inprogress

[jalview.git] / forester / java / src / org / forester / phylogeny / PhylogenyMethods.java

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
index 08fe7f0..a916d89 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -36,9 +36,9 @@ import java.util.HashMap;
 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.Pattern;
 
 import org.forester.io.parsers.PhylogenyParser;
 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
@@ -411,6 +411,26 @@ public class PhylogenyMethods {
         phy.externalNodesHaveChanged();
     }
 
+    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 );
+        }
+        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.getIndicator() != 0 ) {
+                continue;
+            }
+            l.add( divideIntoSubTreesHelper( n, min_distance_to_root ) );
+            if ( l.isEmpty() ) {
+                throw new RuntimeException( "this should not have happened" );
+            }
+        }
+        return l;
+    }
+
     public static List<PhylogenyNode> getAllDescendants( final PhylogenyNode node ) {
         final List<PhylogenyNode> descs = new ArrayList<PhylogenyNode>();
         final Set<Long> encountered = new HashSet<Long>();
@@ -711,9 +731,9 @@ public class PhylogenyMethods {
      * null is returned.
      * 
      */
-    public static SortedMap<Taxonomy, Integer> obtainDistinctTaxonomyCounts( final PhylogenyNode node ) {
+    public static Map<Taxonomy, Integer> obtainDistinctTaxonomyCounts( final PhylogenyNode node ) {
         final List<PhylogenyNode> descs = node.getAllExternalDescendants();
-        final SortedMap<Taxonomy, Integer> tax_map = new TreeMap<Taxonomy, Integer>();
+        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;
@@ -1142,6 +1162,12 @@ public class PhylogenyMethods {
         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). 
@@ -1633,6 +1659,20 @@ public class PhylogenyMethods {
         }
     }
 
+    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 l;
+    }
+
     /**
      * Calculates the distance between PhylogenyNodes n1 and n2.
      * PRECONDITION: n1 is a descendant of n2.
@@ -1670,23 +1710,33 @@ public class PhylogenyMethods {
             return my_s.indexOf( my_query ) >= 0;
         }
         else {
-            return my_s.equals( my_query );
+            return Pattern.compile( "(\\b|_)" + Pattern.quote( my_query ) + "(\\b|_)" ).matcher( my_s ).find();
         }
     }
 
+    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();
+        }
+        return prev;
+    }
+
     public static enum DESCENDANT_SORT_PRIORITY {
-        TAXONOMY, SEQUENCE, NODE_NAME;
+        NODE_NAME, SEQUENCE, TAXONOMY;
     }
 
     public static enum PhylogenyNodeField {
         CLADE_NAME,
+        SEQUENCE_NAME,
+        SEQUENCE_SYMBOL,
         TAXONOMY_CODE,
-        TAXONOMY_SCIENTIFIC_NAME,
         TAXONOMY_COMMON_NAME,
-        SEQUENCE_SYMBOL,
-        SEQUENCE_NAME,
+        TAXONOMY_ID,
         TAXONOMY_ID_UNIPROT_1,
         TAXONOMY_ID_UNIPROT_2,
-        TAXONOMY_ID;
+        TAXONOMY_SCIENTIFIC_NAME;
     }
 }