new option

diff --git a/forester/java/src/org/forester/application/strip.java b/forester/java/src/org/forester/application/phylostrip.java
similarity index 68%
rename from forester/java/src/org/forester/application/strip.java
rename to forester/java/src/org/forester/application/phylostrip.java
index 14aa69e..2981cd9 100644 (file)
--- a/forester/java/src/org/forester/application/strip.java
+++ b/forester/java/src/org/forester/application/phylostrip.java
@@ -27,26 +27,31 @@ package org.forester.application;
 
 import java.io.File;
 import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
 
 import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
 import org.forester.io.parsers.util.ParserUtils;
 import org.forester.io.writers.PhylogenyWriter;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.data.Taxonomy;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
 import org.forester.phylogeny.factories.PhylogenyFactory;
 
-public class strip {
+public class phylostrip {
 
     public static void main( final String args[] ) {
         if ( args.length < 4 ) {
             System.out.println( "\nstrip: Wrong number of arguments.\n" );
             System.out
-                    .println( "Usage: \"strip <infile> <outfile> <options> [name1] [name2] ... OR [phylogenyfile]\"\n" );
-            System.out.println( " Options: -k to keep listed nodes" );
-            System.out.println( "          -r to remove listed nodes" );
-            System.out.println( "          -kp to keep nodes found in [phylogenyfile]" );
-            System.out.println( "          -rp to remove nodes found in [phylogenyfile]\n" );
+                    .println( "Usage: \"phylostrip <in-tree> <out-tree> <options> [name1] [name2] ... OR [ref-tree]\"\n" );
+            System.out.println( " Options: -knn to keep listed nodes" );
+            System.out.println( "          -rnn to remove listed nodes" );
+            System.out.println( "          -knnp to keep nodes found in [ref-tree]" );
+            System.out.println( "          -rnnp to remove nodes found in [ref-tree]" );
+            System.out.println( "          -ktc to keep only nodes from listed taxonomy codes\n" );
             System.exit( -1 );
         }
         final File infile = new File( args[ 0 ] );
@@ -64,23 +69,27 @@ public class strip {
         }
         boolean keep = false;
         boolean from_p0 = false;
-        if ( options.trim().toLowerCase().equals( "-k" ) ) {
+        boolean ktc = false;
+        if ( options.trim().toLowerCase().equals( "-knn" ) ) {
             keep = true;
         }
-        else if ( options.trim().toLowerCase().equals( "-kp" ) ) {
+        else if ( options.trim().toLowerCase().equals( "-knnp" ) ) {
             keep = true;
             from_p0 = true;
         }
-        else if ( options.trim().toLowerCase().equals( "-rp" ) ) {
+        else if ( options.trim().toLowerCase().equals( "-rnnp" ) ) {
             from_p0 = true;
         }
-        else if ( !options.trim().toLowerCase().equals( "-r" ) ) {
+        else if ( options.trim().toLowerCase().equals( "-ktc" ) ) {
+            ktc = true;
+        }
+        else if ( !options.trim().toLowerCase().equals( "-rnn" ) ) {
             System.out.println( "\nUnknown option \"" + options + "\"\n" );
             System.exit( -1 );
         }
         String[] names = null;
         if ( from_p0 ) {
-            names = strip.readInNamesFromPhylogeny( args[ 3 ] );
+            names = phylostrip.readInNamesFromPhylogeny( args[ 3 ] );
         }
         else {
             names = new String[ args.length - 3 ];
@@ -88,7 +97,22 @@ public class strip {
                 names[ i ] = args[ i + 3 ];
             }
         }
-        if ( keep ) {
+        if ( ktc ) {
+            final List<Taxonomy> taxonomies_to_keep = new ArrayList<Taxonomy>();
+            for( final String n : names ) {
+                final Taxonomy t = new Taxonomy();
+                try {
+                    t.setTaxonomyCode( n );
+                }
+                catch ( final PhyloXmlDataFormatException e ) {
+                    System.out.println( e.getMessage() );
+                    System.exit( -1 );
+                }
+                taxonomies_to_keep.add( t );
+            }
+            PhylogenyMethods.deleteExternalNodesPositiveSelectionT( taxonomies_to_keep, p );
+        }
+        else if ( keep ) {
             PhylogenyMethods.deleteExternalNodesPositiveSelection( names, p );
         }
         else {
@@ -96,7 +120,7 @@ public class strip {
         }
         try {
             final PhylogenyWriter w = new PhylogenyWriter();
-            w.toPhyloXML( outfile, p, 1 );
+            w.toPhyloXML( outfile, p, 0 );
         }
         catch ( final IOException e ) {
             System.out.println( "\nFailure to write output [" + e.getMessage() + "]\n" );

diff --git a/forester/java/src/org/forester/archaeopteryx/simple_node_processor.java b/forester/java/src/org/forester/application/simple_node_processor.java
similarity index 99%
rename from forester/java/src/org/forester/archaeopteryx/simple_node_processor.java
rename to forester/java/src/org/forester/application/simple_node_processor.java
index 711cbd0..d1e0c11 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/simple_node_processor.java
+++ b/forester/java/src/org/forester/application/simple_node_processor.java
@@ -1,5 +1,5 @@
 
-package org.forester.archaeopteryx;
+package org.forester.application;
 
 import java.io.File;
 

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
index f14efd3..cc140e4 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -309,9 +309,8 @@ public class PhylogenyMethods {
         return nodes;
     }
 
-    public static void deleteExternalNodesNegativeSelection( final Set<Integer> to_delete, final Phylogeny phy ) {
-        phy.clearHashIdToNodeMap();
-        for( final Integer id : to_delete ) {
+    public static void deleteExternalNodesNegativeSelection( final Set<Long> to_delete, final Phylogeny phy ) {
+        for( final Long id : to_delete ) {
             phy.deleteSubtree( phy.getNode( id ), true );
         }
         phy.clearHashIdToNodeMap();
@@ -339,24 +338,6 @@ public class PhylogenyMethods {
         p.externalNodesHaveChanged();
     }
 
-    public static void deleteExternalNodesPositiveSelection( final Set<Taxonomy> species_to_keep, final Phylogeny phy ) {
-        //   final Set<Integer> to_delete = new HashSet<Integer>();
-        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();
@@ -379,6 +360,22 @@ public class PhylogenyMethods {
         return deleted;
     }
 
+    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" );
+            }
+        }
+        deleteExternalNodesNegativeSelection( to_delete, phy );
+    }
+
     final public static void deleteInternalNodesWithOnlyOneDescendent( final Phylogeny phy ) {
         final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
         for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {