From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Fri, 20 Sep 2013 23:32:37 +0000 (+0000)
Subject: inprogress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=99a50fc42cd1e9b4e799dbd0696c5a8066f2fd77;p=jalview.git

inprogress
---

diff --git a/forester/java/src/org/forester/application/decorator2.java b/forester/java/src/org/forester/application/decorator2.java
new file mode 100644
index 0000000..fbbf41c
--- /dev/null
+++ b/forester/java/src/org/forester/application/decorator2.java
@@ -0,0 +1,85 @@
+// java -Xmx2048m -cp
+// ~/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester/java/forester.jar
+// org.forester.application.decorator2
+// RRMa_ALL_plus_RRMa_ee3_50_hmmalign_05_40_fme_with_seqs_2.phylo.xml
+// nature12311-s3_cz_4.txt x
+
+package org.forester.application;
+
+import java.io.File;
+
+import org.forester.io.parsers.phyloxml.PhyloXmlParser;
+import org.forester.io.writers.PhylogenyWriter;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Annotation;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.util.BasicTable;
+import org.forester.util.BasicTableParser;
+import org.forester.util.CommandLineArguments;
+
+public class decorator2 {
+
+    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 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" );
+                System.exit( -1 );
+            }
+            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+            final PhyloXmlParser xml_parser = new PhyloXmlParser();
+            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();
+            int i = 0;
+            while ( it.hasNext() ) {
+                final PhylogenyNode node = it.next();
+                if ( node.isExternal() ) {
+                    processNode( node, t );
+                }
+                i++;
+            }
+            final PhylogenyWriter writer = new PhylogenyWriter();
+            writer.toPhyloXML( outtree, 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();
+        boolean found = false;
+        for( int col = 0; col < t.getNumberOfRows(); ++col ) {
+            String table_seq = t.getValueAsString( SEQ_COLUMN, col ).toUpperCase();
+            if ( table_seq.contains( node_seq ) ) {
+                if ( found ) {
+                    throw new Exception( "Sequence from node " + node + " is not unique: " + node_seq );
+                }
+                found = true;
+                Annotation annotation = new Annotation( "target:" + t.getValueAsString( TARGET_COLUMN, col ) );
+                node.getNodeData().getSequence().addAnnotation( annotation );
+                System.out.println( node + "->" + annotation );
+            }
+        }
+        // if ( !found ) {
+        //     throw new Exception( "Sequence from node " + node + " not found: " + node_seq );
+        // }
+    }
+}