+ }
+ }
+ if ( !match && node.getNodeData().isHasSequence()
+ && match( node.getNodeData().getSequence().getName(), query, case_sensitive, partial ) ) {
+ match = true;
+ }
+ if ( !match && node.getNodeData().isHasSequence()
+ && match( node.getNodeData().getSequence().getGeneName(), query, case_sensitive, partial ) ) {
+ match = true;
+ }
+ if ( !match && node.getNodeData().isHasSequence()
+ && match( node.getNodeData().getSequence().getSymbol(), query, case_sensitive, partial ) ) {
+ match = true;
+ }
+ if ( !match
+ && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getAccession() != null )
+ && match( node.getNodeData().getSequence().getAccession().getValue(),
+ query,
+ case_sensitive,
+ partial ) ) {
+ match = true;
+ }
+ if ( search_domains && !match && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
+ final DomainArchitecture da = node.getNodeData().getSequence().getDomainArchitecture();
+ I: for( int i = 0; i < da.getNumberOfDomains(); ++i ) {
+ if ( match( da.getDomain( i ).getName(), query, case_sensitive, partial ) ) {
+ match = true;
+ break I;
+ }
+ }
+ }
+ //
+ if ( !match && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getAnnotations() != null ) ) {
+ for( final Annotation ann : node.getNodeData().getSequence().getAnnotations() ) {
+ if ( match( ann.getDesc(), query, case_sensitive, partial ) ) {
+ match = true;
+ break;
+ }
+ if ( match( ann.getRef(), query, case_sensitive, partial ) ) {
+ match = true;
+ break;
+ }
+ }
+ }
+ if ( !match && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getCrossReferences() != null ) ) {
+ for( final Accession x : node.getNodeData().getSequence().getCrossReferences() ) {
+ if ( match( x.getComment(), query, case_sensitive, partial ) ) {
+ match = true;
+ break;
+ }
+ if ( match( x.getSource(), query, case_sensitive, partial ) ) {
+ match = true;
+ break;
+ }
+ if ( match( x.getValue(), query, case_sensitive, partial ) ) {
+ match = true;
+ break;
+ }
+ }
+ }
+ //
+ if ( !match && ( node.getNodeData().getBinaryCharacters() != null ) ) {
+ Iterator<String> it = node.getNodeData().getBinaryCharacters().getPresentCharacters().iterator();
+ I: while ( it.hasNext() ) {
+ if ( match( it.next(), query, case_sensitive, partial ) ) {
+ match = true;
+ break I;
+ }
+ }
+ it = node.getNodeData().getBinaryCharacters().getGainedCharacters().iterator();
+ I: while ( it.hasNext() ) {
+ if ( match( it.next(), query, case_sensitive, partial ) ) {
+ match = true;
+ break I;
+ }
+ }
+ }
+ if ( !match ) {
+ all_matched = false;
+ break;
+ }
+ }
+ if ( all_matched ) {
+ nodes.add( node );
+ }
+ }
+ return nodes;
+ }
+
+ public static void setAllIndicatorsToZero( final Phylogeny phy ) {
+ for( final PhylogenyNodeIterator it = phy.iteratorPostorder(); it.hasNext(); ) {
+ it.next().setIndicator( ( byte ) 0 );
+ }
+ }
+
+ /**
+ * Convenience method.
+ * Sets value for the first confidence value (created if not present, values overwritten otherwise).
+ */
+ public static void setBootstrapConfidence( final PhylogenyNode node, final double bootstrap_confidence_value ) {
+ setConfidence( node, bootstrap_confidence_value, "bootstrap" );
+ }
+
+ public static void setBranchColorValue( final PhylogenyNode node, final Color color ) {
+ if ( node.getBranchData().getBranchColor() == null ) {
+ node.getBranchData().setBranchColor( new BranchColor() );
+ }
+ node.getBranchData().getBranchColor().setValue( color );
+ }
+
+ /**
+ * Convenience method
+ */
+ public static void setBranchWidthValue( final PhylogenyNode node, final double branch_width_value ) {
+ node.getBranchData().setBranchWidth( new BranchWidth( branch_width_value ) );
+ }
+
+ /**
+ * Convenience method.
+ * Sets value for the first confidence value (created if not present, values overwritten otherwise).
+ */
+ public static void setConfidence( final PhylogenyNode node, final double confidence_value ) {
+ setConfidence( node, confidence_value, "" );
+ }
+
+ /**
+ * Convenience method.
+ * Sets value for the first confidence value (created if not present, values overwritten otherwise).
+ */
+ public static void setConfidence( final PhylogenyNode node, final double confidence_value, final String type ) {
+ Confidence c = null;
+ if ( node.getBranchData().getNumberOfConfidences() > 0 ) {
+ c = node.getBranchData().getConfidence( 0 );
+ }
+ else {
+ c = new Confidence();
+ node.getBranchData().addConfidence( c );
+ }
+ c.setType( type );
+ c.setValue( confidence_value );
+ }
+
+ public static void setScientificName( final PhylogenyNode node, final String scientific_name ) {
+ if ( !node.getNodeData().isHasTaxonomy() ) {
+ node.getNodeData().setTaxonomy( new Taxonomy() );
+ }
+ node.getNodeData().getTaxonomy().setScientificName( scientific_name );
+ }
+
+ /**
+ * Convenience method to set the taxonomy code of a phylogeny node.
+ *
+ *
+ * @param node
+ * @param taxonomy_code
+ * @throws PhyloXmlDataFormatException
+ */
+ public static void setTaxonomyCode( final PhylogenyNode node, final String taxonomy_code )
+ throws PhyloXmlDataFormatException {
+ if ( !node.getNodeData().isHasTaxonomy() ) {
+ node.getNodeData().setTaxonomy( new Taxonomy() );
+ }
+ node.getNodeData().getTaxonomy().setTaxonomyCode( taxonomy_code );
+ }
+
+ final static public void sortNodeDescendents( final PhylogenyNode node, final DESCENDANT_SORT_PRIORITY pri ) {
+ class PhylogenyNodeSortTaxonomyPriority implements Comparator<PhylogenyNode> {
+
+ @Override
+ public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
+ if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
+ return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
+ .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
+ }
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
+ return n1.getNodeData().getTaxonomy().getTaxonomyCode()
+ .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
+ }
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {
+ return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()
+ .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );
+ }
+ }
+ if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
+ return n1.getNodeData().getSequence().getName().toLowerCase()
+ .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
+ }
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
+ return n1.getNodeData().getSequence().getSymbol()
+ .compareTo( n2.getNodeData().getSequence().getSymbol() );
+ }
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
+ return n1.getNodeData().getSequence().getGeneName()
+ .compareTo( n2.getNodeData().getSequence().getGeneName() );
+ }
+ if ( ( n1.getNodeData().getSequence().getAccession() != null )
+ && ( n2.getNodeData().getSequence().getAccession() != null )
+ && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
+ && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {
+ return n1.getNodeData().getSequence().getAccession().getValue()
+ .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );
+ }
+ }
+ if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
+ return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
+ }
+ return 0;
+ }
+ }
+ class PhylogenyNodeSortSequencePriority implements Comparator<PhylogenyNode> {
+
+ @Override
+ public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
+ if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
+ return n1.getNodeData().getSequence().getName().toLowerCase()
+ .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
+ }
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
+ return n1.getNodeData().getSequence().getSymbol()
+ .compareTo( n2.getNodeData().getSequence().getSymbol() );
+ }
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
+ return n1.getNodeData().getSequence().getGeneName()
+ .compareTo( n2.getNodeData().getSequence().getGeneName() );
+ }
+ if ( ( n1.getNodeData().getSequence().getAccession() != null )
+ && ( n2.getNodeData().getSequence().getAccession() != null )
+ && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
+ && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {
+ return n1.getNodeData().getSequence().getAccession().getValue()
+ .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );
+ }
+ }
+ if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
+ return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
+ .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
+ }
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
+ return n1.getNodeData().getTaxonomy().getTaxonomyCode()
+ .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
+ }
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {
+ return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()
+ .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );
+ }
+ }
+ if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
+ return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
+ }
+ return 0;
+ }
+ }
+ class PhylogenyNodeSortNodeNamePriority implements Comparator<PhylogenyNode> {
+
+ @Override
+ public int compare( final PhylogenyNode n1, final PhylogenyNode n2 ) {
+ if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
+ return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
+ }
+ if ( n1.getNodeData().isHasTaxonomy() && n2.getNodeData().isHasTaxonomy() ) {
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getScientificName() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getScientificName() ) ) ) {
+ return n1.getNodeData().getTaxonomy().getScientificName().toLowerCase()
+ .compareTo( n2.getNodeData().getTaxonomy().getScientificName().toLowerCase() );
+ }
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
+ return n1.getNodeData().getTaxonomy().getTaxonomyCode()
+ .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
+ }
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getCommonName() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getCommonName() ) ) ) {
+ return n1.getNodeData().getTaxonomy().getCommonName().toLowerCase()
+ .compareTo( n2.getNodeData().getTaxonomy().getCommonName().toLowerCase() );
+ }
+ }
+ if ( n1.getNodeData().isHasSequence() && n2.getNodeData().isHasSequence() ) {
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getName() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getName() ) ) ) {
+ return n1.getNodeData().getSequence().getName().toLowerCase()
+ .compareTo( n2.getNodeData().getSequence().getName().toLowerCase() );
+ }
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
+ return n1.getNodeData().getSequence().getSymbol()
+ .compareTo( n2.getNodeData().getSequence().getSymbol() );
+ }
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
+ return n1.getNodeData().getSequence().getGeneName()
+ .compareTo( n2.getNodeData().getSequence().getGeneName() );
+ }
+ if ( ( n1.getNodeData().getSequence().getAccession() != null )
+ && ( n2.getNodeData().getSequence().getAccession() != null )
+ && !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getAccession().getValue() )
+ && !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getAccession().getValue() ) ) {
+ return n1.getNodeData().getSequence().getAccession().getValue()
+ .compareTo( n2.getNodeData().getSequence().getAccession().getValue() );
+ }
+ }
+ return 0;
+ }
+ }
+ Comparator<PhylogenyNode> c;
+ switch ( pri ) {
+ case SEQUENCE:
+ c = new PhylogenyNodeSortSequencePriority();
+ break;
+ case NODE_NAME:
+ c = new PhylogenyNodeSortNodeNamePriority();
+ break;
+ default:
+ c = new PhylogenyNodeSortTaxonomyPriority();
+ }
+ final List<PhylogenyNode> descs = node.getDescendants();
+ Collections.sort( descs, c );
+ int i = 0;
+ for( final PhylogenyNode desc : descs ) {
+ node.setChildNode( i++, desc );
+ }
+ }
+
+ /**
+ * Removes from Phylogeny to_be_stripped all external Nodes which are
+ * associated with a species NOT found in Phylogeny reference.
+ *
+ * @param reference
+ * a reference Phylogeny
+ * @param to_be_stripped
+ * Phylogeny to be stripped
+ * @return nodes removed from to_be_stripped
+ */
+ public static List<PhylogenyNode> taxonomyBasedDeletionOfExternalNodes( final Phylogeny reference,
+ final Phylogeny to_be_stripped ) {
+ final Set<String> ref_ext_taxo = new HashSet<String>();
+ for( final PhylogenyNodeIterator it = reference.iteratorExternalForward(); it.hasNext(); ) {
+ final PhylogenyNode n = it.next();
+ if ( !n.getNodeData().isHasTaxonomy() ) {
+ throw new IllegalArgumentException( "no taxonomic data in node: " + n );
+ }
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+ ref_ext_taxo.add( n.getNodeData().getTaxonomy().getScientificName() );
+ }
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+ ref_ext_taxo.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );
+ }
+ if ( ( n.getNodeData().getTaxonomy().getIdentifier() != null )
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getIdentifier().getValue() ) ) {
+ ref_ext_taxo.add( n.getNodeData().getTaxonomy().getIdentifier().getValuePlusProvider() );
+ }
+ }
+ final ArrayList<PhylogenyNode> nodes_to_delete = new ArrayList<PhylogenyNode>();
+ for( final PhylogenyNodeIterator it = to_be_stripped.iteratorExternalForward(); it.hasNext(); ) {
+ final PhylogenyNode n = it.next();
+ if ( !n.getNodeData().isHasTaxonomy() ) {
+ nodes_to_delete.add( n );
+ }
+ else if ( !( ref_ext_taxo.contains( n.getNodeData().getTaxonomy().getScientificName() ) )
+ && !( ref_ext_taxo.contains( n.getNodeData().getTaxonomy().getTaxonomyCode() ) )
+ && !( ( n.getNodeData().getTaxonomy().getIdentifier() != null ) && ref_ext_taxo.contains( n
+ .getNodeData().getTaxonomy().getIdentifier().getValuePlusProvider() ) ) ) {
+ nodes_to_delete.add( n );
+ }
+ }
+ for( final PhylogenyNode n : nodes_to_delete ) {
+ to_be_stripped.deleteSubtree( n, true );
+ }
+ to_be_stripped.clearHashIdToNodeMap();
+ to_be_stripped.externalNodesHaveChanged();
+ return nodes_to_delete;
+ }
+
+ final static public void transferInternalNamesToBootstrapSupport( final Phylogeny phy ) {
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ while ( it.hasNext() ) {
+ final PhylogenyNode n = it.next();
+ if ( !n.isExternal() && !ForesterUtil.isEmpty( n.getName() ) ) {
+ double value = -1;
+ try {
+ value = Double.parseDouble( n.getName() );
+ }
+ catch ( final NumberFormatException e ) {
+ throw new IllegalArgumentException( "failed to parse number from [" + n.getName() + "]: "
+ + e.getLocalizedMessage() );
+ }
+ if ( value >= 0.0 ) {
+ n.getBranchData().addConfidence( new Confidence( value, "bootstrap" ) );
+ n.setName( "" );
+ }
+ }
+ }
+ }
+
+ final static public void transferInternalNodeNamesToConfidence( final Phylogeny phy ) {
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ while ( it.hasNext() ) {
+ final PhylogenyNode n = it.next();
+ if ( !n.isExternal() && !n.getBranchData().isHasConfidences() ) {
+ if ( !ForesterUtil.isEmpty( n.getName() ) ) {
+ double d = -1.0;
+ try {
+ d = Double.parseDouble( n.getName() );
+ }
+ catch ( final Exception e ) {
+ d = -1.0;
+ }
+ if ( d >= 0.0 ) {
+ n.getBranchData().addConfidence( new Confidence( d, "" ) );
+ n.setName( "" );
+ }
+ }
+ }
+ }
+ }
+
+ final static public void transferNodeNameToField( final Phylogeny phy,
+ final PhylogenyNodeField field,
+ final boolean external_only ) throws PhyloXmlDataFormatException {
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ while ( it.hasNext() ) {
+ final PhylogenyNode n = it.next();
+ if ( external_only && n.isInternal() ) {
+ continue;
+ }
+ final String name = n.getName().trim();
+ if ( !ForesterUtil.isEmpty( name ) ) {
+ switch ( field ) {
+ case TAXONOMY_CODE:
+ n.setName( "" );
+ setTaxonomyCode( n, name );
+ break;
+ case TAXONOMY_SCIENTIFIC_NAME:
+ n.setName( "" );
+ if ( !n.getNodeData().isHasTaxonomy() ) {
+ n.getNodeData().setTaxonomy( new Taxonomy() );
+ }
+ n.getNodeData().getTaxonomy().setScientificName( name );
+ break;
+ case TAXONOMY_COMMON_NAME:
+ n.setName( "" );
+ if ( !n.getNodeData().isHasTaxonomy() ) {
+ n.getNodeData().setTaxonomy( new Taxonomy() );
+ }
+ n.getNodeData().getTaxonomy().setCommonName( name );
+ break;
+ case SEQUENCE_SYMBOL:
+ n.setName( "" );
+ if ( !n.getNodeData().isHasSequence() ) {
+ n.getNodeData().setSequence( new Sequence() );
+ }
+ n.getNodeData().getSequence().setSymbol( name );
+ break;
+ case SEQUENCE_NAME:
+ n.setName( "" );
+ if ( !n.getNodeData().isHasSequence() ) {
+ n.getNodeData().setSequence( new Sequence() );
+ }
+ n.getNodeData().getSequence().setName( name );
+ break;
+ case TAXONOMY_ID_UNIPROT_1: {
+ if ( !n.getNodeData().isHasTaxonomy() ) {
+ n.getNodeData().setTaxonomy( new Taxonomy() );
+ }
+ String id = name;
+ final int i = name.indexOf( '_' );
+ if ( i > 0 ) {
+ id = name.substring( 0, i );
+ }
+ else {
+ n.setName( "" );