node.getNodeData().addSequence( ns );
final PhylogenyNode n = nodes.get( 0 ); if ( !n.getNodeData().isHasSequence() ) { n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() );
org.forester.phylogeny.data.Sequence seq = new org.forester.phylogeny.data.Sequence(); seq.setSymbol( "K1PYK7_CRAGI" ); n.getNodeData().addSequence( seq ); if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) { return false; seq = new org.forester.phylogeny.data.Sequence(); seq.setName( "K1PYK7_CRAGI" ); n.getNodeData().addSequence( seq ); if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) { return false; seq = new org.forester.phylogeny.data.Sequence(); seq.setAccession( new Accession( "K1PYK8_CRAGI", "?" ) ); n.getNodeData().addSequence( seq ); if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK8_CRAGI" ) ) { return false; seq = new org.forester.phylogeny.data.Sequence(); seq.setAccession( new Accession( "tr|B3RJ64", "?" ) ); n.getNodeData().addSequence( seq ); if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) { return false;
private final static void addSeqs2Tree( final Msa msa, final Phylogeny phy ) { for( int i = 0; i < msa.getNumberOfSequences(); ++i ) { final MolecularSequence seq = msa.getSequence( i ); final String seq_name = seq.getIdentifier(); final PhylogenyNode n = phy.getNode( seq_name ); if ( !n.getNodeData().isHasSequence() ) { n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() ); } else { throw new IllegalArgumentException( "this should not have happened" ); } n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() ); n.getNodeData().getSequence().setMolecularSequenceAligned( true ); n.getNodeData().getSequence().setName( seq_name ); } }
public static void addMolecularSeqsToTree( final Phylogeny phy, final Msa msa ) { for( int s = 0; s < msa.getNumberOfSequences(); ++s ) { final org.forester.sequence.MolecularSequence seq = msa.getSequence( s ); final PhylogenyNode node = phy.getNode( seq.getIdentifier() ); final org.forester.phylogeny.data.Sequence new_seq = new Sequence(); new_seq.setMolecularSequenceAligned( true ); new_seq.setMolecularSequence( seq.getMolecularSequenceAsString() ); new_seq.setName( seq.getIdentifier() ); try { new_seq.setType( PhyloXmlUtil.SEQ_TYPE_PROTEIN ); } catch ( final PhyloXmlDataFormatException ignore ) { // do nothing } node.getNodeData().addSequence( new_seq ); } }
node.getNodeData().addSequence( sequence );
for( final Sequence s : getSequences() ) { if ( s != null ) { new_data.addSequence( ( Sequence ) s.copy() );
static void processTreeBaseTrees( final Phylogeny phy ) { phy.setDescription( TREE_BASE_DESC ); final PhylogenyNodeIterator it = phy.iteratorExternalForward(); while ( it.hasNext() ) { final PhylogenyNode n = it.next(); if ( !ForesterUtil.isEmpty( n.getName() ) ) { final Accession acc = SequenceAccessionTools.parseAccessorFromString( n.getName() ); if ( acc != null ) { if ( !n.getNodeData().isHasSequence() ) { n.getNodeData().addSequence( new Sequence() ); } final Sequence s = n.getNodeData().getSequence(); if ( s.getAccession() == null ) { s.setAccession( acc ); } } } } }
d1.getNodeData().addSequence( s1 ); final Sequence s2 = new Sequence(); s2.setName( "Bcl-2" ); d2.getNodeData().addSequence( s2 );
private void createNodes( final DefaultMutableTreeNode top, final PhylogenyNode phylogeny_node ) { if ( !phylogeny_node.getNodeData().isHasTaxonomy() ) { phylogeny_node.getNodeData().addTaxonomy( new Taxonomy() ); } if ( !phylogeny_node.getNodeData().isHasSequence() ) { phylogeny_node.getNodeData().addSequence( new Sequence() ); } if ( !phylogeny_node.getNodeData().isHasDistribution() ) { phylogeny_node.getNodeData().addDistribution( new Distribution( "" ) ); } if ( !phylogeny_node.getNodeData().isHasReference() ) { phylogeny_node.getNodeData().addReference( new Reference( "" ) ); } addBasics( top, phylogeny_node, NodePanel.BASIC ); addTaxonomy( top, phylogeny_node.getNodeData().getTaxonomy(), NodePanel.TAXONOMY ); addSequence( top, phylogeny_node.getNodeData().getSequence(), NodePanel.SEQUENCE ); if ( !phylogeny_node.isExternal() ) { addEvents( top, phylogeny_node.getNodeData().getEvent(), NodePanel.EVENTS ); } addDate( top, phylogeny_node.getNodeData().getDate(), NodePanel.DATE ); addDistribution( top, phylogeny_node.getNodeData().getDistribution(), NodePanel.DISTRIBUTION ); addReference( top, phylogeny_node.getNodeData().getReference(), NodePanel.LIT_REFERENCE ); // addProperties( top, phylogeny_node.getNodeData().getProperties(), "Properties" ); }
if ( acc != null ) { if ( !n.getNodeData().isHasSequence() ) { n.getNodeData().addSequence( new Sequence() );