElement) { - rootNodes = new ArrayList(); - if(inputElement instanceof Set){ - for (Object o: (Set)inputElement) { - if(o instanceof SpecimenOrObservationBase){ - SpecimenOrObservationBase rootElement = (SpecimenOrObservationBase)o; - if(rootElement!=null){ - rootNodes.add(new TreeNode(rootElement)); - } - } - } - } - return rootNodes.toArray(); - } - - @Override - public Object[] getChildren(Object element) { - TreeNode currentnode = null; - Object value = null; - if(element instanceof TreeNode){ - currentnode = (TreeNode) element; - value = ((TreeNode) element).getValue(); - } - Set children = new LinkedHashSet(); - if(value instanceof DnaSample && ((DnaSample) value).getRecordBasis()==SpecimenOrObservationType.DnaSample){ - DnaSample dnaSample = (DnaSample)value; - Set sequences = dnaSample.getSequences(); - for (Sequence sequence : sequences) { - TreeNode node = new TreeNode(sequence); - node.setParent(currentnode); - children.add(node); - } - } - else if(value instanceof Sequence){ - Set singleReads = ((Sequence) value).getSingleReads(); - for(SingleRead singleRead:singleReads){ - TreeNode node = new TreeNode(singleRead); - node.setParent(currentnode); - children.add(node); - } - return children.toArray(); - } - - if(value instanceof SpecimenOrObservationBase){ - List derivates = getDerivates((SpecimenOrObservationBase) value); - for (DerivedUnit derivedUnit:derivates) { - TreeNode node = new TreeNode(derivedUnit); - node.setParent(currentnode); - children.add(node); - } - return children.toArray(); - } - return null; - } - - @Override - public Object getParent(Object element) { - if(element instanceof TreeNode){ - return ((TreeNode) element).getParent(); - } - return null; - } - - @Override - public boolean hasChildren(Object element) { - if(element instanceof TreeNode){ - element = ((TreeNode) element).getValue(); - } - - if(element instanceof DnaSample && ((DnaSample) element).getRecordBasis()==SpecimenOrObservationType.DnaSample){ - DnaSample dnaSample = (DnaSample)element; - if(!dnaSample.getSequences().isEmpty()){// || !dnaSample.getAmplifications().isEmpty()){ - return true; - } - } - else if(element instanceof Sequence){ - return !((Sequence)element).getSingleReads().isEmpty(); - } - - if(element instanceof SpecimenOrObservationBase){ - SpecimenOrObservationBase specimenOrObservation = (SpecimenOrObservationBase)element; - for(DerivationEvent event:specimenOrObservation.getDerivationEvents()){ - if(!event.getDerivatives().isEmpty()){ - return true; - } - } - } - return false; - } - - private List getDerivates(SpecimenOrObservationBase specimenOrObservation){ - List derivates = new ArrayList(); - for(DerivationEvent derivationEvent:specimenOrObservation.getDerivationEvents()){ - derivates.addAll(derivationEvent.getDerivatives()); - } - return derivates; - } - -} diff --git a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/searchFilter/DerivateLabelProvider.java b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/searchFilter/DerivateLabelProvider.java deleted file mode 100644 index 42b1d5cc0..000000000 --- a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/searchFilter/DerivateLabelProvider.java +++ /dev/null @@ -1,388 +0,0 @@ -// $Id$ -/** -* Copyright (C) 2013 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.taxeditor.editor.view.derivate.searchFilter; - -import java.util.List; -import java.util.Set; -import java.util.UUID; - -import org.eclipse.jface.viewers.ColumnLabelProvider; -import org.eclipse.jface.viewers.TreeNode; -import org.eclipse.swt.graphics.Image; -import org.hibernate.LazyInitializationException; - -import eu.etaxonomy.cdm.api.conversation.ConversationHolder; -import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper; -import eu.etaxonomy.cdm.model.common.CdmBase; -import eu.etaxonomy.cdm.model.common.DefinedTerm; -import eu.etaxonomy.cdm.model.common.Identifier; -import eu.etaxonomy.cdm.model.molecular.DnaSample; -import eu.etaxonomy.cdm.model.molecular.Sequence; -import eu.etaxonomy.cdm.model.molecular.SingleRead; -import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; -import eu.etaxonomy.cdm.model.occurrence.FieldUnit; -import eu.etaxonomy.cdm.model.occurrence.GatheringEvent; -import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen; -import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase; -import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType; -import eu.etaxonomy.taxeditor.model.ImageResources; -import eu.etaxonomy.taxeditor.store.CdmStore; - -/** - * Label provider for the views to show {@link SpecimenOrObservationBase}s.
- *
- * Note: If you use this label provider you need to assure that you - * created a {@link ConversationHolder} resp. have an open session because - * the labels are generated from various fields of the derivate hierarchy which - * are lazy loaded and could therefore throw a {@link LazyInitializationException}.
- * Use {@link #setConversation(ConversationHolder)} to assign the session to this provider. - */ -public class DerivateLabelProvider extends ColumnLabelProvider { - - private static final String NO_SAMPLE_DESIGNATION = "[no sample designation]"; - - private Set multiLinkSingleReads; - - private ConversationHolder conversation; - - private static DefinedTerm photoTerm = null; - private static DefinedTerm drawingTerm = null; - private static DefinedTerm specimenScanTerm = null; - private static DefinedTerm detailImageTerm = null; - private static DefinedTerm sampleDesignationTerm = null; - - //FIXME: move static term getters to new singleton utility class - private static void initializeTerms() { - List preferredTerms = CdmStore.getTermManager().getPreferredTerms(DefinedTerm.class); - for (DefinedTerm definedTerm : preferredTerms) { - if(definedTerm.getUuid().equals(UUID.fromString("c5c59c42-f254-471e-96c6-09f459f7c903"))){ - photoTerm = definedTerm; - } - else if(definedTerm.getUuid().equals(UUID.fromString("669b0409-4aa4-4695-aae4-a95ed27bad4c"))){ - drawingTerm = definedTerm; - } - else if(definedTerm.getUuid().equals(UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03"))){ - specimenScanTerm = definedTerm; - } - else if(definedTerm.getUuid().equals(UUID.fromString("31eb8d02-bf5d-437c-bcc6-87a626445f34"))){ - detailImageTerm = definedTerm; - } - else if(definedTerm.getUuid().equals(UUID.fromString("fadeba12-1be3-4bc7-9ff5-361b088d86fc"))){ - sampleDesignationTerm = definedTerm; - } - } - } - - public static DefinedTerm getLivingPlantPhotoTerm(){ - if(photoTerm==null){ - initializeTerms(); - } - return photoTerm; - } - - public static DefinedTerm getArtworkTerm(){ - if(drawingTerm==null){ - initializeTerms(); - } - return drawingTerm; - } - - public static DefinedTerm getSpecimenScanTerm(){ - if(specimenScanTerm==null){ - initializeTerms(); - } - return specimenScanTerm; - } - - public static DefinedTerm getDetailImageTerm(){ - if(detailImageTerm==null){ - initializeTerms(); - } - return detailImageTerm; - } - - public static DefinedTerm getSampleDesignationTerm(){ - if(sampleDesignationTerm==null){ - initializeTerms(); - } - return sampleDesignationTerm; - } - - - /** {@inheritDoc} */ - @Override - public String getText(Object element) { - return getDerivateText(element); - } - - /** {@inheritDoc} */ - @Override - public String getToolTipText(Object element) { - return getDerivateText(element); - } - - /** - * @param conversation the conversation to set - */ - public void setConversation(ConversationHolder conversation) { - this.conversation = conversation; - } - - public String getDerivateText(Object element){ - return getDerivateText(element, conversation); - } - - public static String getDerivateText(Object element, ConversationHolder conversation){ - //TODO: use list of strings to assemble labels to avoid adding the separator every time and to allow null values - TreeNode parentNode = null; - TreeNode node = null; - Object derivate = element; - if(element instanceof TreeNode){ - node = (TreeNode) element; - parentNode = node.getParent(); - //unwrap specimen from TreeNode - derivate = node.getValue(); - } - - conversation.bind(); - - final String emptyString = ""; - final String separator = " "; - - String label = emptyString; - - //Field Unit - if(derivate instanceof FieldUnit){ - FieldUnit fieldUnit = (FieldUnit)derivate; - if(fieldUnit.getGatheringEvent()!=null){ - GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent(); - label += gatheringEvent.getCountry()!=null?gatheringEvent.getCountry().getLabel()+separator:emptyString; - label += gatheringEvent.getLocality()!=null?gatheringEvent.getLocality().getText()+separator:emptyString; - label += gatheringEvent.getGatheringDate()!=null?gatheringEvent.getGatheringDate()+separator:emptyString; - label += gatheringEvent.getCollector()!=null?gatheringEvent.getCollector()+separator:emptyString; - } - label += fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber():emptyString; - } - //MediaSpecimen - else if(derivate instanceof MediaSpecimen){ - MediaSpecimen mediaSpecimen = (MediaSpecimen)derivate; - if(mediaSpecimen.getMediaSpecimen()!=null){ - label += mediaSpecimen.getMediaSpecimen().getTitle()!=null?mediaSpecimen.getMediaSpecimen().getTitle().getText()+separator:"[no motif]"; - label += mediaSpecimen.getMediaSpecimen().getArtist()!=null?mediaSpecimen.getMediaSpecimen().getArtist()+separator:emptyString; - } - eu.etaxonomy.cdm.model.occurrence.Collection collection = mediaSpecimen.getCollection(); - if(collection!=null){ - label += collection.getName()!=null?collection.getName()+" ":emptyString; - label += collection.getCode()!=null?"("+collection.getCode()+")"+separator:emptyString; - } - label += mediaSpecimen.getAccessionNumber()!=null?mediaSpecimen.getAccessionNumber()+separator:emptyString; - label += mediaSpecimen.getBarcode()!=null?mediaSpecimen.getBarcode()+separator:emptyString; - } - //TissueSample + DnaSample - else if(derivate instanceof DnaSample){ - DnaSample dnaSample = (DnaSample)derivate; - if(((DnaSample) derivate).getRecordBasis()==SpecimenOrObservationType.DnaSample){ - Identifier currentSampleDesignation = getCurrentSampleDesignation(dnaSample); - if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){ - label += currentSampleDesignation.getIdentifier()+separator; - } - else{ - label += NO_SAMPLE_DESIGNATION+separator; - } - } - else if(((DnaSample) derivate).getRecordBasis()==SpecimenOrObservationType.TissueSample){ - if(dnaSample.getKindOfUnit()!=null){ - label += dnaSample.getKindOfUnit()+separator; - } - Identifier currentSampleDesignation = getCurrentSampleDesignation(dnaSample); - if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){ - label += currentSampleDesignation.getIdentifier()+separator; - } - else{ - label += NO_SAMPLE_DESIGNATION+separator; - } - } - - } - //DerivedUnit + TissueSample - else if(derivate instanceof DerivedUnit){ - DerivedUnit derivedUnit = (DerivedUnit)derivate; - if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){ - //java.util.Collection fieldUnits = CdmStore.getService(IOccurrenceService.class).getFieldUnits(derivedUnit.getUuid()); - //TODO : This is not generic anymore for performance reasons - Set originals = derivedUnit.getOriginals(); - if(originals!=null && originals.size() ==1) { - SpecimenOrObservationBase specimen = originals.iterator().next(); - if(specimen instanceof FieldUnit) { - FieldUnit fieldUnit = (FieldUnit)specimen; - GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent(); - if(gatheringEvent!=null){ - label += gatheringEvent.getCollector()!=null?gatheringEvent.getCollector()+separator:emptyString; - } - label += fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber()+separator:emptyString; - } - } - - eu.etaxonomy.cdm.model.occurrence.Collection collection = derivedUnit.getCollection(); - if(collection!=null){ - label += collection.getCode()!=null?"("+collection.getCode()+")"+separator:emptyString; - } - String mostSignificantIdentifier = derivedUnit.getMostSignificantIdentifier(); - label += mostSignificantIdentifier!=null?mostSignificantIdentifier+separator:emptyString; - } - else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){ - //TissueSample should only be created by using it's own class - //in future using only one class with different SpecimenOrObservationTypes is desired -// label += derivedUnit.getKindOfUnit() + NO_SAMPLE_DESIGNATION; - } - } - //Sequence - else if(derivate instanceof Sequence){ - Sequence sequence = (Sequence)derivate; - Identifier currentSampleDesignation = getCurrentSampleDesignation(sequence); - if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){ - label += currentSampleDesignation.getIdentifier()+separator; - } - else{ - label += NO_SAMPLE_DESIGNATION+separator; - } - label += sequence.getDnaMarker()!=null?sequence.getDnaMarker():emptyString; - } - //SingleRead - else if(derivate instanceof SingleRead){ - SingleRead singleRead = (SingleRead)derivate; - if(parentNode!=null && parentNode.getValue() instanceof Sequence){ - Sequence sequence = (Sequence) parentNode.getValue(); - Identifier currentSampleDesignation = getCurrentSampleDesignation(sequence); - if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){ - label = currentSampleDesignation.getIdentifier()+separator; - } - else{ - label += NO_SAMPLE_DESIGNATION+separator; - } - label += singleRead.getPrimer()!=null?singleRead.getPrimer().getLabel()+separator:emptyString; - if(sequence!=null && sequence.getDnaMarker()!=null){ - label += sequence.getDnaMarker()+separator; - } - if(singleRead.getAmplificationResult()!=null && singleRead.getAmplificationResult().getAmplification()!=null){ - label += singleRead.getAmplificationResult().getAmplification().getLabelCache()+separator; - } - } - } - //SOOB - else if(derivate instanceof SpecimenOrObservationBase){ - SpecimenOrObservationBase specimen = (SpecimenOrObservationBase) derivate; - SpecimenOrObservationType type = specimen.getRecordBasis(); - return specimen.getTitleCache() + (type!=null?" ["+type.toString()+"]":emptyString); - } - if(label.isEmpty()){ - label = derivate.toString(); - } - //remove last comma - else if(label.endsWith(separator)){ - label = label.substring(0, label.length()-separator.length()); - } - return label; - } - - /* (non-Javadoc) - * @see org.eclipse.jface.viewers.ColumnLabelProvider#getImage(java.lang.Object) - */ - @Override - public Image getImage(Object element) { - if(element instanceof TreeNode){ - element = ((TreeNode) element).getValue(); - } - if(element instanceof CdmBase){ - CdmBase cdmBase = (CdmBase)element; - boolean hasCharacterData = false; - if(cdmBase.isInstanceOf(SpecimenOrObservationBase.class)){ - SpecimenOrObservationBase specimen = HibernateProxyHelper.deproxy(cdmBase, SpecimenOrObservationBase.class); - if(specimen.hasCharacterData()){ - hasCharacterData = true; - } - } - if(cdmBase.isInstanceOf(FieldUnit.class)){ - return hasCharacterData?ImageResources.getImage(ImageResources.FIELD_UNIT_CHARACTER_DATA):ImageResources.getImage(ImageResources.FIELD_UNIT); - } - else if(cdmBase.isInstanceOf(DerivedUnit.class)){ - DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(element, DerivedUnit.class); - if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.FieldUnit){ - return hasCharacterData?ImageResources.getImage(ImageResources.FIELD_UNIT_CHARACTER_DATA):ImageResources.getImage(ImageResources.FIELD_UNIT); - } - else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.DnaSample){ - return hasCharacterData?ImageResources.getImage(ImageResources.DNA_SAMPLE_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.DNA_SAMPLE_DERIVATE); - } - else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){ - return hasCharacterData?ImageResources.getImage(ImageResources.TISSUE_SAMPLE_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.TISSUE_SAMPLE_DERIVATE); - } - else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){ - return hasCharacterData?ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE); - } - else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.Media){ - if(derivedUnit.getKindOfUnit()!=null){ - if(derivedUnit.getKindOfUnit().equals(getArtworkTerm())){ - return hasCharacterData?ImageResources.getImage(ImageResources.ARTWORK_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.ARTWORK_DERIVATE); - } - else if(derivedUnit.getKindOfUnit().equals(getLivingPlantPhotoTerm())){ - return hasCharacterData?ImageResources.getImage(ImageResources.LIVING_PLANT_PHOTO_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.LIVING_PLANT_PHOTO_DERIVATE); - } - else if(derivedUnit.getKindOfUnit().equals(getSpecimenScanTerm())){ - return hasCharacterData?ImageResources.getImage(ImageResources.SPECIMEN_SCAN_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.SPECIMEN_SCAN_DERIVATE); - } - else if(derivedUnit.getKindOfUnit().equals(getDetailImageTerm())){ - return hasCharacterData?ImageResources.getImage(ImageResources.DETAIL_IMAGE_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.DETAIL_IMAGE_DERIVATE); - } - } - } - } - else if(cdmBase.isInstanceOf(Sequence.class)){ - return ImageResources.getImage(ImageResources.SEQUENCE_DERIVATE); - } - - else if(cdmBase.isInstanceOf(SingleRead.class)){ - if(multiLinkSingleReads.contains(element)){ - return ImageResources.getImage(ImageResources.SINGLE_READ_DERIVATE_MULTILINK); - } - else{ - return ImageResources.getImage(ImageResources.SINGLE_READ_DERIVATE); - } - } - } - return super.getImage(element); - } - - public static Identifier getCurrentSampleDesignation(CdmBase entity) { - if(entity.isInstanceOf(DnaSample.class)){ - DnaSample dnaSample = HibernateProxyHelper.deproxy(entity, DnaSample.class); - for (Identifier identifier : dnaSample.getIdentifiers()) { - if(identifier.getType()!=null && identifier.getType().equals(DerivateLabelProvider.getSampleDesignationTerm())){ - //first sample designation is the current - return identifier; - } - } - } - else if(entity.isInstanceOf(Sequence.class)){ - Sequence sequence = HibernateProxyHelper.deproxy(entity, Sequence.class); - if(sequence.getDnaSample()!=null){ - return getCurrentSampleDesignation(sequence.getDnaSample()); - } - } - return null; - } - - /** - * @param multiLinkSingleReads2 - */ - public void setMultiLinkSingleReads(Set multiLinkSingleReads) { - this.multiLinkSingleReads = multiLinkSingleReads; - } - -}