Revision 731fe9ff
Added by Andreas Müller over 12 years ago
cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/name/NonViralNameDefaultCacheStrategy.java | ||
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import eu.etaxonomy.cdm.model.agent.Team; |
24 | 24 |
import eu.etaxonomy.cdm.model.common.Language; |
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import eu.etaxonomy.cdm.model.common.Representation; |
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import eu.etaxonomy.cdm.model.name.BotanicalName; |
|
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import eu.etaxonomy.cdm.model.name.HybridRelationship; |
27 | 28 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatus; |
28 | 29 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType; |
... | ... | |
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|
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|
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/** |
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* This class is a default implementation for the INonViralNameCacheStrategy<T extends NonViralName> interface. |
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* The method actually implements a cache strategy for botanical names so no method has to be overwritten by |
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* This class is a default implementation for the INonViralNameCacheStrategy<T extends NonViralName> |
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* interface.<BR> |
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* The method implements a cache strategy for botanical names so no method has to be overwritten by |
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* a subclass for botanic names. |
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* Where differing from this Default BotanicNameCacheStrategy other subclasses should overwrite the existing methods
|
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* e.g. a CacheStrategy for zoological names should overwrite getAuthorAndExAuthor |
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* Where differing from this default botanic name strategy other subclasses should overwrite the
|
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* existing methods, e.g. a CacheStrategy for zoological names should overwrite getAuthorAndExAuthor
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* @author a.mueller |
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*/ |
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/** |
... | ... | |
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} |
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|
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public void setBasionymAuthorCombinationAuthorSeperator( |
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CharSequence basionymAuthorCombinationAuthorSeperator) { |
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public void setBasionymAuthorCombinationAuthorSeperator( CharSequence basionymAuthorCombinationAuthorSeperator) { |
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BasionymAuthorCombinationAuthorSeperator = basionymAuthorCombinationAuthorSeperator; |
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} |
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|
... | ... | |
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} |
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} |
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|
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|
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public String getTitleCache_OLD(T nonViralName) { |
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if (nonViralName == null){ |
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return null; |
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} |
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|
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if (nonViralName.isProtectedTitleCache()){ |
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return nonViralName.getTitleCache(); |
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} |
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String result = ""; |
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if (nonViralName.isHybridFormula()){ |
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//hybrid formula |
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result = null; |
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String hybridSeparator = " " + NonViralNameParserImplRegExBase.hybridSign + " "; |
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List<HybridRelationship> rels = nonViralName.getOrderedChildRelationships(); |
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for (HybridRelationship rel: rels){ |
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result = CdmUtils.concat(hybridSeparator, result, rel.getParentName().getTitleCache()).trim(); |
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} |
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return result; |
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}else if (nonViralName.isAutonym()){ |
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//Autonym |
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result = handleAutonym(nonViralName); |
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}else{ //not Autonym |
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String nameCache = nonViralName.getNameCache(); //OLD: CdmUtils.Nz(getNameCache(nonViralName)); |
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if (nameIncludesAuthorship(nonViralName)){ |
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String authorCache = CdmUtils.Nz(getAuthorshipCache(nonViralName)); |
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result = CdmUtils.concat(NameAuthorSeperator, nameCache, authorCache); |
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}else{ |
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result = nameCache; |
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} |
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} |
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return result; |
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} |
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|
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/** |
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* Creates a string from tagged text. |
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* @param tags |
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* @return |
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*/ |
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private String createString(List<TaggedText> tags) { |
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StringBuffer result = new StringBuffer(); |
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boolean isSeparator; |
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boolean wasSeparator = true; //true for start tag |
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for (TaggedText tag: tags){ |
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isSeparator = tag.getType().equals(TagEnum.separator); |
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if (! wasSeparator && ! isSeparator ){ |
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result.append(" "); |
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} |
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result.append(tag.getText()); |
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wasSeparator = isSeparator; |
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} |
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return result.toString(); |
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} |
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|
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/** |
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* @param nonViralName |
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* @param speciesPart |
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* @return |
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*/ |
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private List<TaggedText> handleTaggedAutonym(T nonViralName) { |
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|
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//species part |
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List<TaggedText> tags = getSpeciesTaggedNameCache(nonViralName); |
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|
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//author |
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//TODO should this include basionym authors and ex authors |
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INomenclaturalAuthor author = nonViralName.getCombinationAuthorTeam(); |
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String authorPart = ""; |
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if (author != null){ |
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authorPart = CdmUtils.Nz(author.getNomenclaturalTitle()); |
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} |
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INomenclaturalAuthor basAuthor = nonViralName.getBasionymAuthorTeam(); |
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String basAuthorPart = ""; |
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if (basAuthor != null){ |
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basAuthorPart = CdmUtils.Nz(basAuthor.getNomenclaturalTitle()); |
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} |
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if (! "".equals(basAuthorPart)){ |
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authorPart = "("+ basAuthorPart +") " + authorPart; |
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} |
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if (StringUtils.isNotBlank(authorPart)){ |
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tags.add(new TaggedText(TagEnum.authors, authorPart)); |
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} |
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|
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|
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//infra species marker |
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if (nonViralName.getRank() == null || !nonViralName.getRank().isInfraSpecific()){ |
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//TODO handle exception |
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logger.warn("Rank for autonym does not exist or is not lower than species !!"); |
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}else{ |
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String infraSpeciesMarker = nonViralName.getRank().getAbbreviation(); |
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if (StringUtils.isNotBlank(infraSpeciesMarker)){ |
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tags.add(new TaggedText(TagEnum.rank, infraSpeciesMarker)); |
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} |
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} |
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|
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//infra species |
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String infraSpeciesPart = CdmUtils.Nz(nonViralName.getInfraSpecificEpithet()).trim().replace("null", ""); |
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if (StringUtils.isNotBlank(infraSpeciesPart)){ |
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tags.add(new TaggedText(TagEnum.name, infraSpeciesPart)); |
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} |
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return tags; |
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} |
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|
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/** |
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* @param nonViralName |
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* @param speciesPart |
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* @return |
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*/ |
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private String handleAutonym(T nonViralName) { |
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String result; |
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String speciesPart = getSpeciesNameCache(nonViralName); |
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//TODO should this include basionym authors and ex authors |
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INomenclaturalAuthor author = nonViralName.getCombinationAuthorTeam(); |
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String authorPart = ""; |
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if (author != null){ |
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authorPart = CdmUtils.Nz(author.getNomenclaturalTitle()); |
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} |
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INomenclaturalAuthor basAuthor = nonViralName.getBasionymAuthorTeam(); |
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String basAuthorPart = ""; |
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if (basAuthor != null){ |
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basAuthorPart = CdmUtils.Nz(basAuthor.getNomenclaturalTitle()); |
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} |
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if (! "".equals(basAuthorPart)){ |
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authorPart = "("+ basAuthorPart +") " + authorPart; |
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} |
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String infraSpeciesPart = (CdmUtils.Nz(nonViralName.getInfraSpecificEpithet())); |
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|
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String infraSpeciesSeparator = ""; |
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if (nonViralName.getRank() == null || !nonViralName.getRank().isInfraSpecific()){ |
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//TODO handle exception |
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logger.warn("Rank for autonym does not exist or is not lower than species !!"); |
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}else{ |
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infraSpeciesSeparator = nonViralName.getRank().getAbbreviation(); |
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} |
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|
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result = CdmUtils.concat(" ", new String[]{speciesPart, authorPart, infraSpeciesSeparator, infraSpeciesPart}); |
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result = result.trim().replace("null", ""); |
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return result; |
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} |
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|
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protected boolean nameIncludesAuthorship(NonViralName<?> nonViralName){ |
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Rank rank = nonViralName.getRank(); |
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if (rank != null && rank.isSpeciesAggregate()){ |
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return false; |
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}else{ |
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return true; |
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} |
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} |
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|
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.strategy.cache.name.NameCacheStrategyBase#getFullTitleCache(eu.etaxonomy.cdm.model.name.TaxonNameBase) |
338 | 185 |
*/ |
... | ... | |
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return result; |
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} |
348 | 195 |
} |
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|
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|
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public String getFullTitleCache_OLD(T nonViralName) { |
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//null |
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if (nonViralName == null){ |
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return null; |
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} |
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//full title cache |
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if (nonViralName.isProtectedFullTitleCache() == true) { |
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return nonViralName.getFullTitleCache(); |
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} |
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|
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String result = ""; |
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//title cache |
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String titleCache = nonViralName.getTitleCache(); // OLD: getTitleCache(nonViralName); |
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|
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String microReference = nonViralName.getNomenclaturalMicroReference(); |
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INomenclaturalReference ref = nonViralName.getNomenclaturalReference(); |
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String referenceBaseCache = null; |
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if (ref != null){ |
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INomenclaturalReference nomenclaturalReference = HibernateProxyHelper.deproxy(ref, INomenclaturalReference.class); |
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nomenclaturalReference.setCacheStrategy(nomenclaturalReference.getType().getCacheStrategy()); |
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referenceBaseCache = nomenclaturalReference.getNomenclaturalCitation(microReference); |
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} |
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|
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//make nomenclatural status |
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String ncStatusCache = ""; |
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Set<NomenclaturalStatus> ncStati = nonViralName.getStatus(); |
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Iterator<NomenclaturalStatus> iterator = ncStati.iterator(); |
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while (iterator.hasNext()) { |
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NomenclaturalStatus ncStatus = (NomenclaturalStatus)iterator.next(); |
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// since the NewInstance method of nomencatural status allows null as parameter |
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// we have to check for null values here |
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String suffix = "not defined"; |
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if(ncStatus.getType() != null){ |
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NomenclaturalStatusType statusType = ncStatus.getType(); |
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Language lang = Language.LATIN(); |
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Representation repr = statusType.getRepresentation(lang); |
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if (repr != null){ |
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suffix = repr.getAbbreviatedLabel(); |
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}else{ |
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String message = "No latin representation available for nom. status. " + statusType.getTitleCache(); |
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logger.warn(message); |
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throw new IllegalStateException(message); |
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} |
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}else if(ncStatus.getRuleConsidered() != null && ! ncStatus.getRuleConsidered().equals("")){ |
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suffix = ncStatus.getRuleConsidered(); |
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} |
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ncStatusCache = ", " + suffix; |
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} |
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String refConcat = " "; |
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if (referenceBaseCache != null && ! referenceBaseCache.trim().startsWith("in ")){ |
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refConcat = ", "; |
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} |
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result = CdmUtils.concat(refConcat, titleCache, referenceBaseCache); |
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result = CdmUtils.concat("", result, ncStatusCache); |
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return result; |
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} |
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|
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/** |
... | ... | |
421 | 209 |
} |
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} |
423 | 211 |
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public String getNameCache_OLD(T nonViralName) { |
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if (nonViralName == null){ |
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return null; |
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} |
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String result; |
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Rank rank = nonViralName.getRank(); |
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|
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if (nonViralName.isProtectedNameCache()){ |
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result = nonViralName.getNameCache(); |
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}else if (rank == null){ |
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result = getRanklessNameCache(nonViralName); |
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// }else if (nonViralName.isInfragenericUnranked()){ |
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// result = getUnrankedInfragenericNameCache(nonViralName); |
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}else if (rank.isInfraSpecific()){ |
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result = getInfraSpeciesNameCache(nonViralName); |
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}else if (rank.isSpecies()){ |
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result = getSpeciesNameCache(nonViralName); |
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}else if (rank.isInfraGeneric()){ |
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result = getInfraGenusNameCache(nonViralName); |
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}else if (rank.isGenus()){ |
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result = getGenusOrUninomialNameCache(nonViralName); |
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}else if (rank.isSupraGeneric()){ |
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result = getGenusOrUninomialNameCache(nonViralName); |
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}else{ |
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logger.warn("Name Strategy for Name (UUID: " + nonViralName.getUuid() + ") not yet implemented"); |
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result = ""; |
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} |
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return result; |
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} |
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|
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454 | 212 |
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private String getUnrankedInfragenericNameCache(T nonViralName) { |
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String result; |
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Rank rank = nonViralName.getRank(); |
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if (rank.isSpeciesAggregate()){ |
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return getSpeciesAggregateCache(nonViralName); |
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/** |
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* Creates a string from tagged text. |
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* @param tags |
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* @return |
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*/ |
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218 |
protected String createString(List<TaggedText> tags) { |
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219 |
StringBuffer result = new StringBuffer(); |
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220 |
|
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221 |
boolean isSeparator; |
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boolean wasSeparator = true; //true for start tag |
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for (TaggedText tag: tags){ |
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isSeparator = tag.getType().equals(TagEnum.separator); |
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225 |
if (! wasSeparator && ! isSeparator ){ |
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226 |
result.append(" "); |
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227 |
} |
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228 |
result.append(tag.getText()); |
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wasSeparator = isSeparator; |
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460 | 230 |
} |
461 |
String infraGenericMarker = rank.getAbbreviation(); |
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result = CdmUtils.Nz(nonViralName.getGenusOrUninomial()).trim(); |
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result += " " + infraGenericMarker + " " + (CdmUtils.Nz(nonViralName.getInfraGenericEpithet())).trim().replace("null", ""); |
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result = addAppendedPhrase(result, nonViralName).trim(); |
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return result; |
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231 |
return result.toString(); |
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466 | 232 |
} |
467 |
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|
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// ******************* Authorship ******************************/ |
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235 |
|
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468 | 236 |
|
469 | 237 |
/* (non-Javadoc) |
470 | 238 |
* @see eu.etaxonomy.cdm.strategy.cache.INonViralNameCacheStrategy#getAuthorCache(eu.etaxonomy.cdm.model.name.NonViralName) |
... | ... | |
528 | 296 |
} |
529 | 297 |
result = exAuthorString + authorString; |
530 | 298 |
return result; |
531 |
|
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532 | 299 |
} |
533 | 300 |
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534 |
// ************* TAGGED NAME ***************************************/ |
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535 | 301 |
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302 |
/** |
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303 |
* Checks if the given name should include the author in it's cached version.<BR> |
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304 |
* This is usually the case but not for <i>species aggregates</i>. |
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305 |
* @param nonViralName |
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306 |
* @return |
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307 |
*/ |
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308 |
protected boolean nameIncludesAuthorship(NonViralName<?> nonViralName){ |
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309 |
Rank rank = nonViralName.getRank(); |
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310 |
if (rank != null && rank.isSpeciesAggregate()){ |
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return false; |
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312 |
}else{ |
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313 |
return true; |
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314 |
} |
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315 |
} |
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316 |
|
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317 |
// ************* TAGGED NAME ***************************************/ |
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318 |
|
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536 | 319 |
/* (non-Javadoc) |
537 |
* @see eu.etaxonomy.cdm.strategy.cache.name.NameCacheStrategyBase#getTaggedTitle(eu.etaxonomy.cdm.model.name.TaxonNameBase) |
|
320 |
* @see eu.etaxonomy.cdm.strategy.cache.name.NameCacheStrategyBase#getTaggedFullTitle(eu.etaxonomy.cdm.model.name.TaxonNameBase)
|
|
538 | 321 |
*/ |
539 | 322 |
@Override |
540 | 323 |
public List<TaggedText> getTaggedFullTitle(T nonViralName) { |
... | ... | |
607 | 390 |
|
608 | 391 |
} |
609 | 392 |
|
393 |
/* (non-Javadoc) |
|
394 |
* @see eu.etaxonomy.cdm.strategy.cache.name.NameCacheStrategyBase#getTaggedTitle(eu.etaxonomy.cdm.model.name.TaxonNameBase) |
|
395 |
*/ |
|
610 | 396 |
public List<TaggedText> getTaggedTitle(T nonViralName) { |
611 | 397 |
if (nonViralName == null){ |
612 | 398 |
return null; |
... | ... | |
653 | 439 |
|
654 | 440 |
|
655 | 441 |
/** |
656 |
* Returns the name part (without author and reference) of this name in tagged mode.
|
|
442 |
* Returns the tag list of the name part (without author and reference).
|
|
657 | 443 |
* @param nonViralName |
658 | 444 |
* @return |
659 | 445 |
*/ |
660 |
private List<TaggedText> getTaggedName(T nonViralName) {
|
|
446 |
public List<TaggedText> getTaggedName(T nonViralName) {
|
|
661 | 447 |
if (nonViralName == null){ |
662 | 448 |
return null; |
663 | 449 |
} |
... | ... | |
691 | 477 |
} |
692 | 478 |
|
693 | 479 |
|
694 |
//Old: may be replaced once getTagged(Full)Title is fully tested |
|
695 |
/* (non-Javadoc) |
|
696 |
* @see eu.etaxonomy.cdm.strategy.INameCacheStrategy#getTaggedName(eu.etaxonomy.cdm.model.common.CdmBase) |
|
480 |
|
|
481 |
|
|
482 |
//***************************** PRIVATES ***************************************/ |
|
483 |
|
|
484 |
|
|
485 |
/** |
|
486 |
* Returns the tag list for an autonym taxon. |
|
487 |
* |
|
488 |
* @see NonViralName#isAutonym() |
|
489 |
* @see BotanicalName#isAutonym() |
|
490 |
* @param nonViralName |
|
491 |
* @return |
|
697 | 492 |
*/ |
698 |
@Override |
|
699 |
@Deprecated |
|
700 |
public List<Object> getTaggedNameDeprecated(T nonViralName) { |
|
701 |
List<Object> tags = new ArrayList<Object>(); |
|
493 |
private List<TaggedText> handleTaggedAutonym(T nonViralName) { |
|
702 | 494 |
|
703 |
if (nonViralName.isProtectedNameCache() || |
|
704 |
nonViralName.isProtectedAuthorshipCache() || |
|
705 |
nonViralName.isProtectedFullTitleCache() || |
|
706 |
nonViralName.isProtectedTitleCache()){ |
|
707 |
tags.add(nonViralName.getTitleCache()); |
|
708 |
return tags; |
|
709 |
} |
|
710 |
|
|
711 |
// Why does it make sense to add the nameCache in case of non existing genusOrUninomial? |
|
712 |
// if (nonViralName.getGenusOrUninomial() == null){ |
|
713 |
// tags.add(nonViralName.getNameCache()); |
|
714 |
// }else{ |
|
495 |
//species part |
|
496 |
List<TaggedText> tags = getSpeciesTaggedNameCache(nonViralName); |
|
715 | 497 |
|
716 |
if (nonViralName.getGenusOrUninomial() != null) { |
|
717 |
tags.add(nonViralName.getGenusOrUninomial()); |
|
498 |
//author |
|
499 |
//TODO should this include basionym authors and ex authors |
|
500 |
INomenclaturalAuthor author = nonViralName.getCombinationAuthorTeam(); |
|
501 |
String authorPart = ""; |
|
502 |
if (author != null){ |
|
503 |
authorPart = CdmUtils.Nz(author.getNomenclaturalTitle()); |
|
718 | 504 |
} |
719 |
if (nonViralName.isSpecies() || nonViralName.isInfraSpecific()){ |
|
720 |
tags.add(nonViralName.getSpecificEpithet()); |
|
505 |
INomenclaturalAuthor basAuthor = nonViralName.getBasionymAuthorTeam(); |
|
506 |
String basAuthorPart = ""; |
|
507 |
if (basAuthor != null){ |
|
508 |
basAuthorPart = CdmUtils.Nz(basAuthor.getNomenclaturalTitle()); |
|
721 | 509 |
} |
722 |
|
|
723 |
// No autonym |
|
724 |
if (nonViralName.isInfraSpecific() && ! nonViralName.getSpecificEpithet().equals(nonViralName.getInfraSpecificEpithet())){ |
|
725 |
tags.add(nonViralName.getRank()); |
|
726 |
tags.add(nonViralName.getInfraSpecificEpithet()); |
|
510 |
if (! "".equals(basAuthorPart)){ |
|
511 |
authorPart = "("+ basAuthorPart +") " + authorPart; |
|
727 | 512 |
} |
728 |
|
|
729 |
if (nonViralName.isInfraGeneric()){ |
|
730 |
//TODO choose right strategy or generic approach? |
|
731 |
// --- strategy 1 --- |
|
732 |
|
|
733 |
if (nonViralName.getRank().isSpeciesAggregate()){ |
|
734 |
tags.add(nonViralName.getSpecificEpithet()); |
|
735 |
tags.add(getSpeciesAggregateEpithet(nonViralName)); |
|
736 |
}else{ |
|
737 |
tags.add(nonViralName.getRank()); |
|
738 |
tags.add(nonViralName.getInfraGenericEpithet()); |
|
739 |
} |
|
740 |
// --- strategy 2 --- |
|
741 |
// tags.add('('+nvn.getInfraGenericEpithet()+')'); |
|
513 |
if (StringUtils.isNotBlank(authorPart)){ |
|
514 |
tags.add(new TaggedText(TagEnum.authors, authorPart)); |
|
742 | 515 |
} |
743 |
Team authorTeam = Team.NewInstance(); |
|
744 |
authorTeam.setProtectedTitleCache(true); |
|
745 |
authorTeam.setTitleCache(nonViralName.getAuthorshipCache(), true); |
|
746 |
tags.add(authorTeam); |
|
747 | 516 |
|
748 |
// Name is an autonym. Rank and infraspecific epitheton follow the author |
|
749 |
if (nonViralName.isInfraSpecific() && nonViralName.getSpecificEpithet().equals(nonViralName.getInfraSpecificEpithet())){ |
|
750 |
tags.add(nonViralName.getRank()); |
|
751 |
tags.add(nonViralName.getInfraSpecificEpithet()); |
|
517 |
|
|
518 |
//infra species marker |
|
519 |
if (nonViralName.getRank() == null || !nonViralName.getRank().isInfraSpecific()){ |
|
520 |
//TODO handle exception |
|
521 |
logger.warn("Rank for autonym does not exist or is not lower than species !!"); |
|
522 |
}else{ |
|
523 |
String infraSpeciesMarker = nonViralName.getRank().getAbbreviation(); |
|
524 |
if (StringUtils.isNotBlank(infraSpeciesMarker)){ |
|
525 |
tags.add(new TaggedText(TagEnum.rank, infraSpeciesMarker)); |
|
526 |
} |
|
752 | 527 |
} |
753 | 528 |
|
754 |
if(! "".equals(nonViralName.getAppendedPhrase())&& (nonViralName.getAppendedPhrase() != null)){ |
|
755 |
tags.add(nonViralName.getAppendedPhrase()); |
|
529 |
//infra species |
|
530 |
String infraSpeciesPart = CdmUtils.Nz(nonViralName.getInfraSpecificEpithet()).trim().replace("null", ""); |
|
531 |
if (StringUtils.isNotBlank(infraSpeciesPart)){ |
|
532 |
tags.add(new TaggedText(TagEnum.name, infraSpeciesPart)); |
|
756 | 533 |
} |
757 | 534 |
|
758 | 535 |
return tags; |
759 | 536 |
} |
760 | 537 |
|
761 |
|
|
762 |
//***************************** PRIVATES ***************************************/ |
|
763 |
|
|
538 |
|
|
539 |
|
|
540 |
/** |
|
541 |
* Returns the tag list for rankless taxa. |
|
542 |
* @param nonViralName |
|
543 |
* @return |
|
544 |
*/ |
|
764 | 545 |
protected List<TaggedText> getRanklessTaggedNameCache(NonViralName<?> nonViralName){ |
765 | 546 |
List<TaggedText> tags = getUninomialTaggedPart(nonViralName); |
766 | 547 |
String speciesEpi = CdmUtils.Nz(nonViralName.getSpecificEpithet()).trim().replace("null", ""); |
... | ... | |
777 | 558 |
addAppendedTaggedPhrase(tags, nonViralName); |
778 | 559 |
return tags; |
779 | 560 |
} |
780 |
|
|
781 |
protected String getRanklessNameCache(NonViralName<?> nonViralName){ |
|
782 |
String result = ""; |
|
783 |
result = (result + (CdmUtils.Nz(nonViralName.getGenusOrUninomial()))).trim().replace("null", ""); |
|
784 |
result += " " + (CdmUtils.Nz(nonViralName.getSpecificEpithet())).trim(); |
|
785 |
result += " " + (CdmUtils.Nz(nonViralName.getInfraSpecificEpithet())).trim(); |
|
786 |
result = result.trim().replace("null", ""); |
|
787 |
//result += " (rankless)"; |
|
788 |
result = addAppendedPhrase(result, nonViralName); |
|
789 |
return result; |
|
790 |
} |
|
791 |
|
|
792 |
|
|
793 |
protected List<TaggedText> getGenusOrUninomialTaggedNameCache(NonViralName<?> nonViralName){ |
|
794 |
List<TaggedText> tags = getUninomialTaggedPart(nonViralName); |
|
795 |
addAppendedTaggedPhrase(tags, nonViralName); |
|
796 |
return tags; |
|
797 |
} |
|
798 |
|
|
799 |
protected String getGenusOrUninomialNameCache(NonViralName<?> nonViralName){ |
|
800 |
String result; |
|
801 |
result = getUninomialPart(nonViralName); |
|
802 |
result = addAppendedPhrase(result, nonViralName).trim(); |
|
803 |
return result; |
|
804 |
} |
|
805 |
|
|
806 | 561 |
|
562 |
/** |
|
563 |
* Returns the tag list for the first epithet (including a hybrid sign if required). |
|
564 |
* @param nonViralName |
|
565 |
* @return |
|
566 |
*/ |
|
807 | 567 |
private List<TaggedText> getUninomialTaggedPart(NonViralName<?> nonViralName) { |
808 | 568 |
List<TaggedText> tags = new ArrayList<TaggedText>(); |
809 | 569 |
|
... | ... | |
819 | 579 |
return tags; |
820 | 580 |
} |
821 | 581 |
|
822 |
private String getUninomialPart(NonViralName<?> nonViralName) { |
|
823 |
String result; |
|
824 |
result = CdmUtils.Nz(nonViralName.getGenusOrUninomial()).trim(); |
|
825 |
if (nonViralName.isMonomHybrid()){ |
|
826 |
result = NonViralNameParserImplRegExBase.hybridSign + result; |
|
827 |
} |
|
828 |
return result; |
|
582 |
/** |
|
583 |
* Returns the tag list for an genus or higher taxon. |
|
584 |
* |
|
585 |
* @param nonViralName |
|
586 |
* @return |
|
587 |
*/ |
|
588 |
protected List<TaggedText> getGenusOrUninomialTaggedNameCache(NonViralName<?> nonViralName){ |
|
589 |
List<TaggedText> tags = getUninomialTaggedPart(nonViralName); |
|
590 |
addAppendedTaggedPhrase(tags, nonViralName); |
|
591 |
return tags; |
|
829 | 592 |
} |
830 | 593 |
|
831 |
|
|
594 |
/** |
|
595 |
* Returns the tag list for an infrageneric taxon (including species aggregates). |
|
596 |
* |
|
597 |
* @see #getSpeciesAggregateTaggedCache(NonViralName) |
|
598 |
* @param nonViralName |
|
599 |
* @return |
|
600 |
*/ |
|
832 | 601 |
protected List<TaggedText> getInfraGenusTaggedNameCache(NonViralName<?> nonViralName){ |
833 | 602 |
Rank rank = nonViralName.getRank(); |
834 | 603 |
if (rank.isSpeciesAggregate()){ |
... | ... | |
859 | 628 |
return tags; |
860 | 629 |
} |
861 | 630 |
|
862 |
protected String getInfraGenusNameCache(NonViralName<?> nonViralName){ |
|
863 |
String result; |
|
864 |
Rank rank = nonViralName.getRank(); |
|
865 |
if (rank.isSpeciesAggregate()){ |
|
866 |
return getSpeciesAggregateCache(nonViralName); |
|
867 |
} |
|
868 |
String infraGenericMarker = "'unhandled infrageneric rank'"; |
|
869 |
if (rank != null){ |
|
870 |
try { |
|
871 |
infraGenericMarker = rank.getInfraGenericMarker(); |
|
872 |
} catch (UnknownCdmTypeException e) { |
|
873 |
infraGenericMarker = "'unhandled infrageneric rank'"; |
|
874 |
} |
|
875 |
} |
|
876 |
result = getUninomialPart(nonViralName); |
|
877 |
result += " " + infraGenericMarker + " " + (CdmUtils.Nz(nonViralName.getInfraGenericEpithet())).trim().replace("null", ""); |
|
878 |
result = addAppendedPhrase(result, nonViralName).trim(); |
|
879 |
return result; |
|
880 |
} |
|
881 |
|
|
882 |
// aggr.|agg.|group |
|
631 |
/** |
|
632 |
* Returns the tag list for a species aggregate (or similar) taxon.<BR> |
|
633 |
* Possible ranks for a <i>species aggregate</i> are "aggr.", "species group", ... |
|
634 |
* @param nonViralName |
|
635 |
* @return |
|
636 |
*/ |
|
883 | 637 |
protected List<TaggedText> getSpeciesAggregateTaggedCache(NonViralName<?> nonViralName){ |
884 | 638 |
List<TaggedText> tags = getGenusAndSpeciesTaggedPart(nonViralName); |
885 | 639 |
|
... | ... | |
888 | 642 |
return tags; |
889 | 643 |
} |
890 | 644 |
|
645 |
/** |
|
646 |
* Adds the aggregate tag to the tag list. |
|
647 |
* @param tags |
|
648 |
* @param nonViralName |
|
649 |
*/ |
|
891 | 650 |
private void addSpeciesAggregateTaggedEpithet(List<TaggedText> tags, NonViralName<?> nonViralName) { |
892 | 651 |
String marker; |
893 | 652 |
try { |
... | ... | |
899 | 658 |
tags.add(new TaggedText(TagEnum.rank, marker)); |
900 | 659 |
} |
901 | 660 |
} |
902 |
|
|
903 |
// aggr.|agg.|group |
|
904 |
protected String getSpeciesAggregateCache(NonViralName<?> nonViralName){ |
|
905 |
String result = getGenusAndSpeciesPart(nonViralName); |
|
906 |
|
|
907 |
result += " " + getSpeciesAggregateEpithet(nonViralName); |
|
908 |
result = addAppendedPhrase(result, nonViralName).trim(); |
|
909 |
return result; |
|
910 |
} |
|
911 |
|
|
912 |
private String getSpeciesAggregateEpithet(NonViralName<?> nonViralName) { |
|
913 |
String marker; |
|
914 |
try { |
|
915 |
marker = nonViralName.getRank().getInfraGenericMarker(); |
|
916 |
} catch (UnknownCdmTypeException e) { |
|
917 |
marker = "'unknown aggregat type'"; |
|
918 |
} |
|
919 |
return marker; |
|
920 |
} |
|
921 | 661 |
|
922 | 662 |
|
663 |
/** |
|
664 |
* Returns the tag list for a species taxon. |
|
665 |
* @param nonViralName |
|
666 |
* @return |
|
667 |
*/ |
|
923 | 668 |
protected List<TaggedText> getSpeciesTaggedNameCache(NonViralName<?> nonViralName){ |
924 | 669 |
List<TaggedText> tags = getGenusAndSpeciesTaggedPart(nonViralName); |
925 | 670 |
addAppendedTaggedPhrase(tags, nonViralName); |
926 | 671 |
return tags; |
927 | 672 |
} |
928 |
|
|
929 |
protected String getSpeciesNameCache(NonViralName<?> nonViralName){ |
|
930 |
String result = getGenusAndSpeciesPart(nonViralName); |
|
931 |
result = addAppendedPhrase(result, nonViralName).trim(); |
|
932 |
result = result.replace("\\s\\", " "); |
|
933 |
return result; |
|
934 |
} |
|
935 | 673 |
|
674 |
/** |
|
675 |
* Creates the tag list for an infraspecific taxon. In include is true the result will contain |
|
676 |
* @param nonViralName |
|
677 |
* @return |
|
678 |
*/ |
|
936 | 679 |
protected List<TaggedText> getInfraSpeciesTaggedNameCache(NonViralName<?> nonViralName){ |
937 | 680 |
return getInfraSpeciesTaggedNameCache(nonViralName, true); |
938 | 681 |
} |
939 | 682 |
|
683 |
/** |
|
684 |
* Creates the tag list for an infraspecific taxon. In include is true the result will contain |
|
685 |
* the infraspecific marker (e.g. "var.") |
|
686 |
* @param nonViralName |
|
687 |
* @param includeMarker |
|
688 |
* @return |
|
689 |
*/ |
|
940 | 690 |
protected List<TaggedText> getInfraSpeciesTaggedNameCache(NonViralName<?> nonViralName, boolean includeMarker){ |
941 | 691 |
List<TaggedText> tags = getGenusAndSpeciesTaggedPart(nonViralName); |
942 | 692 |
if (includeMarker){ |
... | ... | |
968 | 718 |
tags.add(new TaggedText(TagEnum.hybridSign, NonViralNameParserImplRegExBase.hybridSign)); |
969 | 719 |
tags.add(new TaggedText(TagEnum.separator, "")); //no whitespace separator |
970 | 720 |
} |
971 |
|
|
972 |
protected String getInfraSpeciesNameCache(NonViralName<?> nonViralName){ |
|
973 |
return getInfraSpeciesNameCache(nonViralName, true); |
|
974 |
} |
|
975 |
|
|
976 |
|
|
977 |
protected String getInfraSpeciesNameCache(NonViralName<?> nonViralName, boolean includeMarker){ |
|
978 |
String result = getGenusAndSpeciesPart(nonViralName); |
|
979 |
if (includeMarker){ |
|
980 |
result += " " + (nonViralName.getRank().getAbbreviation()).trim().replace("null", ""); |
|
981 |
} |
|
982 |
String infrSpecEpi = CdmUtils.Nz(nonViralName.getInfraSpecificEpithet()); |
|
983 |
if (nonViralName.isTrinomHybrid()){ |
|
984 |
infrSpecEpi = NonViralNameParserImplRegExBase.hybridSign + infrSpecEpi; |
|
985 |
} |
|
986 |
result += " " + (infrSpecEpi).trim().replace("null", ""); |
|
987 |
result = addAppendedPhrase(result, nonViralName).trim(); |
|
988 |
return result; |
|
989 |
} |
|
990 |
|
|
991 | 721 |
|
722 |
/** |
|
723 |
* Creates the tag list for the genus and species part. |
|
724 |
* @param nonViralName |
|
725 |
* @return |
|
726 |
*/ |
|
992 | 727 |
private List<TaggedText> getGenusAndSpeciesTaggedPart(NonViralName<?> nonViralName) { |
993 | 728 |
//Uninomial |
994 | 729 |
List<TaggedText> tags = getUninomialTaggedPart(nonViralName); |
... | ... | |
1017 | 752 |
return tags; |
1018 | 753 |
} |
1019 | 754 |
|
1020 |
private String getGenusAndSpeciesPart(NonViralName<?> nonViralName) { |
|
1021 |
String result; |
|
1022 |
//Uninomial |
|
1023 |
result = getUninomialPart(nonViralName); |
|
1024 |
|
|
1025 |
//InfraGenericEpi |
|
1026 |
boolean hasInfraGenericEpi = StringUtils.isNotBlank(nonViralName.getInfraGenericEpithet()); |
|
1027 |
if (hasInfraGenericEpi){ |
|
1028 |
String infrGenEpi = nonViralName.getInfraGenericEpithet().trim(); |
|
1029 |
if (nonViralName.isBinomHybrid()){ |
|
1030 |
infrGenEpi = NonViralNameParserImplRegExBase.hybridSign + infrGenEpi; |
|
1031 |
} |
|
1032 |
result += " (" + infrGenEpi + ")"; |
|
1033 |
} |
|
1034 |
//Species Epi |
|
1035 |
String specEpi = CdmUtils.Nz(nonViralName.getSpecificEpithet()).trim(); |
|
1036 |
if (! hasInfraGenericEpi && nonViralName.isBinomHybrid() || |
|
1037 |
hasInfraGenericEpi && nonViralName.isTrinomHybrid()){ |
|
1038 |
specEpi = NonViralNameParserImplRegExBase.hybridSign + specEpi; |
|
1039 |
} |
|
1040 |
result += " " + (specEpi).replace("null", ""); |
|
1041 |
return result; |
|
1042 |
} |
|
1043 |
|
|
1044 |
|
|
1045 | 755 |
/** |
1046 | 756 |
* Adds the tag for the appended phrase if an appended phrase exists |
1047 | 757 |
* @param tags |
... | ... | |
1053 | 763 |
tags.add(new TaggedText(TagEnum.name, appendedPhrase)); |
1054 | 764 |
} |
1055 | 765 |
} |
1056 |
|
|
1057 |
protected String addAppendedPhrase(String resultString, NonViralName<?> nonViralName){ |
|
1058 |
String appendedPhrase = nonViralName ==null ? null : nonViralName.getAppendedPhrase(); |
|
1059 |
if (resultString == null){ |
|
1060 |
return appendedPhrase; |
|
1061 |
}else if(appendedPhrase == null || "".equals(appendedPhrase.trim())) { |
|
1062 |
return resultString; |
|
1063 |
}else if ("".equals(resultString)){ |
|
1064 |
return resultString + appendedPhrase; |
|
1065 |
}else { |
|
1066 |
return resultString + " " + appendedPhrase; |
|
1067 |
} |
|
1068 |
} |
|
1069 |
|
|
1070 | 766 |
|
1071 | 767 |
public String getLastEpithet(T taxonNameBase) { |
1072 | 768 |
Rank rank = taxonNameBase.getRank(); |
... | ... | |
1080 | 776 |
return taxonNameBase.getInfraSpecificEpithet(); |
1081 | 777 |
} |
1082 | 778 |
} |
779 |
|
|
780 |
// *************************** DEPRECATED ***************************************************/ |
|
781 |
|
|
782 |
|
|
783 |
//Old: may be replaced once getTagged(Full)Title is fully tested |
|
784 |
/* (non-Javadoc) |
|
785 |
* @see eu.etaxonomy.cdm.strategy.INameCacheStrategy#getTaggedName(eu.etaxonomy.cdm.model.common.CdmBase) |
|
786 |
*/ |
|
787 |
@Override |
|
788 |
@Deprecated |
|
789 |
public List<Object> getTaggedNameDeprecated(T nonViralName) { |
|
790 |
List<Object> tags = new ArrayList<Object>(); |
|
791 |
|
|
792 |
if (nonViralName.isProtectedNameCache() || |
|
793 |
nonViralName.isProtectedAuthorshipCache() || |
|
794 |
nonViralName.isProtectedFullTitleCache() || |
|
795 |
nonViralName.isProtectedTitleCache()){ |
|
796 |
tags.add(nonViralName.getTitleCache()); |
|
797 |
return tags; |
|
798 |
} |
|
799 |
|
|
800 |
// Why does it make sense to add the nameCache in case of non existing genusOrUninomial? |
|
801 |
// if (nonViralName.getGenusOrUninomial() == null){ |
|
802 |
// tags.add(nonViralName.getNameCache()); |
|
803 |
// }else{ |
|
804 |
|
|
805 |
if (nonViralName.getGenusOrUninomial() != null) { |
|
806 |
tags.add(nonViralName.getGenusOrUninomial()); |
|
807 |
} |
|
808 |
if (nonViralName.isSpecies() || nonViralName.isInfraSpecific()){ |
|
809 |
tags.add(nonViralName.getSpecificEpithet()); |
|
810 |
} |
|
811 |
|
|
812 |
// No autonym |
|
813 |
if (nonViralName.isInfraSpecific() && ! nonViralName.getSpecificEpithet().equals(nonViralName.getInfraSpecificEpithet())){ |
|
814 |
tags.add(nonViralName.getRank()); |
|
815 |
tags.add(nonViralName.getInfraSpecificEpithet()); |
|
816 |
} |
|
817 |
|
|
818 |
if (nonViralName.isInfraGeneric()){ |
|
819 |
//TODO choose right strategy or generic approach? |
|
820 |
// --- strategy 1 --- |
|
821 |
|
|
822 |
if (nonViralName.getRank().isSpeciesAggregate()){ |
|
823 |
tags.add(nonViralName.getSpecificEpithet()); |
|
824 |
tags.add(getSpeciesAggregateEpithet(nonViralName)); |
|
825 |
}else{ |
|
826 |
tags.add(nonViralName.getRank()); |
|
827 |
tags.add(nonViralName.getInfraGenericEpithet()); |
|
828 |
} |
|
829 |
// --- strategy 2 --- |
|
830 |
// tags.add('('+nvn.getInfraGenericEpithet()+')'); |
|
831 |
} |
|
832 |
Team authorTeam = Team.NewInstance(); |
|
833 |
authorTeam.setProtectedTitleCache(true); |
|
834 |
authorTeam.setTitleCache(nonViralName.getAuthorshipCache(), true); |
|
835 |
tags.add(authorTeam); |
|
836 |
|
|
837 |
// Name is an autonym. Rank and infraspecific epitheton follow the author |
|
838 |
if (nonViralName.isInfraSpecific() && nonViralName.getSpecificEpithet().equals(nonViralName.getInfraSpecificEpithet())){ |
|
839 |
tags.add(nonViralName.getRank()); |
|
840 |
tags.add(nonViralName.getInfraSpecificEpithet()); |
|
841 |
} |
|
842 |
|
|
843 |
if(! "".equals(nonViralName.getAppendedPhrase())&& (nonViralName.getAppendedPhrase() != null)){ |
|
844 |
tags.add(nonViralName.getAppendedPhrase()); |
|
845 |
} |
|
846 |
|
|
847 |
return tags; |
|
848 |
} |
|
849 |
|
|
850 |
|
|
851 |
/** |
|
852 |
* @deprecated use only for {@link #getTaggedNameDeprecated(NonViralName)}. Delete when the later |
|
853 |
* is deleted. |
|
854 |
*/ |
|
855 |
@Deprecated |
|
856 |
private String getSpeciesAggregateEpithet(NonViralName<?> nonViralName) { |
|
857 |
String marker; |
|
858 |
try { |
|
859 |
marker = nonViralName.getRank().getInfraGenericMarker(); |
|
860 |
} catch (UnknownCdmTypeException e) { |
|
861 |
marker = "'unknown aggregat type'"; |
|
862 |
} |
|
863 |
return marker; |
|
864 |
} |
|
865 |
|
|
866 |
|
|
1083 | 867 |
} |
Also available in: Unified diff
Cleaning up name cache strategies and updating javadoc