Revision 7b1ac952
Added by Andreas Müller over 12 years ago
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/name/NonViralNameDefaultCacheStrategy.java | ||
|---|---|---|
| 29 | 29 |
import eu.etaxonomy.cdm.model.name.NonViralName; |
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import eu.etaxonomy.cdm.model.name.Rank; |
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import eu.etaxonomy.cdm.model.reference.INomenclaturalReference; |
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import eu.etaxonomy.cdm.strategy.TagEnum; |
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import eu.etaxonomy.cdm.strategy.TaggedText; |
|
| 32 | 34 |
import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException; |
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImplRegExBase; |
| 34 | 36 |
|
| ... | ... | |
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return new NonViralNameDefaultCacheStrategy(); |
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} |
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|
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/** |
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* Factory method |
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* @return NonViralNameDefaultCacheStrategy A new instance of NonViralNameDefaultCacheStrategy |
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*/ |
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public static <T extends NonViralName<?>> NonViralNameDefaultCacheStrategy<T> NewInstance(Class<T> clazz){
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return new NonViralNameDefaultCacheStrategy<T>(); |
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} |
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|
|
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/** |
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* Constructor |
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*/ |
| ... | ... | |
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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.INameCacheStrategy#getNameCache()
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* @see eu.etaxonomy.cdm.strategy.cache.name.NameCacheStrategyBase#getTitleCache(eu.etaxonomy.cdm.model.name.TaxonNameBase)
|
|
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*/ |
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@Override |
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public String getTitleCache(T nonViralName) {
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List<TaggedText> tags = getTaggedTitle(nonViralName); |
|
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if (tags == null){
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return null; |
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}else{
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String result = createString(tags); |
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return result; |
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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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|
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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 result; |
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} |
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|
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protected boolean nameIncludesAuthorship(NonViralName nonViralName){
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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; |
| ... | ... | |
| 240 | 333 |
} |
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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) |
|
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*/ |
|
| 247 | 339 |
@Override |
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public String getFullTitleCache(T nonViralName) {
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List<TaggedText> tags = getTaggedFullTitle(nonViralName); |
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if (tags == null){
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return null; |
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}else{
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String result = createString(tags); |
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return result; |
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} |
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} |
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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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return result; |
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} |
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|
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|
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|
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/** |
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* Generates and returns the "name cache" (only scientific name without author teams and year). |
| 308 | 412 |
* @see eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy#getNameCache(eu.etaxonomy.cdm.model.name.TaxonNameBase) |
| 309 | 413 |
*/ |
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@Override |
|
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public String getNameCache(T nonViralName) {
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List<TaggedText> tags = getNameTags(nonViralName); |
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if (tags == null){
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return null; |
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}else{
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String result = createString(tags); |
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return result; |
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} |
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} |
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|
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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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} |
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return result; |
| 338 | 453 |
} |
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// |
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// |
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// /** |
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// * @param nonViralName |
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// * @return |
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// */ |
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// private boolean isInfragenericUnranked(T nonViralName) {
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// Rank rank = nonViralName.getRank(); |
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// if (rank == null || ! rank.equals(Rank.UNRANKED())){
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// return false; |
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// } |
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// if (StringUtils.isBlank(nonViralName.getSpecificEpithet()) && StringUtils.isBlank(nonViralName.getInfraSpecificEpithet()) ){
|
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// return true; |
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// }else{
|
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// return false; |
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// } |
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// } |
|
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|
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|
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private String getUnrankedInfragenericNameCache(T nonViralName) {
|
| ... | ... | |
| 434 | 532 |
|
| 435 | 533 |
} |
| 436 | 534 |
|
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// ************* TAGGED NAME ***************************************/ |
|
| 437 | 536 |
|
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/* (non-Javadoc) |
|
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* @see eu.etaxonomy.cdm.strategy.cache.name.NameCacheStrategyBase#getTaggedTitle(eu.etaxonomy.cdm.model.name.TaxonNameBase) |
|
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*/ |
|
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@Override |
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public List<TaggedText> getTaggedFullTitle(T nonViralName) {
|
|
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List<TaggedText> tags = new ArrayList<TaggedText>(); |
|
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|
|
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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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|
|
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//protected full title cache |
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if (nonViralName.isProtectedFullTitleCache()){
|
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tags.add(new TaggedText(TagEnum.fullName, nonViralName.getFullTitleCache())); |
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return tags; |
|
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} |
|
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|
|
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//title cache |
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// String titleCache = nonViralName.getTitleCache(); |
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List<TaggedText> titleTags = getTaggedTitle(nonViralName); |
|
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tags.addAll(titleTags); |
|
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|
|
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|
|
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//reference |
|
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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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//add to tags |
|
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if (StringUtils.isNotBlank(referenceBaseCache)){
|
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if (! referenceBaseCache.trim().startsWith("in ")){
|
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String refConcat = ", "; |
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tags.add(new TaggedText(TagEnum.separator, refConcat)); |
|
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} |
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tags.add(new TaggedText(TagEnum.reference, referenceBaseCache)); |
|
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} |
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|
|
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//nomenclatural status |
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Set<NomenclaturalStatus> ncStati = nonViralName.getStatus(); |
|
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Iterator<NomenclaturalStatus> iterator = ncStati.iterator(); |
|
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List<TaggedText> nomStatusTags = new ArrayList<TaggedText>(); |
|
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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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String statusSeparator = ", "; |
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nomStatusTags.add(new TaggedText(TagEnum.separator, statusSeparator)); |
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nomStatusTags.add(new TaggedText(TagEnum.nomStatus, suffix)); |
|
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} |
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tags.addAll(nomStatusTags); |
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return tags; |
|
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|
|
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} |
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|
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public List<TaggedText> getTaggedTitle(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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List<TaggedText> tags = new ArrayList<TaggedText>(); |
|
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|
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//TODO how to handle protected fullTitleCache here? |
|
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|
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if (nonViralName.isProtectedTitleCache()){
|
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//protected title cache |
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tags.add(new TaggedText(TagEnum.name, nonViralName.getTitleCache())); |
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return tags; |
|
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}else if (nonViralName.isHybridFormula()){
|
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//hybrid formula |
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String hybridSeparator = NonViralNameParserImplRegExBase.hybridSign; |
|
| 627 |
boolean isFirst = true; |
|
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List<HybridRelationship> rels = nonViralName.getOrderedChildRelationships(); |
|
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for (HybridRelationship rel: rels){
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if (! isFirst){
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| 631 |
tags.add(new TaggedText(TagEnum.separator, hybridSeparator)); |
|
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} |
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tags.add(new TaggedText(TagEnum.name, hybridSeparator)); |
|
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isFirst = false; |
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tags.addAll(getTaggedTitle((T)rel.getParentName())); |
|
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} |
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return tags; |
|
| 638 |
}else if (nonViralName.isAutonym()){
|
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| 639 |
//Autonym |
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tags.addAll(handleTaggedAutonym(nonViralName)); |
|
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}else{ //not Autonym
|
|
| 642 |
// String nameCache = nonViralName.getNameCache(); //OLD: CdmUtils.Nz(getNameCache(nonViralName)); |
|
| 643 |
List<TaggedText> nameTags = getNameTags(nonViralName); |
|
| 644 |
tags.addAll(nameTags); |
|
| 645 |
if (nameIncludesAuthorship(nonViralName)){
|
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| 646 |
String authorCache = getAuthorshipCache(nonViralName); |
|
| 647 |
if (StringUtils.isNotBlank(authorCache)){
|
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| 648 |
tags.add(new TaggedText(TagEnum.authors, authorCache)); |
|
| 649 |
} |
|
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} |
|
| 651 |
} |
|
| 652 |
return tags; |
|
| 653 |
|
|
| 654 |
} |
|
| 655 |
|
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| 656 |
|
|
| 657 |
/** |
|
| 658 |
* @param nonViralName |
|
| 659 |
* @return |
|
| 660 |
*/ |
|
| 661 |
private List<TaggedText> getNameTags(T nonViralName) {
|
|
| 662 |
if (nonViralName == null){
|
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| 663 |
return null; |
|
| 664 |
} |
|
| 665 |
List<TaggedText> tags = new ArrayList<TaggedText>(); |
|
| 666 |
Rank rank = nonViralName.getRank(); |
|
| 667 |
|
|
| 668 |
if (nonViralName.isProtectedNameCache()){
|
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| 669 |
tags.add(new TaggedText(TagEnum.name, nonViralName.getNameCache())); |
|
| 670 |
}else if (rank == null){
|
|
| 671 |
tags = getRanklessTaggedNameCache(nonViralName); |
|
| 672 |
// }else if (nonViralName.isInfragenericUnranked()){
|
|
| 673 |
// result = getUnrankedInfragenericNameCache(nonViralName); |
|
| 674 |
}else if (rank.isInfraSpecific()){
|
|
| 675 |
tags = getInfraSpeciesTaggedNameCache(nonViralName); |
|
| 676 |
}else if (rank.isSpecies()){
|
|
| 677 |
tags = getSpeciesTaggedNameCache(nonViralName); |
|
| 678 |
}else if (rank.isInfraGeneric()){
|
|
| 679 |
tags = getInfraGenusTaggedNameCache(nonViralName); |
|
| 680 |
}else if (rank.isGenus()){
|
|
| 681 |
tags = getGenusOrUninomialTaggedNameCache(nonViralName); |
|
| 682 |
}else if (rank.isSupraGeneric()){
|
|
| 683 |
tags = getGenusOrUninomialTaggedNameCache(nonViralName); |
|
| 684 |
}else{
|
|
| 685 |
logger.warn("Name Strategy for Name (UUID: " + nonViralName.getUuid() + ") not yet implemented");
|
|
| 686 |
} |
|
| 687 |
//TODO handle appended phrase here instead of different places, check first if this is true for all |
|
| 688 |
//cases |
|
| 689 |
|
|
| 690 |
return tags; |
|
| 691 |
|
|
| 692 |
} |
|
| 693 |
|
|
| 694 |
|
|
| 695 |
//Old: may be replaced once getTagged(Full)Title is fully tested |
|
| 438 | 696 |
/* (non-Javadoc) |
| 439 | 697 |
* @see eu.etaxonomy.cdm.strategy.INameCacheStrategy#getTaggedName(eu.etaxonomy.cdm.model.common.CdmBase) |
| 440 | 698 |
*/ |
| ... | ... | |
| 503 | 761 |
|
| 504 | 762 |
//***************************** PRIVATES ***************************************/ |
| 505 | 763 |
|
| 506 |
protected String getRanklessNameCache(NonViralName nonViralName){
|
|
| 507 |
String result = ""; |
|
| 508 |
result = (result + (CdmUtils.Nz(nonViralName.getGenusOrUninomial()))).trim().replace("null", "");
|
|
| 509 |
result += " " + (CdmUtils.Nz(nonViralName.getSpecificEpithet())).trim(); |
|
| 510 |
result += " " + (CdmUtils.Nz(nonViralName.getInfraSpecificEpithet())).trim(); |
|
| 511 |
result = result.trim().replace("null", "");
|
|
| 512 |
//result += " (rankless)"; |
|
| 513 |
result = addAppendedPhrase(result, nonViralName); |
|
| 514 |
return result; |
|
| 764 |
protected List<TaggedText> getRanklessTaggedNameCache(NonViralName<?> nonViralName){
|
|
| 765 |
List<TaggedText> tags = getUninomialTaggedPart(nonViralName); |
|
| 766 |
String speciesEpi = CdmUtils.Nz(nonViralName.getSpecificEpithet()).trim().replace("null", "");
|
|
| 767 |
if (StringUtils.isNotBlank(speciesEpi)){
|
|
| 768 |
tags.add(new TaggedText(TagEnum.name, speciesEpi)); |
|
| 515 | 769 |
} |
| 516 |
|
|
| 517 |
|
|
| 518 |
protected String getGenusOrUninomialNameCache(NonViralName nonViralName){
|
|
| 519 |
String result; |
|
| 520 |
result = getUninomialPart(nonViralName); |
|
| 521 |
result = addAppendedPhrase(result, nonViralName).trim(); |
|
| 522 |
return result; |
|
| 770 |
|
|
| 771 |
String infraSpeciesEpi = CdmUtils.Nz(nonViralName.getInfraSpecificEpithet()).trim().replace("null", "");
|
|
| 772 |
if (StringUtils.isNotBlank(infraSpeciesEpi)){
|
|
| 773 |
tags.add(new TaggedText(TagEnum.name, infraSpeciesEpi)); |
|
| 523 | 774 |
} |
| 775 |
|
|
| 776 |
//result += " (rankless)"; |
|
| 777 |
addAppendedTaggedPhrase(tags, nonViralName); |
|
| 778 |
return tags; |
|
| 779 |
} |
|
| 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 |
} |
|
| 524 | 791 |
|
| 792 |
|
|
| 793 |
protected List<TaggedText> getGenusOrUninomialTaggedNameCache(NonViralName<?> nonViralName){
|
|
| 794 |
List<TaggedText> tags = getUninomialTaggedPart(nonViralName); |
|
| 795 |
addAppendedTaggedPhrase(tags, nonViralName); |
|
| 796 |
return tags; |
|
| 797 |
} |
|
| 525 | 798 |
|
| 526 |
private String getUninomialPart(NonViralName nonViralName) {
|
|
| 527 |
String result; |
|
| 528 |
result = CdmUtils.Nz(nonViralName.getGenusOrUninomial()).trim(); |
|
| 529 |
if (nonViralName.isMonomHybrid()){
|
|
| 530 |
result = NonViralNameParserImplRegExBase.hybridSign + result; |
|
| 531 |
} |
|
| 532 |
return result; |
|
| 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 |
|
|
| 807 |
private List<TaggedText> getUninomialTaggedPart(NonViralName<?> nonViralName) {
|
|
| 808 |
List<TaggedText> tags = new ArrayList<TaggedText>(); |
|
| 809 |
|
|
| 810 |
if (nonViralName.isMonomHybrid()){
|
|
| 811 |
addHybridPrefix(tags); |
|
| 533 | 812 |
} |
| 534 | 813 |
|
| 535 |
protected String getInfraGenusNameCache(NonViralName nonViralName){
|
|
| 536 |
String result; |
|
| 537 |
Rank rank = nonViralName.getRank(); |
|
| 538 |
if (rank.isSpeciesAggregate()){
|
|
| 539 |
return getSpeciesAggregateCache(nonViralName); |
|
| 540 |
} |
|
| 541 |
String infraGenericMarker = "'unhandled infrageneric rank'"; |
|
| 542 |
if (rank != null){
|
|
| 543 |
try {
|
|
| 544 |
infraGenericMarker = rank.getInfraGenericMarker(); |
|
| 545 |
} catch (UnknownCdmTypeException e) {
|
|
| 546 |
infraGenericMarker = "'unhandled infrageneric rank'"; |
|
| 547 |
} |
|
| 548 |
} |
|
| 549 |
result = getUninomialPart(nonViralName); |
|
| 550 |
result += " " + infraGenericMarker + " " + (CdmUtils.Nz(nonViralName.getInfraGenericEpithet())).trim().replace("null", "");
|
|
| 551 |
result = addAppendedPhrase(result, nonViralName).trim(); |
|
| 552 |
return result; |
|
| 814 |
String uninomial = CdmUtils.Nz(nonViralName.getGenusOrUninomial()).trim().replace("null", "");
|
|
| 815 |
if (StringUtils.isNotBlank(uninomial)){
|
|
| 816 |
tags.add(new TaggedText(TagEnum.name, uninomial)); |
|
| 553 | 817 |
} |
| 554 |
|
|
| 555 |
// aggr.|agg.|group |
|
| 556 |
protected String getSpeciesAggregateCache(NonViralName nonViralName){
|
|
| 557 |
String result = getGenusAndSpeciesPart(nonViralName); |
|
| 558 | 818 |
|
| 559 |
result += " " + getSpeciesAggregateEpithet(nonViralName); |
|
| 560 |
result = addAppendedPhrase(result, nonViralName).trim(); |
|
| 561 |
return result; |
|
| 819 |
return tags; |
|
| 820 |
} |
|
| 821 |
|
|
| 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; |
|
| 562 | 827 |
} |
| 828 |
return result; |
|
| 829 |
} |
|
| 830 |
|
|
| 831 |
|
|
| 832 |
protected List<TaggedText> getInfraGenusTaggedNameCache(NonViralName<?> nonViralName){
|
|
| 833 |
Rank rank = nonViralName.getRank(); |
|
| 834 |
if (rank.isSpeciesAggregate()){
|
|
| 835 |
return getSpeciesAggregateTaggedCache(nonViralName); |
|
| 836 |
} |
|
| 837 |
|
|
| 838 |
//genus |
|
| 839 |
List<TaggedText> tags = getUninomialTaggedPart(nonViralName); |
|
| 563 | 840 |
|
| 564 |
private String getSpeciesAggregateEpithet(NonViralName nonViralName) {
|
|
| 565 |
String marker; |
|
| 841 |
//marker |
|
| 842 |
String infraGenericMarker = "'unhandled infrageneric rank'"; |
|
| 843 |
if (rank != null){
|
|
| 566 | 844 |
try {
|
| 567 |
marker = nonViralName.getRank().getInfraGenericMarker();
|
|
| 845 |
infraGenericMarker = rank.getInfraGenericMarker();
|
|
| 568 | 846 |
} catch (UnknownCdmTypeException e) {
|
| 569 |
marker = "'unknown aggregat type'";
|
|
| 847 |
infraGenericMarker = "'unhandled infrageneric rank'";
|
|
| 570 | 848 |
} |
| 571 |
return marker; |
|
| 572 | 849 |
} |
| 850 |
tags.add(new TaggedText(TagEnum.rank, infraGenericMarker)); |
|
| 573 | 851 |
|
| 574 |
protected String getSpeciesNameCache(NonViralName nonViralName){
|
|
| 575 |
String result = getGenusAndSpeciesPart(nonViralName); |
|
| 576 |
result = addAppendedPhrase(result, nonViralName).trim(); |
|
| 577 |
result = result.replace("\\s\\", " ");
|
|
| 578 |
return result; |
|
| 852 |
|
|
| 853 |
String infraGenEpi = CdmUtils.Nz(nonViralName.getInfraGenericEpithet()).trim().replace("null", "");
|
|
| 854 |
if (StringUtils.isNotBlank(infraGenEpi)){
|
|
| 855 |
tags.add(new TaggedText(TagEnum.name, infraGenEpi)); |
|
| 579 | 856 |
} |
| 580 | 857 |
|
| 858 |
addAppendedTaggedPhrase(tags, nonViralName); |
|
| 859 |
return tags; |
|
| 860 |
} |
|
| 861 |
|
|
| 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 |
|
| 883 |
protected List<TaggedText> getSpeciesAggregateTaggedCache(NonViralName<?> nonViralName){
|
|
| 884 |
List<TaggedText> tags = getGenusAndSpeciesTaggedPart(nonViralName); |
|
| 581 | 885 |
|
| 582 |
protected String getInfraSpeciesNameCache(NonViralName nonViralName){
|
|
| 583 |
return getInfraSpeciesNameCache(nonViralName, true); |
|
| 886 |
addSpeciesAggregateTaggedEpithet(tags, nonViralName); |
|
| 887 |
addAppendedTaggedPhrase(tags, nonViralName); |
|
| 888 |
return tags; |
|
| 889 |
} |
|
| 890 |
|
|
| 891 |
private void addSpeciesAggregateTaggedEpithet(List<TaggedText> tags, NonViralName<?> nonViralName) {
|
|
| 892 |
String marker; |
|
| 893 |
try {
|
|
| 894 |
marker = nonViralName.getRank().getInfraGenericMarker(); |
|
| 895 |
} catch (UnknownCdmTypeException e) {
|
|
| 896 |
marker = "'unknown aggregat type'"; |
|
| 897 |
} |
|
| 898 |
if (StringUtils.isNotBlank(marker)){
|
|
| 899 |
tags.add(new TaggedText(TagEnum.rank, marker)); |
|
| 584 | 900 |
} |
| 901 |
} |
|
| 902 |
|
|
| 903 |
// aggr.|agg.|group |
|
| 904 |
protected String getSpeciesAggregateCache(NonViralName<?> nonViralName){
|
|
| 905 |
String result = getGenusAndSpeciesPart(nonViralName); |
|
| 585 | 906 |
|
| 586 |
protected String getInfraSpeciesNameCache(NonViralName nonViralName, boolean includeMarker){
|
|
| 587 |
String result = getGenusAndSpeciesPart(nonViralName); |
|
| 588 |
if (includeMarker){
|
|
| 589 |
result += " " + (nonViralName.getRank().getAbbreviation()).trim().replace("null", "");
|
|
| 590 |
} |
|
| 591 |
String infrSpecEpi = CdmUtils.Nz(nonViralName.getInfraSpecificEpithet()); |
|
| 592 |
if (nonViralName.isTrinomHybrid()){
|
|
| 593 |
infrSpecEpi = NonViralNameParserImplRegExBase.hybridSign + infrSpecEpi; |
|
| 594 |
} |
|
| 595 |
result += " " + (infrSpecEpi).trim().replace("null", "");
|
|
| 596 |
result = addAppendedPhrase(result, nonViralName).trim(); |
|
| 597 |
return result; |
|
| 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'"; |
|
| 598 | 918 |
} |
| 919 |
return marker; |
|
| 920 |
} |
|
| 599 | 921 |
|
| 922 |
|
|
| 923 |
protected List<TaggedText> getSpeciesTaggedNameCache(NonViralName<?> nonViralName){
|
|
| 924 |
List<TaggedText> tags = getGenusAndSpeciesTaggedPart(nonViralName); |
|
| 925 |
addAppendedTaggedPhrase(tags, nonViralName); |
|
| 926 |
return tags; |
|
| 927 |
} |
|
| 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 |
} |
|
| 600 | 935 |
|
| 601 |
private String getGenusAndSpeciesPart(NonViralName nonViralName) {
|
|
| 602 |
String result; |
|
| 603 |
//Uninomial |
|
| 604 |
result = getUninomialPart(nonViralName); |
|
| 605 |
|
|
| 606 |
//InfraGenericEpi |
|
| 607 |
boolean hasInfraGenericEpi = StringUtils.isNotBlank(nonViralName.getInfraGenericEpithet()); |
|
| 608 |
if (hasInfraGenericEpi){
|
|
| 609 |
String infrGenEpi = nonViralName.getInfraGenericEpithet().trim(); |
|
| 610 |
if (nonViralName.isBinomHybrid()){
|
|
| 611 |
infrGenEpi = NonViralNameParserImplRegExBase.hybridSign + infrGenEpi; |
|
| 612 |
} |
|
| 613 |
result += " (" + infrGenEpi + ")";
|
|
| 936 |
protected List<TaggedText> getInfraSpeciesTaggedNameCache(NonViralName<?> nonViralName){
|
|
| 937 |
return getInfraSpeciesTaggedNameCache(nonViralName, true); |
|
| 938 |
} |
|
| 939 |
|
|
| 940 |
protected List<TaggedText> getInfraSpeciesTaggedNameCache(NonViralName<?> nonViralName, boolean includeMarker){
|
|
| 941 |
List<TaggedText> tags = getGenusAndSpeciesTaggedPart(nonViralName); |
|
| 942 |
if (includeMarker){
|
|
| 943 |
String marker = (nonViralName.getRank().getAbbreviation()).trim().replace("null", "");
|
|
| 944 |
if (StringUtils.isNotBlank(marker)){
|
|
| 945 |
tags.add(new TaggedText(TagEnum.rank, marker)); |
|
| 614 | 946 |
} |
| 615 |
//Species Epi |
|
| 616 |
String specEpi = CdmUtils.Nz(nonViralName.getSpecificEpithet()).trim(); |
|
| 617 |
if (! hasInfraGenericEpi && nonViralName.isBinomHybrid() || |
|
| 618 |
hasInfraGenericEpi && nonViralName.isTrinomHybrid()){
|
|
| 619 |
specEpi = NonViralNameParserImplRegExBase.hybridSign + specEpi; |
|
| 947 |
} |
|
| 948 |
String infrSpecEpi = CdmUtils.Nz(nonViralName.getInfraSpecificEpithet()); |
|
| 949 |
if (nonViralName.isTrinomHybrid()){
|
|
| 950 |
addHybridPrefix(tags); |
|
| 951 |
} |
|
| 952 |
|
|
| 953 |
infrSpecEpi = infrSpecEpi.trim().replace("null", "");
|
|
| 954 |
if (StringUtils.isNotBlank(infrSpecEpi)){
|
|
| 955 |
tags.add(new TaggedText(TagEnum.name, infrSpecEpi)); |
|
| 956 |
} |
|
| 957 |
|
|
| 958 |
addAppendedTaggedPhrase(tags, nonViralName); |
|
| 959 |
return tags; |
|
| 960 |
} |
|
| 961 |
|
|
| 962 |
|
|
| 963 |
/** |
|
| 964 |
* Adds a tag for the hybrid sign and an empty separator to avoid trailing whitespaces. |
|
| 965 |
* @param tags |
|
| 966 |
*/ |
|
| 967 |
private void addHybridPrefix(List<TaggedText> tags) {
|
|
| 968 |
tags.add(new TaggedText(TagEnum.hybridSign, NonViralNameParserImplRegExBase.hybridSign)); |
|
| 969 |
tags.add(new TaggedText(TagEnum.separator, "")); //no whitespace separator |
|
| 970 |
} |
|
| 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 |
|
|
| 992 |
private List<TaggedText> getGenusAndSpeciesTaggedPart(NonViralName<?> nonViralName) {
|
|
| 993 |
//Uninomial |
|
| 994 |
List<TaggedText> tags = getUninomialTaggedPart(nonViralName); |
|
| 995 |
|
|
| 996 |
//InfraGenericEpi |
|
| 997 |
boolean hasInfraGenericEpi = StringUtils.isNotBlank(nonViralName.getInfraGenericEpithet()); |
|
| 998 |
if (hasInfraGenericEpi){
|
|
| 999 |
String infrGenEpi = nonViralName.getInfraGenericEpithet().trim(); |
|
| 1000 |
if (nonViralName.isBinomHybrid()){
|
|
| 1001 |
// addHybridPrefix(tags); FIXME hybridSign should be tag, but then we need to handle "(" ")" differently.
|
|
| 1002 |
infrGenEpi = NonViralNameParserImplRegExBase.hybridSign + infrGenEpi; |
|
| 620 | 1003 |
} |
| 621 |
result += " " + (specEpi).replace("null", "");
|
|
| 622 |
return result;
|
|
| 1004 |
infrGenEpi = "(" + infrGenEpi + ")";
|
|
| 1005 |
tags.add(new TaggedText(TagEnum.name, infrGenEpi));
|
|
| 623 | 1006 |
} |
| 624 | 1007 |
|
| 1008 |
//Species Epi |
|
| 1009 |
String specEpi = CdmUtils.Nz(nonViralName.getSpecificEpithet()).trim().replace("null", "");
|
|
| 1010 |
if (! hasInfraGenericEpi && nonViralName.isBinomHybrid() || |
|
| 1011 |
hasInfraGenericEpi && nonViralName.isTrinomHybrid()){
|
|
| 1012 |
addHybridPrefix(tags); |
|
| 1013 |
} |
|
| 1014 |
if (StringUtils.isNotBlank(specEpi)){
|
|
| 1015 |
tags.add(new TaggedText(TagEnum.name, specEpi)); |
|
| 1016 |
} |
|
| 1017 |
return tags; |
|
| 1018 |
} |
|
| 1019 |
|
|
| 1020 |
private String getGenusAndSpeciesPart(NonViralName<?> nonViralName) {
|
|
| 1021 |
String result; |
|
| 1022 |
//Uninomial |
|
| 1023 |
result = getUninomialPart(nonViralName); |
|
| 625 | 1024 |
|
| 626 |
protected String addAppendedPhrase(String resultString, NonViralName nonViralName){
|
|
| 627 |
String appendedPhrase = nonViralName ==null ? null : nonViralName.getAppendedPhrase(); |
|
| 628 |
if (resultString == null){
|
|
| 629 |
return appendedPhrase; |
|
| 630 |
}else if(appendedPhrase == null || "".equals(appendedPhrase.trim())) {
|
|
| 631 |
return resultString; |
|
| 632 |
}else if ("".equals(resultString)){
|
|
| 633 |
return resultString + appendedPhrase; |
|
| 634 |
}else {
|
|
| 635 |
return resultString + " " + appendedPhrase; |
|
| 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; |
|
| 636 | 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 |
/** |
|
| 1046 |
* Adds the tag for the appended phrase if an appended phrase exists |
|
| 1047 |
* @param tags |
|
| 1048 |
* @param nonViralName |
|
| 1049 |
*/ |
|
| 1050 |
protected void addAppendedTaggedPhrase(List<TaggedText> tags, NonViralName<?> nonViralName){
|
|
| 1051 |
String appendedPhrase = nonViralName ==null ? null : nonViralName.getAppendedPhrase(); |
|
| 1052 |
if (StringUtils.isNotEmpty(appendedPhrase)){
|
|
| 1053 |
tags.add(new TaggedText(TagEnum.name, appendedPhrase)); |
|
| 1054 |
} |
|
| 1055 |
} |
|
| 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; |
|
| 637 | 1067 |
} |
| 1068 |
} |
|
| 638 | 1069 |
|
| 639 | 1070 |
|
| 640 |
public String getLastEpithet(T taxonNameBase) {
|
|
| 641 |
Rank rank = taxonNameBase.getRank(); |
|
| 642 |
if(rank.isGenus() || rank.isSupraGeneric()) {
|
|
| 643 |
return taxonNameBase.getGenusOrUninomial(); |
|
| 644 |
} else if(rank.isInfraGeneric()) {
|
|
| 645 |
return taxonNameBase.getInfraGenericEpithet(); |
|
| 646 |
} else if(rank.isSpecies()) {
|
|
| 647 |
return taxonNameBase.getSpecificEpithet(); |
|
| 648 |
} else {
|
|
| 649 |
return taxonNameBase.getInfraSpecificEpithet(); |
|
| 650 |
} |
|
| 1071 |
public String getLastEpithet(T taxonNameBase) {
|
|
| 1072 |
Rank rank = taxonNameBase.getRank(); |
|
| 1073 |
if(rank.isGenus() || rank.isSupraGeneric()) {
|
|
| 1074 |
return taxonNameBase.getGenusOrUninomial(); |
|
| 1075 |
} else if(rank.isInfraGeneric()) {
|
|
| 1076 |
return taxonNameBase.getInfraGenericEpithet(); |
|
| 1077 |
} else if(rank.isSpecies()) {
|
|
| 1078 |
return taxonNameBase.getSpecificEpithet(); |
|
| 1079 |
} else {
|
|
| 1080 |
return taxonNameBase.getInfraSpecificEpithet(); |
|
| 651 | 1081 |
} |
| 1082 |
} |
|
| 652 | 1083 |
} |
Also available in: Unified diff
Refactoring nameCacheStrategy. Use same method for both caches (tagged + string)