public static void ensurePresenceOfSequence( final PhylogenyNode node ) { if ( !node.getNodeData().isHasSequence() ) { node.getNodeData().setSequence( new Sequence() ); } }
static void extractSpTremblAccFromNodeName( final Phylogeny phy, final String source ) { final PreorderTreeIterator it = new PreorderTreeIterator( phy ); while ( it.hasNext() ) { final PhylogenyNode n = it.next(); if ( !ForesterUtil.isEmpty( n.getName() ) ) { final String name = n.getName(); final int i = name.lastIndexOf( "/" ); if ( i > 0 ) { final String acc_str = name.substring( 0, i ); if ( !ForesterUtil.isEmpty( acc_str ) ) { final Sequence seq = new Sequence(); final Accession acc = new Accession( acc_str, source ); seq.setAccession( acc ); n.getNodeData().setSequence( seq ); } } } } }
final MolecularSequence s = _seqs.get( node.getName() ); final Sequence ns = new Sequence( s ); ns.setMolecularSequenceAligned( true ); //TODO need to check if all same length 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 ); seq = new org.forester.phylogeny.data.Sequence(); seq.setName( "K1PYK7_CRAGI" ); n.getNodeData().addSequence( seq ); seq = new org.forester.phylogeny.data.Sequence(); seq.setAccession( new Accession( "K1PYK8_CRAGI", "?" ) ); n.getNodeData().addSequence( seq ); seq = new org.forester.phylogeny.data.Sequence(); seq.setAccession( new Accession( "tr|B3RJ64", "?" ) ); n.getNodeData().addSequence( seq );
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 ); } }
@Override public Sequence parse( final XmlElement element ) throws PhyloXmlDataFormatException { final Sequence sequence = new Sequence(); if ( element.isHasAttribute( PhyloXmlMapping.SEQUENCE_TYPE ) ) { sequence.setType( element.getAttribute( PhyloXmlMapping.SEQUENCE_TYPE ) );
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 ); } }
private void addSequence( final DefaultMutableTreeNode top, Sequence seq, final String name ) { if ( seq == null ) { seq = new Sequence();
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 ); } } } } }
final Sequence seq = new Sequence(); seq.setAnnotations( getAnnotations() ); seq.setName( getName() );
final Sequence seq = node.getNodeData().isHasSequence() ? node.getNodeData().getSequence() : new Sequence(); if ( !ForesterUtil.isEmpty( db_entry.getAccession() ) ) { seq.setAccession( new Accession( db_entry.getAccession(), acc.getSource() ) );
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() );