inprogress

diff --git a/forester/java/src/org/forester/application/subtree_feature_count.java b/forester/java/src/org/forester/application/subtree_feature_count.java
deleted file mode 100644 (file)
index da23024..0000000
--- a/forester/java/src/org/forester/application/subtree_feature_count.java
+++ /dev/null
@@ -1,161 +0,0 @@
-
-package org.forester.application;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.SortedSet;
-
-import org.forester.io.parsers.phyloxml.PhyloXmlParser;
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.data.Accession;
-import org.forester.phylogeny.data.Sequence;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
-import org.forester.phylogeny.factories.PhylogenyFactory;
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
-import org.forester.util.CommandLineArguments;
-import org.forester.util.ForesterUtil;
-
-public class subtree_feature_count {
-
-    final static private String DEPTH_OPTION  = "d";
-    final static private String E_MAIL        = "phylosoft@gmail.com";
-    final static private String HELP_OPTION_1 = "help";
-    final static private String HELP_OPTION_2 = "h";
-    final static private String PRG_DATE      = "131120";
-    final static private String PRG_DESC      = "";
-    final static private String PRG_NAME      = "subtree_feature_count";
-    final static private String PRG_VERSION   = "0.90";
-    final static private String WWW           = "sites.google.com/site/cmzmasek/home/software/forester";
-
-    public static void main( final String args[] ) {
-        try {
-            final CommandLineArguments cla = new CommandLineArguments( args );
-            if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length < 2 ) ) {
-                printHelp();
-                System.exit( 0 );
-            }
-            final List<String> allowed_options = new ArrayList<String>();
-            allowed_options.add( DEPTH_OPTION );
-            final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
-            if ( dissallowed_options.length() > 0 ) {
-                ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
-            }
-            final double depth = cla.getOptionValueAsDouble( DEPTH_OPTION );
-            final File intree_file = cla.getFile( 0 );
-            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            final Phylogeny phy = factory.create( intree_file, PhyloXmlParser.createPhyloXmlParserXsdValidating() )[ 0 ];
-            execute( phy, depth );
-        }
-        catch ( final Exception e ) {
-            e.printStackTrace();
-            ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
-        }
-    }
-
-    private static StringBuilder analyzeSubtree( final PhylogenyNode n, final double depth ) {
-        final PhylogenyNode node = moveUp( n, depth );
-        final List<PhylogenyNode> ext_descs = node.getAllExternalDescendants();
-        for( final PhylogenyNode ext : ext_descs ) {
-            if ( ext.getIndicator() != 0 ) {
-                throw new RuntimeException( "this should not have happened" );
-            }
-            ext.setIndicator( ( byte ) 1 );
-        }
-        int xray = 0;
-        int nmr = 0;
-        int model = 0;
-        boolean is_first = true;
-        PhylogenyNode first_node = null;
-        PhylogenyNode last_node = null;
-        int c = 0;
-        for( final PhylogenyNode ext : ext_descs ) {
-            if ( is_first ) {
-                first_node = ext;
-                is_first = false;
-            }
-            last_node = ext;
-            ++c;
-            if ( ext.getNodeData().isHasSequence() ) {
-                final Sequence seq = ext.getNodeData().getSequence();
-                final SortedSet<Accession> xrefs = seq.getCrossReferences();
-                if ( !ForesterUtil.isEmpty( xrefs ) ) {
-                    for( final Accession xref : xrefs ) {
-                        if ( xref.getSource().equalsIgnoreCase( "pdb" ) ) {
-                            if ( xref.getComment().equalsIgnoreCase( "x-ray" )
-                                    || xref.getComment().equalsIgnoreCase( "xray" ) ) {
-                                ++xray;
-                            }
-                            if ( xref.getComment().equalsIgnoreCase( "nmr" ) ) {
-                                ++nmr;
-                            }
-                            if ( xref.getComment().equalsIgnoreCase( "model" ) ) {
-                                ++model;
-                            }
-                        }
-                    }
-                }
-            }
-        }
-        final StringBuilder sb = new StringBuilder();
-        sb.append( String.valueOf( c ) );
-        sb.append( "\t" );
-        sb.append( first_node.getName() );
-        sb.append( "\t" );
-        sb.append( last_node.getName() );
-        sb.append( "\t" );
-        sb.append( String.valueOf( xray ) );
-        sb.append( "\t" );
-        sb.append( String.valueOf( nmr ) );
-        sb.append( "\t" );
-        sb.append( String.valueOf( model ) );
-        return sb;
-    }
-
-    private static void execute( final Phylogeny phy, final double depth ) {
-        setAllIndicatorsToZero( phy );
-        for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
-            final PhylogenyNode n = it.next();
-            if ( n.getIndicator() != 0 ) {
-                continue;
-            }
-            final StringBuilder s = analyzeSubtree( n, depth );
-            System.out.println( s.toString() );
-        }
-    }
-
-    private static PhylogenyNode moveUp( final PhylogenyNode node, final double depth ) {
-        PhylogenyNode n = node;
-        PhylogenyNode prev = node;
-        while ( depth < n.calculateDistanceToRoot() ) {
-            prev = n;
-            n = n.getParent();
-        }
-        return prev;
-    }
-
-    private static void printHelp() {
-        ForesterUtil.printProgramInformation( PRG_NAME,
-                                              PRG_DESC,
-                                              PRG_VERSION,
-                                              PRG_DATE,
-                                              E_MAIL,
-                                              WWW,
-                                              ForesterUtil.getForesterLibraryInformation() );
-        System.out.println( "Usage:" );
-        System.out.println();
-        System.out.println( PRG_NAME + "" );
-        System.out.println();
-        System.out.println( " example: " );
-        System.out.println();
-        System.out.println();
-        System.out.println();
-    }
-
-    private static void setAllIndicatorsToZero( final Phylogeny phy ) {
-        for( final PhylogenyNodeIterator it = phy.iteratorPostorder(); it.hasNext(); ) {
-            it.next().setIndicator( ( byte ) 0 );
-        }
-    }
-}

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
index b644e9e..6086534 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -410,6 +410,26 @@ 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>();
@@ -1141,6 +1161,12 @@ 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). 
@@ -1632,6 +1658,20 @@ 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.
@@ -1673,19 +1713,29 @@ public class PhylogenyMethods {
         }
     }
 
+    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;
     }
 }