From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Thu, 15 Sep 2011 23:07:20 +0000 (+0000)
Subject: new app
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=945e6d8e21440c458d2210ff0c0aeac49d78df6c;p=jalview.git

new app
---

diff --git a/forester/java/src/org/forester/application/get_subtree_specific_chars.java b/forester/java/src/org/forester/application/get_subtree_specific_chars.java
new file mode 100644
index 0000000..22bd780
--- /dev/null
+++ b/forester/java/src/org/forester/application/get_subtree_specific_chars.java
@@ -0,0 +1,126 @@
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2011 Christian M. Zmasek
+// Copyright (C) 2008-2011 Burnham Institute for Medical Research
+// All rights reserved
+//
+// This library is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License along with this library; if not, write to the Free Software
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+//
+// Contact: phylosoft @ gmail . com
+// WWW: www.phylosoft.org/forester
+
+package org.forester.application;
+
+import java.io.File;
+import java.util.List;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.util.ForesterUtil;
+
+public class get_subtree_specific_chars {
+
+    public static void main( final String args[] ) {
+        if ( args.length != 1 ) {
+            System.err.println();
+            System.err.println( "get_subtree_specific_chars: wrong number of arguments" );
+            System.err.println( "Usage: \"get_subtree_specific_chars <intree>" );
+            System.err.println();
+            System.exit( -1 );
+        }
+        final File infile = new File( args[ 0 ] );
+        Phylogeny phy = null;
+        try {
+            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+            phy = factory.create( infile, ForesterUtil.createParserDependingOnFileType( infile, true ) )[ 0 ];
+        }
+        catch ( final Exception e ) {
+            System.err.println( e + "\nCould not read " + infile + "\n" );
+            System.exit( -1 );
+        }
+        final SortedSet<Integer> all_external_ids = getAllExternalDescendantsNodeIds( phy.getRoot() );
+        final SortedSet<String> all_chars = getAllExternalPresentAndGainedCharacters( phy.getRoot() );
+        System.out.println( "Sum of all external characters" + all_chars.size() );
+        System.out.println();
+        for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {
+            final PhylogenyNode node = iter.next();
+            if ( !node.isRoot() ) {
+                System.out.println();
+                if ( node.getNodeData().isHasTaxonomy()
+                        && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) {
+                    System.out.print( node.getName() + " " + node.getNodeData().getTaxonomy().getScientificName() );
+                }
+                else {
+                    System.out.print( node.getName() );
+                }
+                System.out.println( ":" );
+                final SortedSet<Integer> external_ids = getAllExternalDescendantsNodeIds( node );
+                final SortedSet<Integer> not_external_ids = copy( all_external_ids );
+                not_external_ids.removeAll( external_ids );
+                final SortedSet<String> not_node_chars = new TreeSet<String>();
+                for( final Integer id : not_external_ids ) {
+                    not_node_chars.addAll( getAllExternalPresentAndGainedCharacters( phy.getNode( id ) ) );
+                }
+                final SortedSet<String> node_chars = getAllExternalPresentAndGainedCharacters( node );
+                final SortedSet<String> unique_chars = new TreeSet<String>();
+                for( final String node_char : node_chars ) {
+                    if ( !not_node_chars.contains( node_char ) ) {
+                        unique_chars.add( node_char );
+                    }
+                }
+                System.out.println( "\tSUM:\t" + unique_chars.size() );
+                int counter = 1;
+                for( final String unique_char : unique_chars ) {
+                    System.out.println( "\t" + counter + ":\t" + unique_char );
+                    ++counter;
+                }
+            }
+        }
+    }
+
+    private static SortedSet<Integer> copy( final SortedSet<Integer> set ) {
+        final SortedSet<Integer> copy = new TreeSet<Integer>();
+        for( final Integer i : set ) {
+            copy.add( i );
+        }
+        return copy;
+    }
+
+    private static SortedSet<Integer> getAllExternalDescendantsNodeIds( final PhylogenyNode node ) {
+        final SortedSet<Integer> ids = new TreeSet<Integer>();
+        final List<PhylogenyNode> descs = node.getAllExternalDescendants();
+        for( final PhylogenyNode desc : descs ) {
+            ids.add( desc.getId() );
+        }
+        return ids;
+    }
+
+    private static SortedSet<String> getAllExternalPresentAndGainedCharacters( final PhylogenyNode node ) {
+        final SortedSet<String> chars = new TreeSet<String>();
+        final List<PhylogenyNode> descs = node.getAllExternalDescendants();
+        for( final PhylogenyNode desc : descs ) {
+            chars.addAll( desc.getNodeData().getBinaryCharacters().getGainedCharacters() );
+            chars.addAll( desc.getNodeData().getBinaryCharacters().getPresentCharacters() );
+        }
+        return chars;
+    }
+}