@Override public StringBuffer asText() { final StringBuffer sb = new StringBuffer( getName() ); sb.append( " [" ); sb.append( getLength() ); if ( !ForesterUtil.isEmpty( getId() ) ) { sb.append( " " ); sb.append( getId() ); } if ( getConfidence() >= 0 ) { sb.append( " " ); sb.append( getConfidence() ); } sb.append( "]" ); return sb; }
@Override public StringBuffer toNHX() { final StringBuffer sb = new StringBuffer(); sb.append( ":" ); sb.append( NHXtags.DOMAIN_STRUCTURE ); sb.append( getTotalLength() ); if ( getDomains() != null ) { for( int i = 0; i < getDomains().size(); ++i ) { sb.append( DomainArchitecture.NHX_SEPARATOR ); sb.append( getDomain( i ).getFrom() ); sb.append( DomainArchitecture.NHX_SEPARATOR ); sb.append( getDomain( i ).getTo() ); sb.append( DomainArchitecture.NHX_SEPARATOR ); sb.append( getDomain( i ).getConfidence() ); sb.append( DomainArchitecture.NHX_SEPARATOR ); sb.append( ForesterUtil.replaceIllegalNhxCharacters( getDomain( i ).getName() ) ); } } return sb; }
@Override public PhylogenyData copy() { if ( getId() == null ) { return new ProteinDomain( getName(), getFrom(), getTo(), getConfidence() ); } return new ProteinDomain( getName(), getFrom(), getTo(), getId(), getConfidence() ); }
@Override public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException { writer.write( ForesterUtil.LINE_SEPARATOR ); writer.write( indentation ); if ( getId() != null ) { PhylogenyDataUtil.appendOpen( writer, PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_DOMAIN, PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_FROM, getFrom() + "", PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_TO, getTo() + "", PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_CONFIDENCE, getConfidence() + "", PhyloXmlMapping.IDENTIFIER, getId() ); } else { PhylogenyDataUtil.appendOpen( writer, PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_DOMAIN, PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_FROM, getFrom() + "", PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_TO, getTo() + "", PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_CONFIDENCE, getConfidence() + "" ); } writer.write( getName() ); PhylogenyDataUtil.appendClose( writer, PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_DOMAIN ); }
for( int i = 0; i < _domain_structure.getDomains().size(); ++i ) { final ProteinDomain d = _domain_structure.getDomain( i ); if ( ( d.getConfidence() <= Math.pow( 10, _e_value_threshold_exp ) ) || ( TreePanel.SPECIAL_DOMAIN_COLORING && ( d.getName().equals( SPECIAL_DOMAIN ) ) && ( ( d .getConfidence() <= 1 ) ) ) ) { if ( TreePanel.SPECIAL_DOMAIN_COLORING && ( d.getName().equals( SPECIAL_DOMAIN ) ) ) { special_domain_count++;
for( int i = 0; i < da.getDomains().size(); ++i ) { final ProteinDomain d = da.getDomain( i ); if ( d.getConfidence() <= Math.pow( 10, getDomainStructureEvalueThresholdExp() ) ) { final String name = d.getName(); if ( !( s.contains( name ) ) ) {
.getConfidence() != 0 ) { return false;
final DomainArchitecture da = node.getNodeData().getSequence().getDomainArchitecture(); I: for( int i = 0; i < da.getNumberOfDomains(); ++i ) { if ( ( da.getDomain( i ).getConfidence() <= domains_confidence_threshold ) && match( da.getDomain( i ).getName(), query, case_sensitive, partial, false ) ) { match = true;
final DomainArchitecture da = node.getNodeData().getSequence().getDomainArchitecture(); I: for( int i = 0; i < da.getNumberOfDomains(); ++i ) { if ( ( da.getDomain( i ).getConfidence() <= domains_confidence_threshold ) && ( match( da.getDomain( i ).getName(), my_query, case_sensitive, partial, regex ) ) ) { match = true;