forester_applications/src/org/forester/applications/reinv_count.java

   1
   2 package org.forester.applications;
   3
   4 // $Id:
   5 // FORESTER -- software libraries and applications
   6 // for evolutionary biology research and applications.
   7 //
   8 // Copyright (C) 2008-2011 Christian M. Zmasek
   9 // Copyright (C) 2008-2011 Burnham Institute for Medical Research
  10 // All rights reserved
  11 //
  12 // This library is free software; you can redistribute it and/or
  13 // modify it under the terms of the GNU Lesser General Public
  14 // License as published by the Free Software Foundation; either
  15 // version 2.1 of the License, or (at your option) any later version.
  16 //
  17 // This library is distributed in the hope that it will be useful,
  18 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  19 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  20 // Lesser General Public License for more details.
  21 //
  22 // You should have received a copy of the GNU Lesser General Public
  23 // License along with this library; if not, write to the Free Software
  24 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  25 //
  26 // Contact: phylosoft @ gmail . com
  27 // WWW: www.phylosoft.org/forester
  28 // javac -cp ~/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester/java/forester.jar
  29 // ~/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester_applications/src/org/forester/applications/reinv_count.java
  30 // java -Xmx2048m -cp
  31 // /home/czmasek/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester_applications/src/:/home/czmasek/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester/java/forester.jar
  32 // org.forester.applications.reinv_count
  33 import java.io.File;
  34 import java.util.List;
  35 import java.util.SortedSet;
  36 import java.util.TreeSet;
  37
  38 import org.forester.phylogeny.Phylogeny;
  39 import org.forester.phylogeny.PhylogenyNode;
  40 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  41 import org.forester.phylogeny.factories.PhylogenyFactory;
  42 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  43
  44 public class reinv_count {
  45
  46     public static void main( final String args[] ) {
  47         if ( args.length != 2 ) {
  48             System.err.println();
  49             System.err.println( "reinv_count: wrong number of arguments" );
  50             System.err.println( "Usage: \"reinv_count <intree> <name>" );
  51             System.err.println();
  52             System.exit( -1 );
  53         }
  54         final File infile = new File( args[ 0 ] );
  55         final String node_name = args[ 1 ];
  56         Phylogeny phy = null;
  57         try {
  58             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
  59             phy = factory.create( infile, org.forester.io.parsers.util.ParserUtils
  60                                   .createParserDependingOnFileType( infile, true ) )[ 0 ];
  61         }
  62         catch ( final Exception e ) {
  63             System.err.println( e + "\nCould not read " + infile + "\n" );
  64             System.exit( -1 );
  65         }
  66         for( final PhylogenyNodeIterator ite = phy.iteratorExternalForward(); ite.hasNext(); ) {
  67             final PhylogenyNode target_node = ite.next();
  68             final SortedSet<String> target_dcs = getAllExternalPresentAndGainedCharacters( target_node );
  69             //System.out.println( "Target DCs:" + target_dcs.size() );
  70             int counter = 0;
  71             final SortedSet<String> reinv = new TreeSet<String>();
  72             for( final String target_dc : target_dcs ) {
  73                 int c = 0;
  74                 for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
  75                     final PhylogenyNode n = it.next();
  76                     final SortedSet<String> n_gained_dcs = n.getNodeData().getBinaryCharacters().getGainedCharacters();
  77                     if ( n_gained_dcs.contains( target_dc ) ) {
  78                         c++;
  79                     }
  80                 }
  81                 if ( c > 1 ) {
  82                     counter++;
  83                     reinv.add( target_dc );
  84                 }
  85             }
  86             // System.out.println();
  87             //System.out.println( "reinv:" + reinv );
  88             //System.out.println();
  89             // System.out.println( "Target DCs:" + target_dcs.size() );
  90             // System.out.println( "reinv size:" + reinv.size() );
  91             // System.out.println( ">1:" + counter );
  92             final double ratio = ( double ) counter / target_dcs.size();
  93             System.out.println( target_node.getName() + "\t" + counter + "/" + target_dcs.size() + "\t" + ratio );
  94         }
  95     }
  96
  97     private static SortedSet<String> getAllExternalPresentAndGainedCharacters( final PhylogenyNode node ) {
  98         final SortedSet<String> chars = new TreeSet<String>();
  99         final List<PhylogenyNode> descs = node.getAllExternalDescendants();
 100         for( final PhylogenyNode desc : descs ) {
 101             chars.addAll( desc.getNodeData().getBinaryCharacters().getGainedCharacters() );
 102             chars.addAll( desc.getNodeData().getBinaryCharacters().getPresentCharacters() );
 103         }
 104         return chars;
 105     }
 106 }