forester/java/src/org/forester/application/decoratorX.java

   1 // java -Xmx2048m -cp
   2 // ~/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester/java/forester.jar
   3 // org.forester.application.decorator2
   4 // RRMa_ALL_plus_RRMa_ee3_50_hmmalign_05_40_fme_with_seqs_2.phylo.xml
   5 // nature12311-s3_cz_4.txt x
   6
   7 package org.forester.application;
   8
   9 import java.io.File;
  10
  11 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
  12 import org.forester.io.writers.PhylogenyWriter;
  13 import org.forester.phylogeny.Phylogeny;
  14 import org.forester.phylogeny.PhylogenyNode;
  15 import org.forester.phylogeny.data.Annotation;
  16 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  17 import org.forester.phylogeny.factories.PhylogenyFactory;
  18 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  19 import org.forester.util.BasicTable;
  20 import org.forester.util.BasicTableParser;
  21 import org.forester.util.CommandLineArguments;
  22
  23 public class decoratorX {
  24
  25     private static final int SEQ_COLUMN    = 3;
  26     private static final int TARGET_COLUMN = 4;
  27
  28     public static void main( final String args[] ) {
  29         File intree = null;
  30         File outtree = null;
  31         File intable = null;
  32         try {
  33             CommandLineArguments cla = null;
  34             cla = new CommandLineArguments( args );
  35             intree = cla.getFile( 0 );
  36             intable = cla.getFile( 1 );
  37             outtree = cla.getFile( 2 );
  38             if ( outtree.exists() ) {
  39                 System.out.println( outtree + " already exists" );
  40                 System.exit( -1 );
  41             }
  42             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
  43             final PhyloXmlParser xml_parser = new PhyloXmlParser();
  44             final Phylogeny phy = factory.create( intree, xml_parser )[ 0 ];
  45             final BasicTable<String> t = BasicTableParser.parse( intable, '\t' );
  46             System.out.println( t.toString() );
  47             final PhylogenyNodeIterator it = phy.iteratorPostorder();
  48             int i = 0;
  49             while ( it.hasNext() ) {
  50                 final PhylogenyNode node = it.next();
  51                 if ( node.isExternal() ) {
  52                     processNode( node, t );
  53                 }
  54                 i++;
  55             }
  56             final PhylogenyWriter writer = new PhylogenyWriter();
  57             writer.toPhyloXML( outtree, phy, 0 );
  58         }
  59         catch ( final Exception e ) {
  60             System.out.println( e.getLocalizedMessage() );
  61             e.printStackTrace();
  62             System.exit( -1 );
  63         }
  64     }
  65
  66     private static void processNode( final PhylogenyNode node, BasicTable<String> t ) throws Exception {
  67         String node_seq = node.getNodeData().getSequence().getMolecularSequence().toUpperCase();
  68         boolean found = false;
  69         for( int col = 0; col < t.getNumberOfRows(); ++col ) {
  70             String table_seq = t.getValueAsString( SEQ_COLUMN, col ).toUpperCase();
  71             if ( table_seq.contains( node_seq ) ) {
  72                 if ( found ) {
  73                     throw new Exception( "Sequence from node " + node + " is not unique: " + node_seq );
  74                 }
  75                 found = true;
  76                 Annotation annotation = new Annotation( "target:" + t.getValueAsString( TARGET_COLUMN, col ) );
  77                 node.getNodeData().getSequence().addAnnotation( annotation );
  78                 System.out.println( node + "->" + annotation );
  79             }
  80         }
  81         // if ( !found ) {
  82         //     throw new Exception( "Sequence from node " + node + " not found: " + node_seq );
  83         // }
  84     }
  85 }