import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
+import java.util.Comparator;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
}
}
}
-
-
-
- final static public void sortNodeDescendents( PhylogenyNode node ) {
+
+ 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 ( ( 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 ( ( 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 ( ( 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( arg0, comparator );
- Collections.sort( descs );
-
+ Collections.sort( descs, c );
int i = 0;
- for( PhylogenyNode desc : descs ) {
+ for( final PhylogenyNode desc : descs ) {
node.setChildNode( i++, desc );
}
-
}
-
final static public void transferNodeNameToField( final Phylogeny phy,
final PhylogenyMethods.PhylogenyNodeField field ) {
.setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
break;
}
+ case TAXONOMY_ID: {
+ if ( !n.getNodeData().isHasTaxonomy() ) {
+ n.getNodeData().setTaxonomy( new Taxonomy() );
+ }
+ n.getNodeData().getTaxonomy().setIdentifier( new Identifier( name ) );
+ break;
+ }
}
}
}
return stats;
}
- public static DescriptiveStatistics calculatConfidenceStatistics( final Phylogeny phy ) {
+ public static DescriptiveStatistics calculatBranchLengthStatistics( final Phylogeny phy ) {
final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
final PhylogenyNode n = iter.next();
- if ( !n.isExternal() ) {
+ if ( !n.isRoot() && ( n.getDistanceToParent() >= 0.0 ) ) {
+ stats.addValue( n.getDistanceToParent() );
+ }
+ }
+ return stats;
+ }
+
+ public static List<DescriptiveStatistics> calculatConfidenceStatistics( final Phylogeny phy ) {
+ final List<DescriptiveStatistics> stats = new ArrayList<DescriptiveStatistics>();
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+ final PhylogenyNode n = iter.next();
+ if ( !n.isExternal() && !n.isRoot() ) {
if ( n.getBranchData().isHasConfidences() ) {
- stats.addValue( n.getBranchData().getConfidence( 0 ).getValue() );
+ for( int i = 0; i < n.getBranchData().getConfidences().size(); ++i ) {
+ final Confidence c = n.getBranchData().getConfidences().get( i );
+ if ( ( i > ( stats.size() - 1 ) ) || ( stats.get( i ) == null ) ) {
+ stats.add( i, new BasicDescriptiveStatistics() );
+ }
+ if ( !ForesterUtil.isEmpty( c.getType() ) ) {
+ if ( !ForesterUtil.isEmpty( stats.get( i ).getDescription() ) ) {
+ if ( !stats.get( i ).getDescription().equalsIgnoreCase( c.getType() ) ) {
+ throw new IllegalArgumentException( "support values in node [" + n.toString()
+ + "] appear inconsistently ordered" );
+ }
+ }
+ stats.get( i ).setDescription( c.getType() );
+ }
+ stats.get( i ).addValue( ( ( c != null ) && ( c.getValue() >= 0 ) ) ? c.getValue() : 0 );
+ }
}
}
}
return nodes_to_delete.size();
}
+ /**
+ * Arranges the order of childern for each node of this Phylogeny in such a
+ * way that either the branch with more children is on top (right) or on
+ * bottom (left), dependent on the value of boolean order.
+ *
+ * @param order
+ * decides in which direction to order
+ * @param pri
+ */
+ public static void orderAppearance( final PhylogenyNode n,
+ final boolean order,
+ final boolean order_ext_alphabetically,
+ final DESCENDANT_SORT_PRIORITY pri ) {
+ if ( n.isExternal() ) {
+ return;
+ }
+ else {
+ PhylogenyNode temp = null;
+ if ( ( n.getNumberOfDescendants() == 2 )
+ && ( n.getChildNode1().getNumberOfExternalNodes() != n.getChildNode2().getNumberOfExternalNodes() )
+ && ( ( n.getChildNode1().getNumberOfExternalNodes() < n.getChildNode2().getNumberOfExternalNodes() ) == order ) ) {
+ temp = n.getChildNode1();
+ n.setChild1( n.getChildNode2() );
+ n.setChild2( temp );
+ }
+ else if ( order_ext_alphabetically ) {
+ boolean all_ext = true;
+ for( final PhylogenyNode i : n.getDescendants() ) {
+ if ( !i.isExternal() ) {
+ all_ext = false;
+ break;
+ }
+ }
+ if ( all_ext ) {
+ PhylogenyMethods.sortNodeDescendents( n, pri );
+ }
+ }
+ for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
+ orderAppearance( n.getChildNode( i ), order, order_ext_alphabetically, pri );
+ }
+ }
+ }
+
public static enum PhylogenyNodeField {
CLADE_NAME,
TAXONOMY_CODE,
SEQUENCE_SYMBOL,
SEQUENCE_NAME,
TAXONOMY_ID_UNIPROT_1,
- TAXONOMY_ID_UNIPROT_2;
+ TAXONOMY_ID_UNIPROT_2,
+ TAXONOMY_ID;
}
public static enum TAXONOMY_EXTRACTION {
NO, YES, PFAM_STYLE_ONLY;
}
+
+ public static enum DESCENDANT_SORT_PRIORITY {
+ TAXONOMY, SEQUENCE, NODE_NAME;
+ }
}
git://source.jalview.org / jalview.git / blobdiff