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

   1
   2 package org.forester.applications;
   3
   4 import java.io.File;
   5 import java.util.Set;
   6 import java.util.SortedSet;
   7 import java.util.TreeSet;
   8
   9 import org.forester.io.parsers.util.ParserUtils;
  10 import org.forester.phylogeny.Phylogeny;
  11 import org.forester.phylogeny.PhylogenyNode;
  12 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  13 import org.forester.util.ForesterUtil;
  14
  15 // javac -cp ~/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester/java/forester.jar
  16 // ~/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester_applications/src/org/forester/applications/domainloss_replacement.java
  17 // java -Xmx2048m -cp
  18 // /home/czmasek/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester_applications/src/:/home/czmasek/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester/java/forester.jar
  19 // org.forester.applications.domainloss_replacement
  20 public class domainloss_replacement {
  21
  22     public static void main( final String args[] ) {
  23         try {
  24             if ( args.length != 2 ) {
  25                 System.out
  26                 .println( "Usage: domainloss_replacement <phylogeny file> <file with replacement characters>" );
  27                 System.exit( -1 );
  28             }
  29             final Phylogeny p = ParserUtils.readPhylogenies( args[ 0 ] )[ 0 ];
  30             final Set<String> replacement_domains = ForesterUtil.file2set( new File( args[ 1 ] ) );
  31             for( final PhylogenyNodeIterator it = p.iteratorExternalForward(); it.hasNext(); ) {
  32                 PhylogenyNode n = it.next();
  33                 String name = null;
  34                 if ( n.getNodeData().isHasTaxonomy()
  35                         && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
  36                     name = n.getNodeData().getTaxonomy().getScientificName();
  37                 }
  38                 else {
  39                     name = n.getName();
  40                 }
  41                 final SortedSet<String> lost_chars = new TreeSet<String>();
  42                 while ( !n.isRoot() ) {
  43                     lost_chars.addAll( n.getNodeData().getBinaryCharacters().getLostCharacters() );
  44                     n = n.getParent();
  45                 }
  46                 final int losses = lost_chars.size();
  47                 lost_chars.retainAll( replacement_domains );
  48                 final int intersection = lost_chars.size();
  49                 final double percentage = ( 100.0 * intersection ) / losses;
  50                 System.out.println( name + "\t" + intersection + "\t" + losses + "\t"
  51                         + ForesterUtil.round( percentage, 3 ) );
  52             }
  53         }
  54         catch ( final Exception e ) {
  55             e.printStackTrace();
  56             System.exit( -1 );
  57         }
  58     }
  59 }