@Override public StringBuffer asSimpleText() { return new StringBuffer( getName() ); }
@Override public boolean isEqual( final PhylogenyData protein_domain ) { if ( protein_domain == null ) { return false; } if ( !( protein_domain instanceof ProteinDomain ) ) { return false; } else if ( ( ( ProteinDomain ) protein_domain ).getLength() != getLength() ) { return false; } else if ( !( ( ProteinDomain ) protein_domain ).getName().equals( getName() ) ) { return false; } return true; }
@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; }
/** * Returns true if the names and the order of the domains match (domain and * linker lengths are ignored). * * */ @Override public boolean isEqual( final PhylogenyData domain_architecture ) { if ( domain_architecture == null ) { return false; } if ( !( domain_architecture instanceof DomainArchitecture ) ) { return false; } final DomainArchitecture d = ( DomainArchitecture ) domain_architecture; if ( getDomains().size() != d.getDomains().size() ) { return false; } for( int i = 0; i < getDomains().size(); ++i ) { if ( !getDomain( i ).getName().equals( d.getDomain( i ).getName() ) ) { return false; } } return true; }
@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; }
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++; g.setColor( Constants.DOMAIN_LABEL_COLOR_FOR_PDF ); g.drawString( d.getName(), xa, y1 + tree_panel.getMainPanel().getTreeFontSet().getFontMetricsSmall().getAscent() + _rendering_height ); && ( d.getName().equals( SPECIAL_DOMAIN ) ) && ( _node_name.indexOf( "~" + special_domain_count + "-" ) < 1 ) ) { drawDomainGrey( xa, y1, xb - xa, _rendering_height, d.getName(), g, to_pdf ); drawDomain( xa, y1, xb - xa, _rendering_height, d.getName(), g, to_pdf );
@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 ); }
final ProteinDomain pd2 = new ProteinDomain( pd0.getName(), pd0.getFrom(), pd0.getTo(), "id" ); final ProteinDomain pd3 = ( ProteinDomain ) pd2.copy(); if ( !pd3.isEqual( pd3 ) ) {
final ProteinDomain d = da.getDomain( i ); if ( d.getConfidence() <= Math.pow( 10, getDomainStructureEvalueThresholdExp() ) ) { final String name = d.getName(); if ( !( s.contains( name ) ) ) { data.add( name );
.getName().equals( "B" ) ) { return false;
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; break I;
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; break I;