// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.phylogeny;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
+import java.util.Map;
import java.util.Set;
-import java.util.SortedMap;
-import java.util.TreeMap;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+import java.util.regex.PatternSyntaxException;
+import org.forester.archaeopteryx.TreePanelUtil;
+import org.forester.io.parsers.FastaParser;
import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
import org.forester.io.parsers.util.PhylogenyParserException;
+import org.forester.msa.Msa;
+import org.forester.phylogeny.data.Accession;
+import org.forester.phylogeny.data.Annotation;
import org.forester.phylogeny.data.BranchColor;
import org.forester.phylogeny.data.BranchWidth;
import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.phylogeny.iterators.PreorderTreeIterator;
import org.forester.util.BasicDescriptiveStatistics;
import org.forester.util.DescriptiveStatistics;
import org.forester.util.FailedConditionCheckException;
import org.forester.util.ForesterUtil;
+import org.forester.util.TaxonomyUtil;
public class PhylogenyMethods {
- private static PhylogenyMethods _instance = null;
- private PhylogenyNode _farthest_1 = null;
- private PhylogenyNode _farthest_2 = null;
+ private static boolean _order_changed;
private PhylogenyMethods() {
// Hidden constructor.
}
- /**
- * Calculates the distance between PhylogenyNodes node1 and node2.
- *
- *
- * @param node1
- * @param node2
- * @return distance between node1 and node2
- */
- public double calculateDistance( final PhylogenyNode node1, final PhylogenyNode node2 ) {
- final PhylogenyNode lca = calculateLCA( node1, node2 );
- final PhylogenyNode n1 = node1;
- final PhylogenyNode n2 = node2;
- return ( PhylogenyMethods.getDistance( n1, lca ) + PhylogenyMethods.getDistance( n2, lca ) );
- }
-
- public double calculateFurthestDistance( final Phylogeny phylogeny ) {
- if ( phylogeny.getNumberOfExternalNodes() < 2 ) {
- return 0.0;
- }
- _farthest_1 = null;
- _farthest_2 = null;
- PhylogenyNode node_1 = null;
- PhylogenyNode node_2 = null;
- double farthest_d = -Double.MAX_VALUE;
- final PhylogenyMethods methods = PhylogenyMethods.getInstance();
- final List<PhylogenyNode> ext_nodes = phylogeny.getRoot().getAllExternalDescendants();
- for( int i = 1; i < ext_nodes.size(); ++i ) {
- for( int j = 0; j < i; ++j ) {
- final double d = methods.calculateDistance( ext_nodes.get( i ), ext_nodes.get( j ) );
- if ( d < 0.0 ) {
- throw new RuntimeException( "distance cannot be negative" );
- }
- if ( d > farthest_d ) {
- farthest_d = d;
- node_1 = ext_nodes.get( i );
- node_2 = ext_nodes.get( j );
- }
- }
- }
- _farthest_1 = node_1;
- _farthest_2 = node_2;
- return farthest_d;
- }
-
- final public static Event getEventAtLCA( final PhylogenyNode n1, final PhylogenyNode n2 ) {
- return calculateLCA( n1, n2 ).getNodeData().getEvent();
- }
-
@Override
public Object clone() throws CloneNotSupportedException {
throw new CloneNotSupportedException();
}
- public PhylogenyNode getFarthestNode1() {
- return _farthest_1;
+ public static boolean extractFastaInformation( final Phylogeny phy ) {
+ boolean could_extract = false;
+ for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
+ final PhylogenyNode node = iter.next();
+ if ( !ForesterUtil.isEmpty( node.getName() ) ) {
+ final Matcher name_m = FastaParser.FASTA_DESC_LINE.matcher( node.getName() );
+ if ( name_m.lookingAt() ) {
+ could_extract = true;
+ final String acc_source = name_m.group( 1 );
+ final String acc = name_m.group( 2 );
+ final String seq_name = name_m.group( 3 );
+ final String tax_sn = name_m.group( 4 );
+ if ( !ForesterUtil.isEmpty( acc_source ) && !ForesterUtil.isEmpty( acc ) ) {
+ ForesterUtil.ensurePresenceOfSequence( node );
+ node.getNodeData().getSequence( 0 ).setAccession( new Accession( acc, acc_source ) );
+ }
+ if ( !ForesterUtil.isEmpty( seq_name ) ) {
+ ForesterUtil.ensurePresenceOfSequence( node );
+ node.getNodeData().getSequence( 0 ).setName( seq_name );
+ }
+ if ( !ForesterUtil.isEmpty( tax_sn ) ) {
+ ForesterUtil.ensurePresenceOfTaxonomy( node );
+ node.getNodeData().getTaxonomy( 0 ).setScientificName( tax_sn );
+ }
+ }
+ }
+ }
+ return could_extract;
}
- public PhylogenyNode getFarthestNode2() {
- return _farthest_2;
+ public static DescriptiveStatistics calculateBranchLengthStatistics( final Phylogeny phy ) {
+ final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+ final PhylogenyNode n = iter.next();
+ if ( !n.isRoot() && ( n.getDistanceToParent() >= 0.0 ) ) {
+ stats.addValue( n.getDistanceToParent() );
+ }
+ }
+ return stats;
}
- final public static void deleteNonOrthologousExternalNodes( final Phylogeny phy, final PhylogenyNode n ) {
- if ( n.isInternal() ) {
- throw new IllegalArgumentException( "node is not external" );
- }
- final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
- for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
- final PhylogenyNode i = it.next();
- if ( !PhylogenyMethods.getEventAtLCA( n, i ).isSpeciation() ) {
- to_delete.add( i );
+ public static List<DescriptiveStatistics> calculateConfidenceStatistics( 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() ) {
+ 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 );
+ }
+ }
}
}
- for( final PhylogenyNode d : to_delete ) {
- phy.deleteSubtree( d, true );
- }
- phy.clearHashIdToNodeMap();
- phy.externalNodesHaveChanged();
+ return stats;
+ }
+
+ /**
+ * Calculates the distance between PhylogenyNodes node1 and node2.
+ *
+ *
+ * @param node1
+ * @param node2
+ * @return distance between node1 and node2
+ */
+ public static double calculateDistance( final PhylogenyNode node1, final PhylogenyNode node2 ) {
+ final PhylogenyNode lca = calculateLCA( node1, node2 );
+ final PhylogenyNode n1 = node1;
+ final PhylogenyNode n2 = node2;
+ return ( PhylogenyMethods.getDistance( n1, lca ) + PhylogenyMethods.getDistance( n2, lca ) );
}
/**
* Returns the LCA of PhylogenyNodes node1 and node2.
- *
- *
+ *
+ *
* @param node1
* @param node2
* @return LCA of node1 and node2
*/
public final static PhylogenyNode calculateLCA( PhylogenyNode node1, PhylogenyNode node2 ) {
+ if ( node1 == null ) {
+ throw new IllegalArgumentException( "first argument (node) is null" );
+ }
+ if ( node2 == null ) {
+ throw new IllegalArgumentException( "second argument (node) is null" );
+ }
if ( node1 == node2 ) {
return node1;
}
throw new IllegalArgumentException( "illegal attempt to calculate LCA of two nodes which do not share a common root" );
}
- public static final void preOrderReId( final Phylogeny phy ) {
- if ( phy.isEmpty() ) {
- return;
- }
- phy.setIdToNodeMap( null );
- int i = PhylogenyNode.getNodeCount();
- for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
- it.next().setId( i++ );
- }
- PhylogenyNode.setNodeCount( i );
- }
-
/**
* Returns the LCA of PhylogenyNodes node1 and node2.
* Precondition: ids are in pre-order (or level-order).
- *
- *
+ *
+ *
* @param node1
* @param node2
* @return LCA of node1 and node2
*/
public final static PhylogenyNode calculateLCAonTreeWithIdsInPreOrder( PhylogenyNode node1, PhylogenyNode node2 ) {
+ if ( node1 == null ) {
+ throw new IllegalArgumentException( "first argument (node) is null" );
+ }
+ if ( node2 == null ) {
+ throw new IllegalArgumentException( "second argument (node) is null" );
+ }
while ( node1 != node2 ) {
if ( node1.getId() > node2.getId() ) {
node1 = node1.getParent();
return node1;
}
- /**
- * Returns all orthologs of the external PhylogenyNode n of this Phylogeny.
- * Orthologs are returned as List of node references.
- * <p>
- * PRECONDITION: This tree must be binary and rooted, and speciation -
- * duplication need to be assigned for each of its internal Nodes.
- * <p>
- * Returns null if this Phylogeny is empty or if n is internal.
- * @param n
- * external PhylogenyNode whose orthologs are to be returned
- * @return Vector of references to all orthologous Nodes of PhylogenyNode n
- * of this Phylogeny, null if this Phylogeny is empty or if n is
- * internal
- */
- public final static List<PhylogenyNode> getOrthologousNodes( final Phylogeny phy, final PhylogenyNode node ) {
- final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
- PhylogenyMethods.preOrderReId( phy );
- final PhylogenyNodeIterator it = phy.iteratorExternalForward();
- while ( it.hasNext() ) {
- final PhylogenyNode temp_node = it.next();
- if ( ( temp_node != node ) && !calculateLCAonTreeWithIdsInPreOrder( node, temp_node ).isDuplication() ) {
- nodes.add( temp_node );
+ public static short calculateMaxBranchesToLeaf( final PhylogenyNode node ) {
+ if ( node.isExternal() ) {
+ return 0;
+ }
+ short max = 0;
+ for( PhylogenyNode d : node.getAllExternalDescendants() ) {
+ short steps = 0;
+ while ( d != node ) {
+ if ( d.isCollapse() ) {
+ steps = 0;
+ }
+ else {
+ steps++;
+ }
+ d = d.getParent();
+ }
+ if ( max < steps ) {
+ max = steps;
}
}
- return nodes;
+ return max;
}
- public static final HashMap<String, PhylogenyNode> createNameToExtNodeMap( final Phylogeny phy ) {
- final HashMap<String, PhylogenyNode> nodes = new HashMap<String, PhylogenyNode>();
+ public static int calculateMaxDepth( final Phylogeny phy ) {
+ int max = 0;
for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
- final PhylogenyNode n = iter.next();
- nodes.put( n.getName(), n );
+ final PhylogenyNode node = iter.next();
+ final int steps = node.calculateDepth();
+ if ( steps > max ) {
+ max = steps;
+ }
}
- return nodes;
+ return max;
}
-
- public final static Phylogeny[] readPhylogenies( final PhylogenyParser parser, final File file ) throws IOException {
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final Phylogeny[] trees = factory.create( file, parser );
- if ( ( trees == null ) || ( trees.length == 0 ) ) {
- throw new PhylogenyParserException( "Unable to parse phylogeny from file: " + file );
+
+ public static String[] obtainPresentRanksSorted( final Phylogeny phy ) {
+ final Set<String> present_ranks = new HashSet<String>();
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+ final PhylogenyNode node = iter.next();
+ if ( !node.isExternal() && !node.isRoot() && ( node.getNodeData().getTaxonomy() != null )
+ && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getRank() ) ) {
+ final String current_rank = node.getNodeData().getTaxonomy().getRank();
+ if ( TaxonomyUtil.RANK_TO_INT.containsKey( current_rank ) ) {
+ present_ranks.add( current_rank );
+ }
+ }
}
- return trees;
+ final String ordered_ranks[] = new String[present_ranks.size() + 1];
+ int c = 0;
+ for( final String rank : TaxonomyUtil.RANKS ) {
+ if ( present_ranks.contains( rank ) ) {
+ ordered_ranks[ c++ ] = rank;
+ }
+ }
+ ordered_ranks[ c ] = "off";
+ return ordered_ranks;
}
- public final static Phylogeny[] readPhylogenies( final PhylogenyParser parser, final List<File> files )
- throws IOException {
- final List<Phylogeny> tree_list = new ArrayList<Phylogeny>();
- for( final File file : files ) {
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final Phylogeny[] trees = factory.create( file, parser );
- if ( ( trees == null ) || ( trees.length == 0 ) ) {
- throw new PhylogenyParserException( "Unable to parse phylogeny from file: " + file );
+ public static int calculateMaxDepthConsiderCollapsed( final Phylogeny phy ) {
+ int max = 0;
+ for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
+ PhylogenyNode n = iter.next();
+ int steps = 0;
+ while ( n.getParent() != null ) {
+ if ( !n.isCollapse() ) {
+ steps++;
+ }
+ n = n.getParent();
+ }
+ if ( steps > max ) {
+ max = steps;
}
- tree_list.addAll( Arrays.asList( trees ) );
}
- return tree_list.toArray( new Phylogeny[ tree_list.size() ] );
+ return max;
}
- 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( "" );
- }
- }
+ public static double calculateMaxDistanceToRoot( final Phylogeny phy ) {
+ double max = 0.0;
+ for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
+ final PhylogenyNode node = iter.next();
+ final double d = node.calculateDistanceToRoot();
+ if ( d > max ) {
+ max = d;
}
}
+ return max;
}
- 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( "" );
- }
+ public static PhylogenyNode calculateNodeWithMaxDistanceToRoot( final Phylogeny phy ) {
+ double max = 0.0;
+ PhylogenyNode max_node = phy.getFirstExternalNode();
+ for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
+ final PhylogenyNode node = iter.next();
+ final double d = node.calculateDistanceToRoot();
+ if ( d > max ) {
+ max = d;
+ max_node = node;
}
}
+ return max_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;
+ public static int calculateNumberOfExternalNodesWithoutTaxonomy( final PhylogenyNode node ) {
+ final List<PhylogenyNode> descs = node.getAllExternalDescendants();
+ int x = 0;
+ for( final PhylogenyNode n : descs ) {
+ if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
+ x++;
}
}
- class PhylogenyNodeSortSequencePriority implements Comparator<PhylogenyNode> {
+ return x;
+ }
- @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;
+ public static DescriptiveStatistics calculateNumberOfDescendantsPerNodeStatistics( final Phylogeny phy ) {
+ final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+ final PhylogenyNode n = iter.next();
+ if ( !n.isExternal() ) {
+ stats.addValue( n.getNumberOfDescendants() );
}
}
- class PhylogenyNodeSortNodeNamePriority implements Comparator<PhylogenyNode> {
+ return stats;
+ }
- @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;
- }
+ public final static void collapseSubtreeStructure( final PhylogenyNode n ) {
+ final List<PhylogenyNode> eds = n.getAllExternalDescendants();
+ final List<Double> d = new ArrayList<Double>();
+ for( final PhylogenyNode ed : eds ) {
+ d.add( calculateDistanceToAncestor( n, ed ) );
}
- 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 );
+ for( int i = 0; i < eds.size(); ++i ) {
+ n.setChildNode( i, eds.get( i ) );
+ eds.get( i ).setDistanceToParent( d.get( i ) );
}
}
- final static public void transferNodeNameToField( final Phylogeny phy,
- final PhylogenyMethods.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( "" );
- }
- n.getNodeData().getTaxonomy()
- .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
- break;
- }
- case TAXONOMY_ID_UNIPROT_2: {
- if ( !n.getNodeData().isHasTaxonomy() ) {
- n.getNodeData().setTaxonomy( new Taxonomy() );
- }
- String id = name;
- final int i = name.indexOf( '_' );
- if ( i > 0 ) {
- id = name.substring( i + 1, name.length() );
- }
- else {
- n.setName( "" );
- }
- n.getNodeData().getTaxonomy()
- .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;
- }
- }
+ public static int countNumberOfOneDescendantNodes( final Phylogeny phy ) {
+ int count = 0;
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+ final PhylogenyNode n = iter.next();
+ if ( !n.isExternal() && ( n.getNumberOfDescendants() == 1 ) ) {
+ count++;
}
}
+ return count;
}
- static double addPhylogenyDistances( final double a, final double b ) {
- if ( ( a >= 0.0 ) && ( b >= 0.0 ) ) {
- return a + b;
- }
- else if ( a >= 0.0 ) {
- return a;
- }
- else if ( b >= 0.0 ) {
- return b;
+ public static int countNumberOfPolytomies( final Phylogeny phy ) {
+ int count = 0;
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+ final PhylogenyNode n = iter.next();
+ if ( !n.isExternal() && ( n.getNumberOfDescendants() > 2 ) ) {
+ count++;
+ }
}
- return PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;
+ return count;
}
- public final static boolean isAllDecendentsAreDuplications( final PhylogenyNode n ) {
- if ( n.isExternal() ) {
- return true;
- }
- else {
- if ( n.isDuplication() ) {
- for( final PhylogenyNode desc : n.getDescendants() ) {
- if ( !isAllDecendentsAreDuplications( desc ) ) {
- return false;
- }
- }
- return true;
- }
- else {
- return false;
- }
+ public static final HashMap<String, PhylogenyNode> createNameToExtNodeMap( final Phylogeny phy ) {
+ final HashMap<String, PhylogenyNode> nodes = new HashMap<String, PhylogenyNode>();
+ final List<PhylogenyNode> ext = phy.getExternalNodes();
+ for( final PhylogenyNode n : ext ) {
+ nodes.put( n.getName(), n );
}
+ return nodes;
}
- public static short calculateMaxBranchesToLeaf( final PhylogenyNode node ) {
- if ( node.isExternal() ) {
- return 0;
+ public static void deleteExternalNodesNegativeSelection( final Set<Long> to_delete, final Phylogeny phy ) {
+ for( final Long id : to_delete ) {
+ phy.deleteSubtree( phy.getNode( id ), true );
}
- short max = 0;
- for( PhylogenyNode d : node.getAllExternalDescendants() ) {
- short steps = 0;
- while ( d != node ) {
- if ( d.isCollapse() ) {
- steps = 0;
- }
- else {
- steps++;
- }
- d = d.getParent();
+ phy.clearHashIdToNodeMap();
+ phy.externalNodesHaveChanged();
+ }
+
+ public static void deleteExternalNodesNegativeSelection( final String[] node_names_to_delete, final Phylogeny p )
+ throws IllegalArgumentException {
+ for( final String element : node_names_to_delete ) {
+ if ( ForesterUtil.isEmpty( element ) ) {
+ continue;
}
- if ( max < steps ) {
- max = steps;
+ List<PhylogenyNode> nodes = null;
+ nodes = p.getNodes( element );
+ final Iterator<PhylogenyNode> it = nodes.iterator();
+ while ( it.hasNext() ) {
+ final PhylogenyNode n = it.next();
+ if ( !n.isExternal() ) {
+ throw new IllegalArgumentException( "attempt to delete non-external node \"" + element + "\"" );
+ }
+ p.deleteSubtree( n, true );
}
}
- return max;
+ p.clearHashIdToNodeMap();
+ p.externalNodesHaveChanged();
}
- public static int calculateMaxDepth( final Phylogeny phy ) {
- int max = 0;
- for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- final int steps = node.calculateDepth();
- if ( steps > max ) {
- max = steps;
+ public static List<String> deleteExternalNodesPositiveSelection( final String[] node_names_to_keep,
+ final Phylogeny p ) {
+ final PhylogenyNodeIterator it = p.iteratorExternalForward();
+ final String[] to_delete = new String[ p.getNumberOfExternalNodes() ];
+ int i = 0;
+ Arrays.sort( node_names_to_keep );
+ while ( it.hasNext() ) {
+ final String curent_name = it.next().getName();
+ if ( Arrays.binarySearch( node_names_to_keep, curent_name ) < 0 ) {
+ to_delete[ i++ ] = curent_name;
}
}
- return max;
- }
-
- public static double calculateMaxDistanceToRoot( final Phylogeny phy ) {
- double max = 0.0;
- for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- final double d = node.calculateDistanceToRoot();
- if ( d > max ) {
- max = d;
+ PhylogenyMethods.deleteExternalNodesNegativeSelection( to_delete, p );
+ final List<String> deleted = new ArrayList<String>();
+ for( final String n : to_delete ) {
+ if ( !ForesterUtil.isEmpty( n ) ) {
+ deleted.add( n );
}
}
- return max;
+ return deleted;
}
- public static int countNumberOfPolytomies( final Phylogeny phy ) {
- int count = 0;
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode n = iter.next();
- if ( !n.isExternal() && ( n.getNumberOfDescendants() > 2 ) ) {
- count++;
+ public static void deleteExternalNodesPositiveSelectionT( final List<Taxonomy> species_to_keep,
+ final Phylogeny phy ) {
+ final Set<Long> to_delete = new HashSet<Long>();
+ for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
+ final PhylogenyNode n = it.next();
+ if ( n.getNodeData().isHasTaxonomy() ) {
+ if ( !species_to_keep.contains( n.getNodeData().getTaxonomy() ) ) {
+ to_delete.add( n.getId() );
+ }
+ }
+ else {
+ throw new IllegalArgumentException( "node " + n.getId() + " has no taxonomic data" );
}
}
- return count;
+ deleteExternalNodesNegativeSelection( to_delete, phy );
}
- public static DescriptiveStatistics calculatNumberOfDescendantsPerNodeStatistics( final Phylogeny phy ) {
- final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+ final public static void deleteInternalNodesWithOnlyOneDescendent( final Phylogeny phy ) {
+ final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
+ for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {
final PhylogenyNode n = iter.next();
- if ( !n.isExternal() ) {
- stats.addValue( n.getNumberOfDescendants() );
+ if ( ( !n.isExternal() ) && ( n.getNumberOfDescendants() == 1 ) ) {
+ to_delete.add( n );
}
}
- return stats;
+ for( final PhylogenyNode d : to_delete ) {
+ PhylogenyMethods.removeNode( d, phy );
+ }
+ phy.clearHashIdToNodeMap();
+ phy.externalNodesHaveChanged();
}
- 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.isRoot() && ( n.getDistanceToParent() >= 0.0 ) ) {
- stats.addValue( n.getDistanceToParent() );
+ final public static void deleteNonOrthologousExternalNodes( final Phylogeny phy, final PhylogenyNode n ) {
+ if ( n.isInternal() ) {
+ throw new IllegalArgumentException( "node is not external" );
+ }
+ final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
+ for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
+ final PhylogenyNode i = it.next();
+ if ( !PhylogenyMethods.getEventAtLCA( n, i ).isSpeciation() ) {
+ to_delete.add( i );
}
}
- return stats;
+ for( final PhylogenyNode d : to_delete ) {
+ phy.deleteSubtree( d, true );
+ }
+ phy.clearHashIdToNodeMap();
+ phy.externalNodesHaveChanged();
}
- 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() ) {
- 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 stats;
- }
-
- /**
- * Returns the set of distinct taxonomies of
- * all external nodes of node.
- * If at least one the external nodes has no taxonomy,
- * null is returned.
- *
- */
- public static Set<Taxonomy> obtainDistinctTaxonomies( final PhylogenyNode node ) {
- final List<PhylogenyNode> descs = node.getAllExternalDescendants();
- final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
- for( final PhylogenyNode n : descs ) {
- if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
- return null;
- }
- tax_set.add( n.getNodeData().getTaxonomy() );
- }
- return tax_set;
- }
-
- /**
- * Returns a map of distinct taxonomies of
- * all external nodes of node.
- * If at least one of the external nodes has no taxonomy,
- * null is returned.
- *
- */
- public static SortedMap<Taxonomy, Integer> obtainDistinctTaxonomyCounts( final PhylogenyNode node ) {
- final List<PhylogenyNode> descs = node.getAllExternalDescendants();
- final SortedMap<Taxonomy, Integer> tax_map = new TreeMap<Taxonomy, Integer>();
- for( final PhylogenyNode n : descs ) {
- if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
- return null;
- }
- final Taxonomy t = n.getNodeData().getTaxonomy();
- if ( tax_map.containsKey( t ) ) {
- tax_map.put( t, tax_map.get( t ) + 1 );
- }
- else {
- tax_map.put( t, 1 );
- }
- }
- return tax_map;
- }
-
- public static int calculateNumberOfExternalNodesWithoutTaxonomy( final PhylogenyNode node ) {
- final List<PhylogenyNode> descs = node.getAllExternalDescendants();
- int x = 0;
- for( final PhylogenyNode n : descs ) {
- if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
- x++;
- }
- }
- return x;
- }
-
- /**
- * Deep copies the phylogeny originating from this node.
- */
- static PhylogenyNode copySubTree( final PhylogenyNode source ) {
- if ( source == null ) {
- return null;
- }
- else {
- final PhylogenyNode newnode = source.copyNodeData();
- if ( !source.isExternal() ) {
- for( int i = 0; i < source.getNumberOfDescendants(); ++i ) {
- newnode.setChildNode( i, PhylogenyMethods.copySubTree( source.getChildNode( i ) ) );
- }
- }
- return newnode;
- }
- }
-
- /**
- * Shallow copies the phylogeny originating from this node.
- */
- static PhylogenyNode copySubTreeShallow( final PhylogenyNode source ) {
- if ( source == null ) {
- return null;
- }
- else {
- final PhylogenyNode newnode = source.copyNodeDataShallow();
- if ( !source.isExternal() ) {
- for( int i = 0; i < source.getNumberOfDescendants(); ++i ) {
- newnode.setChildNode( i, PhylogenyMethods.copySubTreeShallow( source.getChildNode( i ) ) );
- }
- }
- return newnode;
- }
- }
-
- public static void deleteExternalNodesNegativeSelection( final Set<Integer> to_delete, final Phylogeny phy ) {
- phy.clearHashIdToNodeMap();
- for( final Integer id : to_delete ) {
- phy.deleteSubtree( phy.getNode( id ), true );
- }
- phy.clearHashIdToNodeMap();
- phy.externalNodesHaveChanged();
- }
-
- public static void deleteExternalNodesNegativeSelection( final String[] node_names_to_delete, final Phylogeny p )
- throws IllegalArgumentException {
- for( final String element : node_names_to_delete ) {
- if ( ForesterUtil.isEmpty( element ) ) {
- continue;
- }
- List<PhylogenyNode> nodes = null;
- nodes = p.getNodes( element );
- final Iterator<PhylogenyNode> it = nodes.iterator();
- while ( it.hasNext() ) {
- final PhylogenyNode n = it.next();
- if ( !n.isExternal() ) {
- throw new IllegalArgumentException( "attempt to delete non-external node \"" + element + "\"" );
- }
- p.deleteSubtree( n, true );
- }
+ public final static List<List<PhylogenyNode>> divideIntoSubTrees( final Phylogeny phy,
+ final double min_distance_to_root ) {
+ if ( min_distance_to_root <= 0 ) {
+ throw new IllegalArgumentException( "attempt to use min distance to root of: " + min_distance_to_root );
}
- p.clearHashIdToNodeMap();
- p.externalNodesHaveChanged();
- }
-
- public static void deleteExternalNodesPositiveSelection( final Set<Taxonomy> species_to_keep, final Phylogeny phy ) {
- // final Set<Integer> to_delete = new HashSet<Integer>();
+ final List<List<PhylogenyNode>> l = new ArrayList<List<PhylogenyNode>>();
+ setAllIndicatorsToZero( phy );
for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
final PhylogenyNode n = it.next();
- if ( n.getNodeData().isHasTaxonomy() ) {
- if ( !species_to_keep.contains( n.getNodeData().getTaxonomy() ) ) {
- //to_delete.add( n.getNodeId() );
- phy.deleteSubtree( n, true );
- }
- }
- else {
- throw new IllegalArgumentException( "node " + n.getId() + " has no taxonomic data" );
- }
- }
- phy.clearHashIdToNodeMap();
- phy.externalNodesHaveChanged();
- }
-
- public static List<String> deleteExternalNodesPositiveSelection( final String[] node_names_to_keep,
- final Phylogeny p ) {
- final PhylogenyNodeIterator it = p.iteratorExternalForward();
- final String[] to_delete = new String[ p.getNumberOfExternalNodes() ];
- int i = 0;
- Arrays.sort( node_names_to_keep );
- while ( it.hasNext() ) {
- final String curent_name = it.next().getName();
- if ( Arrays.binarySearch( node_names_to_keep, curent_name ) < 0 ) {
- to_delete[ i++ ] = curent_name;
+ if ( n.getIndicator() != 0 ) {
+ continue;
}
- }
- PhylogenyMethods.deleteExternalNodesNegativeSelection( to_delete, p );
- final List<String> deleted = new ArrayList<String>();
- for( final String n : to_delete ) {
- if ( !ForesterUtil.isEmpty( n ) ) {
- deleted.add( n );
+ l.add( divideIntoSubTreesHelper( n, min_distance_to_root ) );
+ if ( l.isEmpty() ) {
+ throw new RuntimeException( "this should not have happened" );
}
}
- return deleted;
+ return l;
}
public static List<PhylogenyNode> getAllDescendants( final PhylogenyNode node ) {
final List<PhylogenyNode> descs = new ArrayList<PhylogenyNode>();
- final Set<Integer> encountered = new HashSet<Integer>();
+ final Set<Long> encountered = new HashSet<Long>();
if ( !node.isExternal() ) {
final List<PhylogenyNode> exts = node.getAllExternalDescendants();
for( PhylogenyNode current : exts ) {
}
/**
- *
+ *
* Convenience method
- *
+ *
* @param node
* @return
*/
return values;
}
- /**
- * Calculates the distance between PhylogenyNodes n1 and n2.
- * PRECONDITION: n1 is a descendant of n2.
- *
- * @param n1
- * a descendant of n2
- * @param n2
- * @return distance between n1 and n2
- */
- private static double getDistance( PhylogenyNode n1, final PhylogenyNode n2 ) {
- double d = 0.0;
- while ( n1 != n2 ) {
- if ( n1.getDistanceToParent() > 0.0 ) {
- d += n1.getDistanceToParent();
- }
- n1 = n1.getParent();
- }
- return d;
+ final public static Event getEventAtLCA( final PhylogenyNode n1, final PhylogenyNode n2 ) {
+ return calculateLCA( n1, n2 ).getNodeData().getEvent();
}
/**
- * Returns taxonomy t if all external descendants have
+ * Returns taxonomy t if all external descendants have
* the same taxonomy t, null otherwise.
- *
+ *
*/
public static Taxonomy getExternalDescendantsTaxonomy( final PhylogenyNode node ) {
final List<PhylogenyNode> descs = node.getAllExternalDescendants();
return farthest;
}
- public static PhylogenyMethods getInstance() {
- if ( PhylogenyMethods._instance == null ) {
- PhylogenyMethods._instance = new PhylogenyMethods();
- }
- return PhylogenyMethods._instance;
- }
-
+ // public static PhylogenyMethods getInstance() {
+ // if ( PhylogenyMethods._instance == null ) {
+ // PhylogenyMethods._instance = new PhylogenyMethods();
+ // }
+ // return PhylogenyMethods._instance;
+ // }
/**
* Returns the largest confidence value found on phy.
*/
}
}
}
- return min;
+ return min;
+ }
+
+ /**
+ * Convenience method for display purposes.
+ * Not intended for algorithms.
+ */
+ public static String getSpecies( final PhylogenyNode node ) {
+ if ( !node.getNodeData().isHasTaxonomy() ) {
+ return "";
+ }
+ else if ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) {
+ return node.getNodeData().getTaxonomy().getScientificName();
+ }
+ if ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+ return node.getNodeData().getTaxonomy().getTaxonomyCode();
+ }
+ else {
+ return node.getNodeData().getTaxonomy().getCommonName();
+ }
+ }
+
+ /**
+ * Convenience method for display purposes.
+ * Not intended for algorithms.
+ */
+ public static String getTaxonomyIdentifier( final PhylogenyNode node ) {
+ if ( !node.getNodeData().isHasTaxonomy() || ( node.getNodeData().getTaxonomy().getIdentifier() == null ) ) {
+ return "";
+ }
+ return node.getNodeData().getTaxonomy().getIdentifier().getValue();
+ }
+
+ public final static boolean isAllDecendentsAreDuplications( final PhylogenyNode n ) {
+ if ( n.isExternal() ) {
+ return true;
+ }
+ else {
+ if ( n.isDuplication() ) {
+ for( final PhylogenyNode desc : n.getDescendants() ) {
+ if ( !isAllDecendentsAreDuplications( desc ) ) {
+ return false;
+ }
+ }
+ return true;
+ }
+ else {
+ return false;
+ }
+ }
+ }
+
+ public static boolean isHasExternalDescendant( final PhylogenyNode node ) {
+ for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
+ if ( node.getChildNode( i ).isExternal() ) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /*
+ * This is case insensitive.
+ *
+ */
+ public synchronized static boolean isTaxonomyHasIdentifierOfGivenProvider( final Taxonomy tax,
+ final String[] providers ) {
+ if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
+ final String my_tax_prov = tax.getIdentifier().getProvider();
+ for( final String provider : providers ) {
+ if ( provider.equalsIgnoreCase( my_tax_prov ) ) {
+ return true;
+ }
+ }
+ return false;
+ }
+ else {
+ return false;
+ }
+ }
+
+ public static void midpointRoot( final Phylogeny phylogeny ) {
+ if ( ( phylogeny.getNumberOfExternalNodes() < 2 ) || ( calculateMaxDistanceToRoot( phylogeny ) <= 0 ) ) {
+ return;
+ }
+ int counter = 0;
+ final int total_nodes = phylogeny.getNodeCount();
+ while ( true ) {
+ if ( ++counter > total_nodes ) {
+ throw new RuntimeException( "this should not have happened: midpoint rooting does not converge" );
+ }
+ PhylogenyNode a = null;
+ double da = 0;
+ double db = 0;
+ for( int i = 0; i < phylogeny.getRoot().getNumberOfDescendants(); ++i ) {
+ final PhylogenyNode f = getFurthestDescendant( phylogeny.getRoot().getChildNode( i ) );
+ final double df = getDistance( f, phylogeny.getRoot() );
+ if ( df > 0 ) {
+ if ( df > da ) {
+ db = da;
+ da = df;
+ a = f;
+ }
+ else if ( df > db ) {
+ db = df;
+ }
+ }
+ }
+ final double diff = da - db;
+ if ( diff < 0.000001 ) {
+ break;
+ }
+ double x = da - ( diff / 2.0 );
+ while ( ( x > a.getDistanceToParent() ) && !a.isRoot() ) {
+ x -= ( a.getDistanceToParent() > 0 ? a.getDistanceToParent() : 0 );
+ a = a.getParent();
+ }
+ phylogeny.reRoot( a, x );
+ }
+ phylogeny.recalculateNumberOfExternalDescendants( true );
+ }
+
+ public static void normalizeBootstrapValues( final Phylogeny phylogeny,
+ final double max_bootstrap_value,
+ final double max_normalized_value ) {
+ for( final PhylogenyNodeIterator iter = phylogeny.iteratorPreorder(); iter.hasNext(); ) {
+ final PhylogenyNode node = iter.next();
+ if ( node.isInternal() ) {
+ final double confidence = getConfidenceValue( node );
+ if ( confidence != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
+ if ( confidence >= max_bootstrap_value ) {
+ setBootstrapConfidence( node, max_normalized_value );
+ }
+ else {
+ setBootstrapConfidence( node, ( confidence * max_normalized_value ) / max_bootstrap_value );
+ }
+ }
+ }
+ }
+ }
+
+ public static List<PhylogenyNode> obtainAllNodesAsList( final Phylogeny phy ) {
+ final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
+ if ( phy.isEmpty() ) {
+ return nodes;
+ }
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+ nodes.add( iter.next() );
+ }
+ return nodes;
+ }
+
+ /**
+ * Returns a map of distinct taxonomies of
+ * all external nodes of node.
+ * If at least one of the external nodes has no taxonomy,
+ * null is returned.
+ *
+ */
+ public static Map<Taxonomy, Integer> obtainDistinctTaxonomyCounts( final PhylogenyNode node ) {
+ final List<PhylogenyNode> descs = node.getAllExternalDescendants();
+ final Map<Taxonomy, Integer> tax_map = new HashMap<Taxonomy, Integer>();
+ for( final PhylogenyNode n : descs ) {
+ if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
+ return null;
+ }
+ final Taxonomy t = n.getNodeData().getTaxonomy();
+ if ( tax_map.containsKey( t ) ) {
+ tax_map.put( t, tax_map.get( t ) + 1 );
+ }
+ else {
+ tax_map.put( t, 1 );
+ }
+ }
+ return tax_map;
+ }
+
+ /**
+ * 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 {
+ if ( ( n.getNumberOfDescendants() == 2 )
+ && ( n.getChildNode1().getNumberOfExternalNodes() != n.getChildNode2().getNumberOfExternalNodes() )
+ && ( ( n.getChildNode1().getNumberOfExternalNodes() < n.getChildNode2()
+ .getNumberOfExternalNodes() ) == order ) ) {
+ final PhylogenyNode temp = n.getChildNode1();
+ n.setChild1( n.getChildNode2() );
+ n.setChild2( temp );
+ _order_changed = true;
+ }
+ 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 synchronized static void orderAppearanceX( final PhylogenyNode n,
+ final boolean order_ext_alphabetically,
+ final DESCENDANT_SORT_PRIORITY pri ) {
+ if ( n.isExternal() ) {
+ return;
+ }
+ else {
+ _order_changed = false;
+ orderAppearance( n, true, order_ext_alphabetically, pri );
+ if ( !_order_changed ) {
+ orderAppearance( n, false, order_ext_alphabetically, pri );
+ }
+ }
+ }
+
+ public static void postorderBranchColorAveragingExternalNodeBased( final Phylogeny p ) {
+ for( final PhylogenyNodeIterator iter = p.iteratorPostorder(); iter.hasNext(); ) {
+ final PhylogenyNode node = iter.next();
+ double red = 0.0;
+ double green = 0.0;
+ double blue = 0.0;
+ int n = 0;
+ if ( node.isInternal() ) {
+ //for( final PhylogenyNodeIterator iterator = node.iterateChildNodesForward(); iterator.hasNext(); ) {
+ for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
+ final PhylogenyNode child_node = node.getChildNode( i );
+ final Color child_color = getBranchColorValue( child_node );
+ if ( child_color != null ) {
+ ++n;
+ red += child_color.getRed();
+ green += child_color.getGreen();
+ blue += child_color.getBlue();
+ }
+ }
+ setBranchColorValue( node,
+ new Color( ForesterUtil.roundToInt( red / n ),
+ ForesterUtil.roundToInt( green / n ),
+ ForesterUtil.roundToInt( blue / n ) ) );
+ }
+ }
+ }
+
+ public static final void preOrderReId( final Phylogeny phy ) {
+ if ( phy.isEmpty() ) {
+ return;
+ }
+ phy.setIdToNodeMap( null );
+ long i = PhylogenyNode.getNodeCount();
+ for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
+ it.next().setId( i++ );
+ }
+ PhylogenyNode.setNodeCount( i );
+ }
+
+ public final static Phylogeny[] readPhylogenies( final PhylogenyParser parser, final File file )
+ throws IOException {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny[] trees = factory.create( file, parser );
+ if ( ( trees == null ) || ( trees.length == 0 ) ) {
+ throw new PhylogenyParserException( "Unable to parse phylogeny from file: " + file );
+ }
+ return trees;
+ }
+
+ public final static Phylogeny[] readPhylogenies( final PhylogenyParser parser, final List<File> files )
+ throws IOException {
+ final List<Phylogeny> tree_list = new ArrayList<Phylogeny>();
+ for( final File file : files ) {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny[] trees = factory.create( file, parser );
+ if ( ( trees == null ) || ( trees.length == 0 ) ) {
+ throw new PhylogenyParserException( "Unable to parse phylogeny from file: " + file );
+ }
+ tree_list.addAll( Arrays.asList( trees ) );
+ }
+ return tree_list.toArray( new Phylogeny[ tree_list.size() ] );
+ }
+
+ public static void removeNode( final PhylogenyNode remove_me, final Phylogeny phylogeny ) {
+ if ( remove_me.isRoot() ) {
+ if ( remove_me.getNumberOfDescendants() == 1 ) {
+ final PhylogenyNode desc = remove_me.getDescendants().get( 0 );
+ desc.setDistanceToParent( addPhylogenyDistances( remove_me.getDistanceToParent(),
+ desc.getDistanceToParent() ) );
+ desc.setParent( null );
+ phylogeny.setRoot( desc );
+ phylogeny.clearHashIdToNodeMap();
+ }
+ else {
+ throw new IllegalArgumentException( "attempt to remove a root node with more than one descendants" );
+ }
+ }
+ else if ( remove_me.isExternal() ) {
+ phylogeny.deleteSubtree( remove_me, false );
+ phylogeny.clearHashIdToNodeMap();
+ phylogeny.externalNodesHaveChanged();
+ }
+ else {
+ final PhylogenyNode parent = remove_me.getParent();
+ final List<PhylogenyNode> descs = remove_me.getDescendants();
+ parent.removeChildNode( remove_me );
+ for( final PhylogenyNode desc : descs ) {
+ parent.addAsChild( desc );
+ desc.setDistanceToParent( addPhylogenyDistances( remove_me.getDistanceToParent(),
+ desc.getDistanceToParent() ) );
+ }
+ remove_me.setParent( null );
+ phylogeny.clearHashIdToNodeMap();
+ phylogeny.externalNodesHaveChanged();
+ }
+ }
+
+ private static enum NDF {
+ NodeName( "NN" ),
+ TaxonomyCode( "TC" ),
+ TaxonomyCommonName( "CN" ),
+ TaxonomyScientificName( "TS" ),
+ TaxonomyIdentifier( "TI" ),
+ TaxonomySynonym( "SY" ),
+ SequenceName( "SN" ),
+ GeneName( "GN" ),
+ SequenceSymbol( "SS" ),
+ SequenceAccession( "SA" ),
+ Domain( "DO" ),
+ Annotation( "AN" ),
+ CrossRef( "XR" ),
+ BinaryCharacter( "BC" ),
+ MolecularSequence( "MS" );
+
+ private final String _text;
+
+ NDF( final String text ) {
+ _text = text;
+ }
+
+ public static NDF fromString( final String text ) {
+ for( final NDF n : NDF.values() ) {
+ if ( text.startsWith( n._text ) ) {
+ return n;
+ }
+ }
+ return null;
+ }
+ }
+
+ public static List<Long> searchData( final String query,
+ final Phylogeny phy,
+ final boolean case_sensitive,
+ final boolean partial,
+ final boolean regex,
+ final boolean search_domains,
+ final double domains_confidence_threshold ) {
+ final List<Long> nodes = new ArrayList<Long>();
+ if ( phy.isEmpty() || ( query == null ) ) {
+ return nodes;
+ }
+ if ( ForesterUtil.isEmpty( query ) ) {
+ return nodes;
+ }
+ String my_query = query;
+ NDF ndf = null;
+ if ( ( my_query.length() > 2 ) && ( my_query.indexOf( ":" ) == 2 ) ) {
+ ndf = NDF.fromString( my_query );
+ if ( ndf != null ) {
+ my_query = my_query.substring( 3 );
+ }
+ }
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+ final PhylogenyNode node = iter.next();
+ boolean match = false;
+ if ( ( ( ndf == null ) || ( ndf == NDF.NodeName ) )
+ && match( node.getName(), my_query, case_sensitive, partial, regex ) ) {
+ match = true;
+ }
+ else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomyCode ) ) && node.getNodeData().isHasTaxonomy()
+ && match( node.getNodeData().getTaxonomy().getTaxonomyCode(),
+ my_query,
+ case_sensitive,
+ partial,
+ regex ) ) {
+ match = true;
+ }
+ else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomyCommonName ) ) && node.getNodeData().isHasTaxonomy()
+ && match( node.getNodeData().getTaxonomy().getCommonName(),
+ my_query,
+ case_sensitive,
+ partial,
+ regex ) ) {
+ match = true;
+ }
+ else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomyScientificName ) ) && node.getNodeData().isHasTaxonomy()
+ && match( node.getNodeData().getTaxonomy().getScientificName(),
+ my_query,
+ case_sensitive,
+ partial,
+ regex ) ) {
+ match = true;
+ }
+ else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomyIdentifier ) ) && node.getNodeData().isHasTaxonomy()
+ && ( node.getNodeData().getTaxonomy().getIdentifier() != null )
+ && match( node.getNodeData().getTaxonomy().getIdentifier().getValue(),
+ my_query,
+ case_sensitive,
+ partial,
+ regex ) ) {
+ match = true;
+ }
+ else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomySynonym ) ) && node.getNodeData().isHasTaxonomy()
+ && !node.getNodeData().getTaxonomy().getSynonyms().isEmpty() ) {
+ final List<String> syns = node.getNodeData().getTaxonomy().getSynonyms();
+ I: for( final String syn : syns ) {
+ if ( match( syn, my_query, case_sensitive, partial, regex ) ) {
+ match = true;
+ break I;
+ }
+ }
+ }
+ if ( !match && ( ( ndf == null ) || ( ndf == NDF.SequenceName ) ) && node.getNodeData().isHasSequence()
+ && match( node.getNodeData().getSequence().getName(), my_query, case_sensitive, partial, regex ) ) {
+ match = true;
+ }
+ if ( !match && ( ( ndf == null ) || ( ndf == NDF.GeneName ) ) && node.getNodeData().isHasSequence()
+ && match( node.getNodeData().getSequence().getGeneName(),
+ my_query,
+ case_sensitive,
+ partial,
+ regex ) ) {
+ match = true;
+ }
+ if ( !match && ( ( ndf == null ) || ( ndf == NDF.SequenceSymbol ) ) && node.getNodeData().isHasSequence()
+ && match( node.getNodeData().getSequence().getSymbol(),
+ my_query,
+ case_sensitive,
+ partial,
+ regex ) ) {
+ match = true;
+ }
+ if ( !match && ( ( ndf == null ) || ( ndf == NDF.SequenceAccession ) ) && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getAccession() != null )
+ && match( node.getNodeData().getSequence().getAccession().getValue(),
+ my_query,
+ case_sensitive,
+ partial,
+ regex ) ) {
+ match = true;
+ }
+ if ( !match && ( ( ( ndf == null ) && search_domains ) || ( ndf == NDF.Domain ) )
+ && 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 ( ( da.getDomain( i ).getConfidence() <= domains_confidence_threshold )
+ && ( match( da.getDomain( i ).getName(), my_query, case_sensitive, partial, regex ) ) ) {
+ match = true;
+ break I;
+ }
+ }
+ }
+ if ( !match && ( ( ndf == null ) || ( ndf == NDF.Annotation ) ) && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getAnnotations() != null ) ) {
+ for( final Annotation ann : node.getNodeData().getSequence().getAnnotations() ) {
+ if ( match( ann.getDesc(), my_query, case_sensitive, partial, regex ) ) {
+ match = true;
+ break;
+ }
+ if ( match( ann.getRef(), my_query, case_sensitive, partial, regex ) ) {
+ match = true;
+ break;
+ }
+ }
+ }
+ if ( !match && ( ( ndf == null ) || ( ndf == NDF.CrossRef ) ) && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getCrossReferences() != null ) ) {
+ for( final Accession x : node.getNodeData().getSequence().getCrossReferences() ) {
+ if ( match( x.getComment(), my_query, case_sensitive, partial, regex ) ) {
+ match = true;
+ break;
+ }
+ if ( match( x.getSource(), my_query, case_sensitive, partial, regex ) ) {
+ match = true;
+ break;
+ }
+ if ( match( x.getValue(), my_query, case_sensitive, partial, regex ) ) {
+ match = true;
+ break;
+ }
+ }
+ }
+ if ( !match && ( ( ndf == null ) || ( ndf == NDF.BinaryCharacter ) )
+ && ( node.getNodeData().getBinaryCharacters() != null ) ) {
+ Iterator<String> it = node.getNodeData().getBinaryCharacters().getPresentCharacters().iterator();
+ I: while ( it.hasNext() ) {
+ if ( match( it.next(), my_query, case_sensitive, partial, regex ) ) {
+ match = true;
+ break I;
+ }
+ }
+ it = node.getNodeData().getBinaryCharacters().getGainedCharacters().iterator();
+ I: while ( it.hasNext() ) {
+ if ( match( it.next(), my_query, case_sensitive, partial, regex ) ) {
+ match = true;
+ break I;
+ }
+ }
+ }
+ if ( !match && ( ndf == NDF.MolecularSequence ) && node.getNodeData().isHasSequence()
+ && match( node.getNodeData().getSequence().getMolecularSequence(),
+ my_query,
+ case_sensitive,
+ true,
+ regex ) ) {
+ match = true;
+ }
+ if ( match ) {
+ nodes.add( node.getId() );
+ }
+ }
+ return nodes;
+ }
+
+ public static List<Long> searchDataLogicalAnd( final String[] queries,
+ final Phylogeny phy,
+ final boolean case_sensitive,
+ final boolean partial,
+ final boolean search_domains,
+ final double domains_confidence_threshold ) {
+ final List<Long> nodes = new ArrayList<Long>();
+ if ( phy.isEmpty() || ( queries == null ) || ( queries.length < 1 ) ) {
+ return nodes;
+ }
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+ final PhylogenyNode node = iter.next();
+ boolean all_matched = true;
+ for( String query : queries ) {
+ if ( query == null ) {
+ continue;
+ }
+ query = query.trim();
+ NDF ndf = null;
+ if ( ( query.length() > 2 ) && ( query.indexOf( ":" ) == 2 ) ) {
+ ndf = NDF.fromString( query );
+ if ( ndf != null ) {
+ query = query.substring( 3 );
+ }
+ }
+ boolean match = false;
+ if ( ForesterUtil.isEmpty( query ) ) {
+ continue;
+ }
+ if ( ( ( ndf == null ) || ( ndf == NDF.NodeName ) )
+ && match( node.getName(), query, case_sensitive, partial, false ) ) {
+ match = true;
+ }
+ else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomyCode ) ) && node.getNodeData().isHasTaxonomy()
+ && match( node.getNodeData().getTaxonomy().getTaxonomyCode(),
+ query,
+ case_sensitive,
+ partial,
+ false ) ) {
+ match = true;
+ }
+ else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomyCommonName ) ) && node.getNodeData().isHasTaxonomy()
+ && match( node.getNodeData().getTaxonomy().getCommonName(),
+ query,
+ case_sensitive,
+ partial,
+ false ) ) {
+ match = true;
+ }
+ else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomyScientificName ) )
+ && node.getNodeData().isHasTaxonomy()
+ && match( node.getNodeData().getTaxonomy().getScientificName(),
+ query,
+ case_sensitive,
+ partial,
+ false ) ) {
+ match = true;
+ }
+ else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomyIdentifier ) ) && node.getNodeData().isHasTaxonomy()
+ && ( node.getNodeData().getTaxonomy().getIdentifier() != null )
+ && match( node.getNodeData().getTaxonomy().getIdentifier().getValue(),
+ query,
+ case_sensitive,
+ partial,
+ false ) ) {
+ match = true;
+ }
+ else if ( ( ( ndf == null ) || ( ndf == NDF.TaxonomySynonym ) ) && node.getNodeData().isHasTaxonomy()
+ && !node.getNodeData().getTaxonomy().getSynonyms().isEmpty() ) {
+ final List<String> syns = node.getNodeData().getTaxonomy().getSynonyms();
+ I: for( final String syn : syns ) {
+ if ( match( syn, query, case_sensitive, partial, false ) ) {
+ match = true;
+ break I;
+ }
+ }
+ }
+ if ( !match && ( ( ndf == null ) || ( ndf == NDF.SequenceName ) ) && node.getNodeData().isHasSequence()
+ && match( node.getNodeData().getSequence().getName(),
+ query,
+ case_sensitive,
+ partial,
+ false ) ) {
+ match = true;
+ }
+ if ( !match && ( ( ndf == null ) || ( ndf == NDF.GeneName ) ) && node.getNodeData().isHasSequence()
+ && match( node.getNodeData().getSequence().getGeneName(),
+ query,
+ case_sensitive,
+ partial,
+ false ) ) {
+ match = true;
+ }
+ if ( !match && ( ( ndf == null ) || ( ndf == NDF.SequenceSymbol ) )
+ && node.getNodeData().isHasSequence() && match( node.getNodeData().getSequence().getSymbol(),
+ query,
+ case_sensitive,
+ partial,
+ false ) ) {
+ match = true;
+ }
+ if ( !match && ( ( ndf == null ) || ( ndf == NDF.SequenceAccession ) )
+ && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getAccession() != null )
+ && match( node.getNodeData().getSequence().getAccession().getValue(),
+ query,
+ case_sensitive,
+ partial,
+ false ) ) {
+ match = true;
+ }
+ if ( !match && ( ( ( ndf == null ) && search_domains ) || ( ndf == NDF.Domain ) )
+ && 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 ( ( da.getDomain( i ).getConfidence() <= domains_confidence_threshold )
+ && match( da.getDomain( i ).getName(), query, case_sensitive, partial, false ) ) {
+ match = true;
+ break I;
+ }
+ }
+ }
+ if ( !match && ( ( ndf == null ) || ( ndf == NDF.Annotation ) ) && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getAnnotations() != null ) ) {
+ for( final Annotation ann : node.getNodeData().getSequence().getAnnotations() ) {
+ if ( match( ann.getDesc(), query, case_sensitive, partial, false ) ) {
+ match = true;
+ break;
+ }
+ if ( match( ann.getRef(), query, case_sensitive, partial, false ) ) {
+ match = true;
+ break;
+ }
+ }
+ }
+ if ( !match && ( ( ndf == null ) || ( ndf == NDF.CrossRef ) ) && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getCrossReferences() != null ) ) {
+ for( final Accession x : node.getNodeData().getSequence().getCrossReferences() ) {
+ if ( match( x.getComment(), query, case_sensitive, partial, false ) ) {
+ match = true;
+ break;
+ }
+ if ( match( x.getSource(), query, case_sensitive, partial, false ) ) {
+ match = true;
+ break;
+ }
+ if ( match( x.getValue(), query, case_sensitive, partial, false ) ) {
+ match = true;
+ break;
+ }
+ }
+ }
+ if ( !match && ( ( ndf == null ) || ( ndf == NDF.BinaryCharacter ) )
+ && ( node.getNodeData().getBinaryCharacters() != null ) ) {
+ Iterator<String> it = node.getNodeData().getBinaryCharacters().getPresentCharacters().iterator();
+ I: while ( it.hasNext() ) {
+ if ( match( it.next(), query, case_sensitive, partial, false ) ) {
+ match = true;
+ break I;
+ }
+ }
+ it = node.getNodeData().getBinaryCharacters().getGainedCharacters().iterator();
+ I: while ( it.hasNext() ) {
+ if ( match( it.next(), query, case_sensitive, partial, false ) ) {
+ match = true;
+ break I;
+ }
+ }
+ }
+ if ( !match && ( ndf == NDF.MolecularSequence ) && node.getNodeData().isHasSequence()
+ && match( node.getNodeData().getSequence().getMolecularSequence(),
+ query,
+ case_sensitive,
+ true,
+ false ) ) {
+ match = true;
+ }
+ if ( !match ) {
+ all_matched = false;
+ break;
+ }
+ }
+ if ( all_matched ) {
+ nodes.add( node.getId() );
+ }
+ }
+ 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 ) {
+ 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 boolean isInternalNamesLookLikeConfidences( final Phylogeny phy ) {
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ while ( it.hasNext() ) {
+ final PhylogenyNode n = it.next();
+ if ( !n.isExternal() && !n.isRoot() ) {
+ if ( !ForesterUtil.isEmpty( n.getName() ) ) {
+ double value = -1;
+ try {
+ value = Double.parseDouble( n.getName() );
+ }
+ catch ( final NumberFormatException e ) {
+ return false;
+ }
+ if ( ( value < 0.0 ) || ( value > 100 ) ) {
+ return false;
+ }
+ }
+ }
+ }
+ return true;
+ }
+
+ final static public void transferInternalNodeNamesToConfidence( final Phylogeny phy,
+ final String confidence_type ) {
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ while ( it.hasNext() ) {
+ transferInternalNodeNameToConfidence( confidence_type, it.next() );
+ }
+ }
+
+ private static void transferInternalNodeNameToConfidence( final String confidence_type, final PhylogenyNode n ) {
+ 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, confidence_type ) );
+ 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( "" );
+ }
+ n.getNodeData().getTaxonomy()
+ .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) );
+ break;
+ }
+ case TAXONOMY_ID_UNIPROT_2: {
+ if ( !n.getNodeData().isHasTaxonomy() ) {
+ n.getNodeData().setTaxonomy( new Taxonomy() );
+ }
+ String id = name;
+ final int i = name.indexOf( '_' );
+ if ( i > 0 ) {
+ id = name.substring( i + 1, name.length() );
+ }
+ else {
+ n.setName( "" );
+ }
+ n.getNodeData().getTaxonomy()
+ .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;
+ }
+ default: {
+ throw new IllegalArgumentException( "don't know what to do with " + field );
+ }
+ }
+ }
+ }
}
- /**
- * Convenience method for display purposes.
- * Not intended for algorithms.
- */
- public static String getSpecies( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasTaxonomy() ) {
- return "";
- }
- else if ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) {
- return node.getNodeData().getTaxonomy().getScientificName();
+ static double addPhylogenyDistances( final double a, final double b ) {
+ if ( ( a >= 0.0 ) && ( b >= 0.0 ) ) {
+ return a + b;
}
- if ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
- return node.getNodeData().getTaxonomy().getTaxonomyCode();
+ else if ( a >= 0.0 ) {
+ return a;
}
- else {
- return node.getNodeData().getTaxonomy().getCommonName();
+ else if ( b >= 0.0 ) {
+ return b;
}
+ return PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;
}
- /**
- * Returns all Nodes which are connected to external PhylogenyNode n of this
- * Phylogeny by a path containing only speciation events. We call these
- * "super orthologs". Nodes are returned as Vector of references to Nodes.
- * <p>
- * PRECONDITION: This tree must be binary and rooted, and speciation -
- * duplication need to be assigned for each of its internal Nodes.
- * <p>
- * Returns null if this Phylogeny is empty or if n is internal.
- * @param n
- * external PhylogenyNode whose strictly speciation related Nodes
- * are to be returned
- * @return References to all strictly speciation related Nodes of
- * PhylogenyNode n of this Phylogeny, null if this Phylogeny is
- * empty or if n is internal
- */
- public static List<PhylogenyNode> getSuperOrthologousNodes( final PhylogenyNode n ) {
- // FIXME
- PhylogenyNode node = n;
- PhylogenyNode deepest = null;
- final List<PhylogenyNode> v = new ArrayList<PhylogenyNode>();
- if ( !node.isExternal() ) {
- return null;
- }
- while ( !node.isRoot() && !node.getParent().isDuplication() ) {
- node = node.getParent();
- }
- deepest = node;
- deepest.setIndicatorsToZero();
- do {
- if ( !node.isExternal() ) {
- if ( node.getIndicator() == 0 ) {
- node.setIndicator( ( byte ) 1 );
- if ( !node.isDuplication() ) {
- node = node.getChildNode1();
- }
- }
- if ( node.getIndicator() == 1 ) {
- node.setIndicator( ( byte ) 2 );
- if ( !node.isDuplication() ) {
- node = node.getChildNode2();
- }
- }
- if ( ( node != deepest ) && ( node.getIndicator() == 2 ) ) {
- node = node.getParent();
+ static double calculateDistanceToAncestor( final PhylogenyNode anc, PhylogenyNode desc ) {
+ double d = 0;
+ boolean all_default = true;
+ while ( anc != desc ) {
+ if ( desc.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
+ d += desc.getDistanceToParent();
+ if ( all_default ) {
+ all_default = false;
}
}
- else {
- if ( node != n ) {
- v.add( node );
- }
- if ( node != deepest ) {
- node = node.getParent();
- }
- else {
- node.setIndicator( ( byte ) 2 );
+ desc = desc.getParent();
+ }
+ if ( all_default ) {
+ return PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;
+ }
+ return d;
+ }
+
+ public static double calculateAverageTreeHeight( final PhylogenyNode node ) {
+ final List<PhylogenyNode> ext = node.getAllExternalDescendants();
+ double s = 0;
+ for( PhylogenyNode n : ext ) {
+ while ( n != node ) {
+ if ( n.getDistanceToParent() > 0 ) {
+ s += n.getDistanceToParent();
}
+ n = n.getParent();
}
- } while ( ( node != deepest ) || ( deepest.getIndicator() != 2 ) );
- return v;
+ }
+ return s / ext.size();
}
/**
- * Convenience method for display purposes.
- * Not intended for algorithms.
+ * Deep copies the phylogeny originating from this node.
*/
- public static String getTaxonomyIdentifier( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasTaxonomy() || ( node.getNodeData().getTaxonomy().getIdentifier() == null ) ) {
- return "";
+ static PhylogenyNode copySubTree( final PhylogenyNode source ) {
+ if ( source == null ) {
+ return null;
+ }
+ else {
+ final PhylogenyNode newnode = source.copyNodeData();
+ if ( !source.isExternal() ) {
+ for( int i = 0; i < source.getNumberOfDescendants(); ++i ) {
+ newnode.setChildNode( i, PhylogenyMethods.copySubTree( source.getChildNode( i ) ) );
+ }
+ }
+ return newnode;
}
- return node.getNodeData().getTaxonomy().getIdentifier().getValue();
}
/**
- * Returns all Nodes which are connected to external PhylogenyNode n of this
- * Phylogeny by a path containing, and leading to, only duplication events.
- * We call these "ultra paralogs". Nodes are returned as Vector of
- * references to Nodes.
- * <p>
- * PRECONDITION: This tree must be binary and rooted, and speciation -
- * duplication need to be assigned for each of its internal Nodes.
- * <p>
- * Returns null if this Phylogeny is empty or if n is internal.
- * <p>
- * (Last modified: 10/06/01)
- *
- * @param n
- * external PhylogenyNode whose ultra paralogs are to be returned
- * @return Vector of references to all ultra paralogs of PhylogenyNode n of
- * this Phylogeny, null if this Phylogeny is empty or if n is
- * internal
+ * Shallow copies the phylogeny originating from this node.
*/
- public static List<PhylogenyNode> getUltraParalogousNodes( final PhylogenyNode n ) {
- // FIXME test me
- PhylogenyNode node = n;
- if ( !node.isExternal() ) {
- throw new IllegalArgumentException( "attempt to get ultra-paralogous nodes of internal node" );
- }
- while ( !node.isRoot() && node.getParent().isDuplication() && isAllDecendentsAreDuplications( node.getParent() ) ) {
- node = node.getParent();
+ static PhylogenyNode copySubTreeShallow( final PhylogenyNode source ) {
+ if ( source == null ) {
+ return null;
}
- final List<PhylogenyNode> nodes = node.getAllExternalDescendants();
- nodes.remove( n );
- return nodes;
- }
-
- public static String inferCommonPartOfScientificNameOfDescendants( final PhylogenyNode node ) {
- final List<PhylogenyNode> descs = node.getDescendants();
- String sn = null;
- for( final PhylogenyNode n : descs ) {
- if ( !n.getNodeData().isHasTaxonomy()
- || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
- return null;
- }
- else if ( sn == null ) {
- sn = n.getNodeData().getTaxonomy().getScientificName().trim();
- }
- else {
- String sn_current = n.getNodeData().getTaxonomy().getScientificName().trim();
- if ( !sn.equals( sn_current ) ) {
- boolean overlap = false;
- while ( ( sn.indexOf( ' ' ) >= 0 ) || ( sn_current.indexOf( ' ' ) >= 0 ) ) {
- if ( ForesterUtil.countChars( sn, ' ' ) > ForesterUtil.countChars( sn_current, ' ' ) ) {
- sn = sn.substring( 0, sn.lastIndexOf( ' ' ) ).trim();
- }
- else {
- sn_current = sn_current.substring( 0, sn_current.lastIndexOf( ' ' ) ).trim();
- }
- if ( sn.equals( sn_current ) ) {
- overlap = true;
- break;
- }
- }
- if ( !overlap ) {
- return null;
- }
+ else {
+ final PhylogenyNode newnode = source.copyNodeDataShallow();
+ if ( !source.isExternal() ) {
+ for( int i = 0; i < source.getNumberOfDescendants(); ++i ) {
+ newnode.setChildNode( i, PhylogenyMethods.copySubTreeShallow( source.getChildNode( i ) ) );
}
}
+ return newnode;
}
- return sn;
}
- public static boolean isHasExternalDescendant( final PhylogenyNode node ) {
- for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
- if ( node.getChildNode( i ).isExternal() ) {
- return true;
+ private final static List<PhylogenyNode> divideIntoSubTreesHelper( final PhylogenyNode node,
+ final double min_distance_to_root ) {
+ final List<PhylogenyNode> l = new ArrayList<PhylogenyNode>();
+ final PhylogenyNode r = moveTowardsRoot( node, min_distance_to_root );
+ for( final PhylogenyNode ext : r.getAllExternalDescendants() ) {
+ if ( ext.getIndicator() != 0 ) {
+ throw new RuntimeException( "this should not have happened" );
}
+ ext.setIndicator( ( byte ) 1 );
+ l.add( ext );
}
- return false;
+ return l;
}
- /*
- * This is case insensitive.
- *
+ /**
+ * Calculates the distance between PhylogenyNodes n1 and n2.
+ * PRECONDITION: n1 is a descendant of n2.
+ *
+ * @param n1
+ * a descendant of n2
+ * @param n2
+ * @return distance between n1 and n2
*/
- public synchronized static boolean isTaxonomyHasIdentifierOfGivenProvider( final Taxonomy tax,
- final String[] providers ) {
- if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
- final String my_tax_prov = tax.getIdentifier().getProvider();
- for( final String provider : providers ) {
- if ( provider.equalsIgnoreCase( my_tax_prov ) ) {
- return true;
- }
+ private static double getDistance( PhylogenyNode n1, final PhylogenyNode n2 ) {
+ double d = 0.0;
+ while ( n1 != n2 ) {
+ if ( n1.getDistanceToParent() > 0.0 ) {
+ d += n1.getDistanceToParent();
}
- return false;
- }
- else {
- return false;
+ n1 = n1.getParent();
}
+ return d;
}
private static boolean match( final String s,
final String query,
final boolean case_sensitive,
- final boolean partial ) {
+ final boolean partial,
+ final boolean regex ) {
if ( ForesterUtil.isEmpty( s ) || ForesterUtil.isEmpty( query ) ) {
return false;
}
String my_s = s.trim();
String my_query = query.trim();
- if ( !case_sensitive ) {
+ if ( !case_sensitive && !regex ) {
my_s = my_s.toLowerCase();
my_query = my_query.toLowerCase();
}
- if ( partial ) {
- return my_s.indexOf( my_query ) >= 0;
- }
- else {
- return my_s.equals( my_query );
- }
- }
-
- public static void midpointRoot( final Phylogeny phylogeny ) {
- if ( phylogeny.getNumberOfExternalNodes() < 2 ) {
- return;
- }
- final PhylogenyMethods methods = getInstance();
- final double farthest_d = methods.calculateFurthestDistance( phylogeny );
- final PhylogenyNode f1 = methods.getFarthestNode1();
- final PhylogenyNode f2 = methods.getFarthestNode2();
- if ( farthest_d <= 0.0 ) {
- return;
- }
- double x = farthest_d / 2.0;
- PhylogenyNode n = f1;
- if ( PhylogenyMethods.getDistance( f1, phylogeny.getRoot() ) < PhylogenyMethods.getDistance( f2, phylogeny
- .getRoot() ) ) {
- n = f2;
- }
- while ( ( x > n.getDistanceToParent() ) && !n.isRoot() ) {
- x -= ( n.getDistanceToParent() > 0 ? n.getDistanceToParent() : 0 );
- n = n.getParent();
- }
- phylogeny.reRoot( n, x );
- phylogeny.recalculateNumberOfExternalDescendants( true );
- final PhylogenyNode a = getFurthestDescendant( phylogeny.getRoot().getChildNode1() );
- final PhylogenyNode b = getFurthestDescendant( phylogeny.getRoot().getChildNode2() );
- final double da = getDistance( a, phylogeny.getRoot() );
- final double db = getDistance( b, phylogeny.getRoot() );
- if ( Math.abs( da - db ) > 0.000001 ) {
- throw new FailedConditionCheckException( "this should not have happened: midpoint rooting failed: da="
- + da + ", db=" + db + ", diff=" + Math.abs( da - db ) );
- }
- }
-
- public static void normalizeBootstrapValues( final Phylogeny phylogeny,
- final double max_bootstrap_value,
- final double max_normalized_value ) {
- for( final PhylogenyNodeIterator iter = phylogeny.iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- if ( node.isInternal() ) {
- final double confidence = getConfidenceValue( node );
- if ( confidence != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
- if ( confidence >= max_bootstrap_value ) {
- setBootstrapConfidence( node, max_normalized_value );
- }
- else {
- setBootstrapConfidence( node, ( confidence * max_normalized_value ) / max_bootstrap_value );
- }
- }
- }
- }
- }
-
- public static List<PhylogenyNode> obtainAllNodesAsList( final Phylogeny phy ) {
- final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
- if ( phy.isEmpty() ) {
- return nodes;
- }
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
- nodes.add( iter.next() );
- }
- return nodes;
- }
-
- public static void postorderBranchColorAveragingExternalNodeBased( final Phylogeny p ) {
- for( final PhylogenyNodeIterator iter = p.iteratorPostorder(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- double red = 0.0;
- double green = 0.0;
- double blue = 0.0;
- int n = 0;
- if ( node.isInternal() ) {
- //for( final PhylogenyNodeIterator iterator = node.iterateChildNodesForward(); iterator.hasNext(); ) {
- for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
- final PhylogenyNode child_node = node.getChildNode( i );
- final Color child_color = getBranchColorValue( child_node );
- if ( child_color != null ) {
- ++n;
- red += child_color.getRed();
- green += child_color.getGreen();
- blue += child_color.getBlue();
- }
+ if ( regex ) {
+ Pattern p = null;
+ try {
+ if ( case_sensitive ) {
+ p = Pattern.compile( my_query );
}
- setBranchColorValue( node,
- new Color( ForesterUtil.roundToInt( red / n ),
- ForesterUtil.roundToInt( green / n ),
- ForesterUtil.roundToInt( blue / n ) ) );
- }
- }
- }
-
- public static void removeNode( final PhylogenyNode remove_me, final Phylogeny phylogeny ) {
- if ( remove_me.isRoot() ) {
- throw new IllegalArgumentException( "ill advised attempt to remove root node" );
- }
- if ( remove_me.isExternal() ) {
- phylogeny.deleteSubtree( remove_me, false );
- phylogeny.clearHashIdToNodeMap();
- phylogeny.externalNodesHaveChanged();
- }
- else {
- final PhylogenyNode parent = remove_me.getParent();
- final List<PhylogenyNode> descs = remove_me.getDescendants();
- parent.removeChildNode( remove_me );
- for( final PhylogenyNode desc : descs ) {
- parent.addAsChild( desc );
- desc.setDistanceToParent( addPhylogenyDistances( remove_me.getDistanceToParent(),
- desc.getDistanceToParent() ) );
- }
- remove_me.setParent( null );
- phylogeny.clearHashIdToNodeMap();
- phylogeny.externalNodesHaveChanged();
- }
- }
-
- public static List<PhylogenyNode> searchData( final String query,
- final Phylogeny phy,
- final boolean case_sensitive,
- final boolean partial,
- final boolean search_domains ) {
- final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
- if ( phy.isEmpty() || ( query == null ) ) {
- return nodes;
- }
- if ( ForesterUtil.isEmpty( query ) ) {
- return nodes;
- }
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- boolean match = false;
- if ( match( node.getName(), query, case_sensitive, partial ) ) {
- match = true;
- }
- else if ( node.getNodeData().isHasTaxonomy()
- && match( node.getNodeData().getTaxonomy().getTaxonomyCode(), query, case_sensitive, partial ) ) {
- match = true;
- }
- else if ( node.getNodeData().isHasTaxonomy()
- && match( node.getNodeData().getTaxonomy().getCommonName(), query, case_sensitive, partial ) ) {
- match = true;
- }
- else if ( node.getNodeData().isHasTaxonomy()
- && match( node.getNodeData().getTaxonomy().getScientificName(), query, case_sensitive, partial ) ) {
- match = true;
- }
- else if ( node.getNodeData().isHasTaxonomy()
- && ( node.getNodeData().getTaxonomy().getIdentifier() != null )
- && match( node.getNodeData().getTaxonomy().getIdentifier().getValue(),
- query,
- case_sensitive,
- partial ) ) {
- match = true;
- }
- else if ( node.getNodeData().isHasTaxonomy() && !node.getNodeData().getTaxonomy().getSynonyms().isEmpty() ) {
- final List<String> syns = node.getNodeData().getTaxonomy().getSynonyms();
- I: for( final String syn : syns ) {
- if ( match( syn, query, case_sensitive, partial ) ) {
- match = true;
- break I;
- }
+ else {
+ p = Pattern.compile( my_query, Pattern.CASE_INSENSITIVE );
}
}
- if ( !match && node.getNodeData().isHasSequence()
- && match( node.getNodeData().getSequence().getName(), query, case_sensitive, partial ) ) {
- match = true;
+ catch ( final PatternSyntaxException e ) {
+ return false;
}
- if ( !match && node.getNodeData().isHasSequence()
- && match( node.getNodeData().getSequence().getSymbol(), query, case_sensitive, partial ) ) {
- match = true;
+ if ( p != null ) {
+ return p.matcher( my_s ).find();
}
- if ( !match
- && node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getAccession() != null )
- && match( node.getNodeData().getSequence().getAccession().getValue(),
- query,
- case_sensitive,
- partial ) ) {
- match = true;
+ else {
+ return false;
}
- 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;
- }
- }
+ }
+ else if ( partial ) {
+ return my_s.indexOf( my_query ) >= 0;
+ }
+ else {
+ Pattern p = null;
+ try {
+ p = Pattern.compile( "(\\b|_)" + Pattern.quote( my_query ) + "(\\b|_)" );
}
- 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;
- }
- }
+ catch ( final PatternSyntaxException e ) {
+ return false;
}
- if ( match ) {
- nodes.add( node );
+ if ( p != null ) {
+ return p.matcher( my_s ).find();
+ }
+ else {
+ return false;
}
}
- return nodes;
}
- public static List<PhylogenyNode> searchDataLogicalAnd( final String[] queries,
- final Phylogeny phy,
- final boolean case_sensitive,
- final boolean partial,
- final boolean search_domains ) {
- final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
- if ( phy.isEmpty() || ( queries == null ) || ( queries.length < 1 ) ) {
- return nodes;
+ private final static PhylogenyNode moveTowardsRoot( final PhylogenyNode node, final double min_distance_to_root ) {
+ PhylogenyNode n = node;
+ PhylogenyNode prev = node;
+ while ( min_distance_to_root < n.calculateDistanceToRoot() ) {
+ prev = n;
+ n = n.getParent();
}
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- boolean all_matched = true;
- for( final String query : queries ) {
- boolean match = false;
- if ( ForesterUtil.isEmpty( query ) ) {
- continue;
- }
- if ( match( node.getName(), query, case_sensitive, partial ) ) {
- match = true;
- }
- else if ( node.getNodeData().isHasTaxonomy()
- && match( node.getNodeData().getTaxonomy().getTaxonomyCode(), query, case_sensitive, partial ) ) {
- match = true;
- }
- else if ( node.getNodeData().isHasTaxonomy()
- && match( node.getNodeData().getTaxonomy().getCommonName(), query, case_sensitive, partial ) ) {
- match = true;
+ return prev;
+ }
+
+ public static enum DESCENDANT_SORT_PRIORITY {
+ NODE_NAME,
+ SEQUENCE,
+ TAXONOMY;
+ }
+
+ public static enum PhylogenyNodeField {
+ CLADE_NAME,
+ SEQUENCE_NAME,
+ SEQUENCE_SYMBOL,
+ TAXONOMY_CODE,
+ TAXONOMY_COMMON_NAME,
+ TAXONOMY_ID,
+ TAXONOMY_ID_UNIPROT_1,
+ TAXONOMY_ID_UNIPROT_2,
+ TAXONOMY_SCIENTIFIC_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 );
+ }
+ }
+
+ final private static 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() );
}
- else if ( node.getNodeData().isHasTaxonomy()
- && match( node.getNodeData().getTaxonomy().getScientificName(), query, case_sensitive, partial ) ) {
- match = true;
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
+ return n1.getNodeData().getTaxonomy().getTaxonomyCode()
+ .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
}
- else if ( node.getNodeData().isHasTaxonomy()
- && ( node.getNodeData().getTaxonomy().getIdentifier() != null )
- && match( node.getNodeData().getTaxonomy().getIdentifier().getValue(),
- query,
- case_sensitive,
- partial ) ) {
- match = true;
+ }
+ 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() );
}
- else if ( node.getNodeData().isHasTaxonomy()
- && !node.getNodeData().getTaxonomy().getSynonyms().isEmpty() ) {
- final List<String> syns = node.getNodeData().getTaxonomy().getSynonyms();
- I: for( final String syn : syns ) {
- if ( match( syn, query, case_sensitive, partial ) ) {
- match = true;
- break I;
- }
- }
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
+ return n1.getNodeData().getSequence().getGeneName()
+ .compareTo( n2.getNodeData().getSequence().getGeneName() );
}
- if ( !match && node.getNodeData().isHasSequence()
- && match( node.getNodeData().getSequence().getName(), query, case_sensitive, partial ) ) {
- match = true;
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
+ return n1.getNodeData().getSequence().getSymbol()
+ .compareTo( n2.getNodeData().getSequence().getSymbol() );
}
- if ( !match && node.getNodeData().isHasSequence()
- && match( node.getNodeData().getSequence().getSymbol(), query, case_sensitive, partial ) ) {
- match = true;
+ }
+ if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
+ return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
+ }
+ return 0;
+ }
+ }
+
+ final private static 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 ( !match
- && node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getAccession() != null )
- && match( node.getNodeData().getSequence().getAccession().getValue(),
- query,
- case_sensitive,
- partial ) ) {
- match = true;
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getGeneName() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
+ return n1.getNodeData().getSequence().getGeneName()
+ .compareTo( n2.getNodeData().getSequence().getGeneName() );
}
- 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 ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
+ return n1.getNodeData().getSequence().getSymbol()
+ .compareTo( n2.getNodeData().getSequence().getSymbol() );
}
- 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 ( 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 ( !match ) {
- all_matched = false;
- break;
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getTaxonomy().getTaxonomyCode() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
+ return n1.getNodeData().getTaxonomy().getTaxonomyCode()
+ .compareTo( n2.getNodeData().getTaxonomy().getTaxonomyCode() );
}
}
- if ( all_matched ) {
- nodes.add( node );
+ if ( ( !ForesterUtil.isEmpty( n1.getName() ) ) && ( !ForesterUtil.isEmpty( n2.getName() ) ) ) {
+ return n1.getName().toLowerCase().compareTo( n2.getName().toLowerCase() );
}
+ return 0;
}
- return nodes;
}
- /**
- * 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" );
- }
+ final private static class PhylogenyNodeSortNodeNamePriority implements Comparator<PhylogenyNode> {
- public static void setBranchColorValue( final PhylogenyNode node, final Color color ) {
- if ( node.getBranchData().getBranchColor() == null ) {
- node.getBranchData().setBranchColor( new BranchColor() );
+ @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 ( 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().getGeneName() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getGeneName() ) ) ) {
+ return n1.getNodeData().getSequence().getGeneName()
+ .compareTo( n2.getNodeData().getSequence().getGeneName() );
+ }
+ if ( ( !ForesterUtil.isEmpty( n1.getNodeData().getSequence().getSymbol() ) )
+ && ( !ForesterUtil.isEmpty( n2.getNodeData().getSequence().getSymbol() ) ) ) {
+ return n1.getNodeData().getSequence().getSymbol()
+ .compareTo( n2.getNodeData().getSequence().getSymbol() );
+ }
+ }
+ return 0;
}
- 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, "" );
+ public final static Map<Long, Integer> calculateDepths( final Phylogeny phy ) {
+ final Map<Long, Integer> depths = new HashMap<Long, Integer>();
+ calculateDepthsHelper( phy.getRoot(), 0, depths );
+ return depths;
}
- /**
- * 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 );
+ private final static void calculateDepthsHelper( final PhylogenyNode n, int d, final Map<Long, Integer> depths ) {
+ depths.put( n.getId(), d );
+ ++d;
+ final List<PhylogenyNode> descs = n.getDescendants();
+ for( final PhylogenyNode desc : descs ) {
+ calculateDepthsHelper( desc, d, depths );
}
- 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() );
+ public final static void collapseToDepth( final Phylogeny phy, final int depth ) {
+ if ( phy.getNumberOfExternalNodes() < 3 ) {
+ return;
}
- node.getNodeData().getTaxonomy().setScientificName( scientific_name );
+ collapseToDepthHelper( phy.getRoot(), 0, depth );
}
- /**
- * 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() );
+ private final static void collapseToDepthHelper( final PhylogenyNode n, int d, final int depth ) {
+ if ( n.isExternal() ) {
+ n.setCollapse( false );
+ return;
}
- node.getNodeData().getTaxonomy().setTaxonomyCode( taxonomy_code );
- }
-
- /**
- * 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 number of external nodes removed from to_be_stripped
- */
- public static int 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 );
- }
- // ref_ext_taxo.add( getSpecies( 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 ( d >= depth ) {
+ n.setCollapse( true );
+ final PhylogenyNodeIterator it = new PreorderTreeIterator( n );
+ while ( it.hasNext() ) {
+ it.next().setCollapse( true );
}
}
- 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() ) ) ) {
- nodes_to_delete.add( n );
+ else {
+ n.setCollapse( false );
+ ++d;
+ final List<PhylogenyNode> descs = n.getDescendants();
+ for( final PhylogenyNode desc : descs ) {
+ collapseToDepthHelper( desc, d, depth );
}
}
- for( final PhylogenyNode phylogenyNode : nodes_to_delete ) {
- to_be_stripped.deleteSubtree( phylogenyNode, true );
+ }
+
+
+
+ public final static void collapseToRank( final Phylogeny phy, final int rank ) {
+ if ( phy.getNumberOfExternalNodes() < 3 ) {
+ return;
}
- to_be_stripped.clearHashIdToNodeMap();
- to_be_stripped.externalNodesHaveChanged();
- return nodes_to_delete.size();
+ if ( rank < 0 || rank >= TaxonomyUtil.RANKS.length ) {
+ throw new IllegalArgumentException( "Rank " + rank + " is out of range" );
+ }
+ collapseToRankHelper( phy.getRoot(), rank );
}
- /**
- * 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 ) {
+ private final static void collapseToRankHelper( final PhylogenyNode n, final int target_rank ) {
if ( n.isExternal() ) {
+ n.setCollapse( false );
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 );
+ if ( ( n.getNodeData().getTaxonomy() != null )
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() ) ) {
+ final String current_rank = n.getNodeData().getTaxonomy().getRank();
+ if ( !TaxonomyUtil.RANK_TO_INT.containsKey( current_rank ) ) {
+ System.out.println( "Don't know rank \"" + current_rank + "\", ignoring." );
}
- else if ( order_ext_alphabetically ) {
- boolean all_ext = true;
- for( final PhylogenyNode i : n.getDescendants() ) {
- if ( !i.isExternal() ) {
- all_ext = false;
- break;
+ else {
+ if ( TaxonomyUtil.RANK_TO_INT.get( current_rank ) >= target_rank ) {
+ n.setCollapse( true );
+
+ final PhylogenyNodeIterator it = new PreorderTreeIterator( n );
+ while ( it.hasNext() ) {
+ it.next().setCollapse( true );
}
+ return;
}
- if ( all_ext ) {
- PhylogenyMethods.sortNodeDescendents( n, pri );
- }
- }
- for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
- orderAppearance( n.getChildNode( i ), order, order_ext_alphabetically, pri );
}
}
+ n.setCollapse( false );
+ final List<PhylogenyNode> descs = n.getDescendants();
+ for( final PhylogenyNode desc : descs ) {
+ collapseToRankHelper( desc, target_rank );
+ }
}
-
- public static enum PhylogenyNodeField {
- CLADE_NAME,
- TAXONOMY_CODE,
- TAXONOMY_SCIENTIFIC_NAME,
- TAXONOMY_COMMON_NAME,
- SEQUENCE_SYMBOL,
- SEQUENCE_NAME,
- TAXONOMY_ID_UNIPROT_1,
- TAXONOMY_ID_UNIPROT_2,
- TAXONOMY_ID;
- }
-
- public static enum TAXONOMY_EXTRACTION {
- NO, YES, PFAM_STYLE_ONLY;
+
+ public final static PhylogenyNode getFirstExternalNode( final PhylogenyNode node ) {
+ PhylogenyNode n = node;
+ while ( n.isInternal() ) {
+ n = n.getFirstChildNode();
+ }
+ return n;
}
-
- public static enum DESCENDANT_SORT_PRIORITY {
- TAXONOMY, SEQUENCE, NODE_NAME;
+
+ public final static PhylogenyNode getLastExternalNode( final PhylogenyNode node ) {
+ PhylogenyNode n = node;
+ while ( n.isInternal() ) {
+ n = n.getLastChildNode();
+ }
+ return n;
}
+
}
git://source.jalview.org / jalview.git / blobdiff