// java -Xmx2048m -cp
// ~/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester/java/forester.jar
-// org.forester.application.decorator2
+// org.forester.application.decoratorX
// RRMa_ALL_plus_RRMa_ee3_50_hmmalign_05_40_fme_with_seqs_2.phylo.xml
-// nature12311-s3_cz_4.txt x
+// nature12311-s3_cz_4.txt x1 x2
package org.forester.application;
public class decoratorX {
- private static final int SEQ_COLUMN = 3;
- private static final int TARGET_COLUMN = 4;
+ private static final int SEQ_NAME_COLUMN = 1;
+ private static final int SPECIES_COLUMN = 2;
+ private static final int SEQ_COLUMN = 3;
+ private static final int TARGET_COLUMN = 4;
public static void main( final String args[] ) {
File intree = null;
- File outtree = null;
+ File outtree1 = null;
+ File outtree2 = null;
File intable = null;
try {
CommandLineArguments cla = null;
cla = new CommandLineArguments( args );
intree = cla.getFile( 0 );
intable = cla.getFile( 1 );
- outtree = cla.getFile( 2 );
- if ( outtree.exists() ) {
- System.out.println( outtree + " already exists" );
+ outtree1 = cla.getFile( 2 );
+ outtree2 = cla.getFile( 3 );
+ if ( outtree1.exists() ) {
+ System.out.println( outtree1 + " already exists" );
+ System.exit( -1 );
+ }
+ if ( outtree2.exists() ) {
+ System.out.println( outtree2 + " already exists" );
System.exit( -1 );
}
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final PhyloXmlParser xml_parser = new PhyloXmlParser();
+ final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
final Phylogeny phy = factory.create( intree, xml_parser )[ 0 ];
final BasicTable<String> t = BasicTableParser.parse( intable, '\t' );
- System.out.println( t.toString() );
- final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ final PhylogenyNodeIterator it = phy.iteratorExternalForward();
int i = 0;
while ( it.hasNext() ) {
final PhylogenyNode node = it.next();
- if ( node.isExternal() ) {
- processNode( node, t );
- }
+ processNode( node, t );
i++;
}
- final PhylogenyWriter writer = new PhylogenyWriter();
- writer.toPhyloXML( outtree, phy, 0 );
+ final PhylogenyWriter writer1 = new PhylogenyWriter();
+ writer1.toPhyloXML( outtree1, phy, 0 );
+ final PhylogenyNodeIterator it2 = phy.iteratorExternalForward();
+ while ( it2.hasNext() ) {
+ final PhylogenyNode node = it2.next();
+ processNode2( node, phy );
+ }
+ final PhylogenyWriter writer2 = new PhylogenyWriter();
+ writer2.toPhyloXML( outtree2, phy, 0 );
}
catch ( final Exception e ) {
System.out.println( e.getLocalizedMessage() );
- e.printStackTrace();
System.exit( -1 );
}
}
- private static void processNode( final PhylogenyNode node, BasicTable<String> t ) throws Exception {
- String node_seq = node.getNodeData().getSequence().getMolecularSequence().toUpperCase();
+ private static void processNode( final PhylogenyNode node, final BasicTable<String> t ) throws Exception {
+ final String node_seq = node.getNodeData().getSequence().getMolecularSequence().toUpperCase();
boolean found = false;
- for( int col = 0; col < t.getNumberOfRows(); ++col ) {
- String table_seq = t.getValueAsString( SEQ_COLUMN, col ).toUpperCase();
+ String found_row = "";
+ String found_protein_name = "";
+ String found_species = "";
+ for( int row = 0; row < t.getNumberOfRows(); ++row ) {
+ final String table_seq = t.getValueAsString( SEQ_COLUMN, row ).toUpperCase();
if ( table_seq.contains( node_seq ) ) {
if ( found ) {
- throw new Exception( "Sequence from node " + node + " is not unique: " + node_seq );
+ if ( !found_protein_name.equals( t.getValueAsString( SEQ_NAME_COLUMN, row ) )
+ || !found_species.equals( t.getValueAsString( SPECIES_COLUMN, row ) ) ) {
+ throw new Exception( "Sequence from node " + node + " is not unique: " + node_seq + "\n"
+ + "Already found in row " + found_row );
+ }
}
- found = true;
- Annotation annotation = new Annotation( "target:" + t.getValueAsString( TARGET_COLUMN, col ) );
+ else {
+ found = true;
+ found_row = t.getRowAsString( row, ", " );
+ found_protein_name = t.getValueAsString( SEQ_NAME_COLUMN, row );
+ found_species = t.getValueAsString( SPECIES_COLUMN, row );
+ }
+ final Annotation annotation = new Annotation( "target", t.getValueAsString( TARGET_COLUMN, row ) );
node.getNodeData().getSequence().addAnnotation( annotation );
System.out.println( node + "->" + annotation );
}
}
- // if ( !found ) {
- // throw new Exception( "Sequence from node " + node + " not found: " + node_seq );
- // }
+ }
+
+ private static void processNode2( final PhylogenyNode node, final Phylogeny t ) {
+ if ( ( node.getNodeData().getSequence().getAnnotations() == null )
+ || node.getNodeData().getSequence().getAnnotations().isEmpty() ) {
+ t.deleteSubtree( node, true );
+ }
}
}