@Override public PhylogenyData copy() { return new Identifier( getValue(), getProvider() ); }
if ( getIdentifier() != null ) { sb.append( "[" ); sb.append( getIdentifier().asSimpleText() ); sb.append( "]" );
@Override public String toString() { return asText().toString(); } }
@Override public boolean isEqual( final PhylogenyData data ) { if ( this == data ) { return true; } if ( ( data == null ) || ( getValue() == null ) ) { return false; } final Identifier a = ( Identifier ) data; if ( ( getProvider() != null ) && ( a.getProvider() != null ) ) { return ( a.getValue().equals( getValue() ) && a.getProvider().equals( getProvider() ) ); } return ( a.getValue().equals( getValue() ) ); }
@Override public int hashCode() { if ( ( getIdentifier() != null ) && !ForesterUtil.isEmpty( getIdentifier().getValue() ) ) { return getIdentifier().hashCode(); } else if ( !ForesterUtil.isEmpty( getTaxonomyCode() ) ) { return getTaxonomyCode().hashCode(); } else if ( !ForesterUtil.isEmpty( getScientificName() ) ) { if ( !ForesterUtil.isEmpty( getAuthority() ) ) { return ( getScientificName().toLowerCase() + getAuthority().toLowerCase() ).hashCode(); } return getScientificName().toLowerCase().hashCode(); } else { return getCommonName().toLowerCase().hashCode(); } }
final Taxonomy t4 = new Taxonomy(); final Taxonomy t5 = new Taxonomy(); t1.setIdentifier( new Identifier( "ecoli" ) ); t1.setTaxonomyCode( "ECOLI" ); t1.setScientificName( "E. coli" ); t2.setIdentifier( new Identifier( "ecoli" ) ); t2.setTaxonomyCode( "OTHER" ); t2.setScientificName( "what" ); t2.setIdentifier( new Identifier( "nemve" ) ); if ( t1.isEqual( t2 ) ) { return false; final Identifier id0 = new Identifier( "123", "pfam" ); final Identifier id1 = ( Identifier ) id0.copy(); if ( !id1.isEqual( id1 ) ) { return false; if ( !id1.isEqual( id0 ) ) { return false; if ( !id0.isEqual( id1 ) ) { return false; id1.asSimpleText(); id1.asText();
@Override public StringBuffer asSimpleText() { return new StringBuffer( getValue() ); }
@Override public PhylogenyData parse( final XmlElement element ) throws PhyloXmlDataFormatException { if ( element.isHasAttribute( PhyloXmlMapping.IDENTIFIER_PROVIDER_ATTR ) ) { return new Identifier( element.getValueAsString(), element.getAttribute( PhyloXmlMapping.IDENTIFIER_PROVIDER_ATTR ) ); } else if ( element.isHasAttribute( TYPE ) ) { return new Identifier( element.getValueAsString(), element.getAttribute( TYPE ) ); } else { return new Identifier( element.getValueAsString() ); } }
@Override public int compareTo( final Taxonomy o ) { if ( equals( o ) ) { return 0; } if ( ( getIdentifier() != null ) && ( o.getIdentifier() != null ) && !ForesterUtil.isEmpty( getIdentifier().getValue() ) && !ForesterUtil.isEmpty( o.getIdentifier().getValue() ) ) { final int x = getIdentifier().getValuePlusProvider().compareTo( o.getIdentifier().getValuePlusProvider() ); if ( x != 0 ) { return x; } } if ( !ForesterUtil.isEmpty( getScientificName() ) && !ForesterUtil.isEmpty( o.getScientificName() ) ) { return getScientificName().compareToIgnoreCase( o.getScientificName() ); } if ( !ForesterUtil.isEmpty( getCommonName() ) && !ForesterUtil.isEmpty( o.getCommonName() ) ) { return getCommonName().compareToIgnoreCase( o.getCommonName() ); } if ( !ForesterUtil.isEmpty( getTaxonomyCode() ) && !ForesterUtil.isEmpty( o.getTaxonomyCode() ) ) { return getTaxonomyCode().compareToIgnoreCase( o.getTaxonomyCode() ); } if ( ( getIdentifier() != null ) && ( o.getIdentifier() != null ) && !ForesterUtil.isEmpty( getIdentifier().getValue() ) && !ForesterUtil.isEmpty( o.getIdentifier().getValue() ) ) { return getIdentifier().getValuePlusProvider().compareTo( o.getIdentifier().getValuePlusProvider() ); } return 1; }
&& ( ( tax.getIdentifier() == null ) || ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) ) { tax.setIdentifier( new Identifier( up_tax.getId(), "uniprot" ) );
writer.write( indentation ); PhylogenyDataUtil.appendOpen( writer, PhyloXmlMapping.TAXONOMY ); if ( ( getIdentifier() != null ) && !ForesterUtil.isEmpty( getIdentifier().getValue() ) ) { getIdentifier().toPhyloXML( writer, level, indentation );
/** * Returns a deep copy of this Phylogeny. * <p> * (The resulting Phylogeny has its references in the external nodes * corrected, if they are lacking/obsolete in this.) */ public Phylogeny copy( final PhylogenyNode source ) { final Phylogeny tree = new Phylogeny(); if ( isEmpty() ) { tree.init(); return tree; } tree._rooted = _rooted; tree._name = new String( _name ); tree._description = new String( _description ); tree._type = new String( _type ); tree._rerootable = _rerootable; tree._distance_unit = new String( _distance_unit ); if ( _confidence != null ) { tree._confidence = ( Confidence ) _confidence.copy(); } if ( _identifier != null ) { tree._identifier = ( Identifier ) _identifier.copy(); } tree.setAllowMultipleParents( isAllowMultipleParents() ); tree._root = PhylogenyMethods.copySubTree( source ); return tree; }
@Override public boolean equals( final Object o ) { if ( this == o ) { return true; } else if ( o == null ) { return false; } else if ( o.getClass() != this.getClass() ) { throw new IllegalArgumentException( "attempt to check [" + this.getClass() + "] equality to " + o + " [" + o.getClass() + "]" ); } else { return isEqual( ( Identifier ) o ); } }
public synchronized static boolean isTaxonomyHasIdentifierOfGivenProvider( final Taxonomy tax, final String[] providers ) { if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) { final String my_tax_prov = tax.getIdentifier().getProvider(); for( final String provider : providers ) { if ( provider.equalsIgnoreCase( my_tax_prov ) ) { return true; } } return false; } else { return false; } }
static String taxonomyToString( final PhylogenyNode n, final TaxonomyComparisonBase base ) { switch ( base ) { case ID: final Identifier id = n.getNodeData().getTaxonomy().getIdentifier(); if ( id == null ) { return null; } return id.getValuePlusProvider(); case CODE: return n.getNodeData().getTaxonomy().getTaxonomyCode(); case SCIENTIFIC_NAME: return n.getNodeData().getTaxonomy().getScientificName(); default: throw new IllegalArgumentException( "unknown comparison base for taxonomies: " + base ); } }
@Override public StringBuffer asText() { final StringBuffer sb = new StringBuffer(); if ( !ForesterUtil.isEmpty( getProvider() ) ) { sb.append( "[" ); sb.append( getProvider() ); sb.append( "] " ); } sb.append( getValue() ); return sb; }
@Override public StringBuffer toNHX() { final StringBuffer sb = new StringBuffer(); if ( getIdentifier() != null ) { sb.append( ':' + NHXtags.TAXONOMY_ID ); sb.append( ForesterUtil.replaceIllegalNhxCharacters( getIdentifier().getValue() ) ); } final StringBuffer species = new StringBuffer(); if ( !ForesterUtil.isEmpty( getTaxonomyCode() ) ) { species.append( ForesterUtil.replaceIllegalNhxCharacters( getTaxonomyCode() ) ); } if ( !ForesterUtil.isEmpty( getScientificName() ) ) { ForesterUtil.appendSeparatorIfNotEmpty( species, '|' ); species.append( ForesterUtil.replaceIllegalNhxCharacters( getScientificName() ) ); } if ( !ForesterUtil.isEmpty( getCommonName() ) ) { ForesterUtil.appendSeparatorIfNotEmpty( species, '|' ); species.append( ForesterUtil.replaceIllegalNhxCharacters( getCommonName() ) ); } if ( species.length() > 0 ) { sb.append( ':' + NHXtags.SPECIES_NAME ); sb.append( species ); } return sb; }
node_to_annotate.getNodeData().setTaxonomy( new Taxonomy() ); node_to_annotate.getNodeData().getTaxonomy().setIdentifier( new Identifier( s.substring( 2 ) ) );
&& !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getIdentifier().getValue() ) ) { ref_ext_taxo.add( n.getNodeData().getTaxonomy().getIdentifier().getValuePlusProvider() ); && !( ref_ext_taxo.contains( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) && !( ( n.getNodeData().getTaxonomy().getIdentifier() != null ) && ref_ext_taxo.contains( n .getNodeData().getTaxonomy().getIdentifier().getValuePlusProvider() ) ) ) { nodes_to_delete.add( n );