public void addDomain( final ProteinDomain pd ) { BigDecimal key = new BigDecimal( "" + pd.getFrom() ); while ( _domains.containsKey( key ) ) { key = new BigDecimal( "" + ( key.doubleValue() + DomainArchitecture.INCREASE_KEY.doubleValue() ) ); } _domains.put( key, pd ); }
public int getLength() { return ( ( getTo() - getFrom() ) + 1 ); }
@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 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 ); }
special_domain_count++; final float xa = start + ( d.getFrom() * f ); final float xb = xa + ( d.getLength() * f ); if ( tree_panel.getMainPanel().getOptions().isShowDomainLabels()
final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" ); final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy(); if ( !pd3.isEqual( pd3 ) ) {
.getFrom() != 21 ) { return false;