import org.forester.io.parsers.phyloxml.PhyloXmlMapping;
import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
import org.forester.util.ForesterUtil;
+import org.forester.util.TaxonomyUtil;
public class Taxonomy implements PhylogenyData, MultipleUris, Comparable<Taxonomy> {
public boolean isEmpty() {
return ( ( getIdentifier() == null ) && ForesterUtil.isEmpty( getTaxonomyCode() )
- && ForesterUtil.isEmpty( getCommonName() ) && ForesterUtil.isEmpty( getScientificName() ) && ForesterUtil
- .isEmpty( _lineage ) );
+ && ForesterUtil.isEmpty( getCommonName() ) && ForesterUtil.isEmpty( getScientificName() )
+ && ForesterUtil.isEmpty( _lineage ) );
}
/**
}
public void setRank( final String rank ) throws PhyloXmlDataFormatException {
- if ( !ForesterUtil.isEmpty( rank ) && !PhyloXmlUtil.TAXONOMY_RANKS_SET.contains( rank ) ) {
+ if ( !ForesterUtil.isEmpty( rank ) && !TaxonomyUtil.TAXONOMY_RANKS_SET.contains( rank ) ) {
throw new PhyloXmlDataFormatException( "illegal rank: [" + rank + "]" );
}
_rank = rank;
&& !PhyloXmlUtil.TAXOMONY_CODE_PATTERN.matcher( taxonomy_code ).matches() ) {
throw new PhyloXmlDataFormatException( "illegal taxonomy code: [" + taxonomy_code + "]" );
}
- //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- //TODO FIXME (added on 13-11-18) remove me eventually
- if ( taxonomy_code.equals( "ACIBL" ) ) {
- taxonomy_code = "KORVE";
- }
- else if ( taxonomy_code.equals( "PYRKO" ) ) {
- taxonomy_code = "THEKO";
- }
- //TODO FIXME (added on 13-11-18) remove me eventually
- //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
_taxonomy_code = taxonomy_code;
}
PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.TAXONOMY_AUTHORITY, getAuthority(), indentation );
}
if ( !ForesterUtil.isEmpty( getCommonName() ) ) {
- PhylogenyDataUtil
- .appendElement( writer, PhyloXmlMapping.TAXONOMY_COMMON_NAME, getCommonName(), indentation );
+ PhylogenyDataUtil.appendElement( writer,
+ PhyloXmlMapping.TAXONOMY_COMMON_NAME,
+ getCommonName(),
+ indentation );
}
if ( _synonyms != null ) {
for( final String syn : getSynonyms() ) {