in progress

diff --git a/forester/java/src/org/forester/application/pfam_go.java b/forester/java/src/org/forester/application/pfam_go.java
index d63ca5f..07e22bb 100644 (file)
--- a/forester/java/src/org/forester/application/pfam_go.java
+++ b/forester/java/src/org/forester/application/pfam_go.java
@@ -29,9 +29,9 @@ import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.HashSet;
 import java.util.List;
-import java.util.Set;
 
 import org.forester.go.PfamToGoMapping;
 import org.forester.go.PfamToGoParser;
@@ -40,20 +40,28 @@ import org.forester.util.ForesterUtil;
 
 public class pfam_go {
 
-    final static private String HELP_OPTION_1 = "help";
-    final static private String HELP_OPTION_2 = "h";
-    final static private String PRG_NAME      = "pfam_go";
-    final static private String PRG_VERSION   = "1.00";
-    final static private String PRG_DATE      = "2010.02.02";
-    final static private String E_MAIL        = "czmasek@burnham.org";
-    final static private String WWW           = "www.phylosoft.org";
+    private static final String ALLOW_DUPLICATES_OPTION = "d";
+    final static private String HELP_OPTION_1           = "help";
+    final static private String HELP_OPTION_2           = "h";
+    final static private String PRG_NAME                = "pfam_go";
+    final static private String PRG_VERSION             = "1.10";
+    final static private String PRG_DATE                = "2011.06.26";
+    final static private String E_MAIL                  = "czmasek@burnham.org";
+    final static private String WWW                     = "www.phylosoft.org";
 
-    private static void doit( final File pfams_file, final List<PfamToGoMapping> mappings ) throws IOException {
+    private static void process( final File pfams_file, final List<PfamToGoMapping> mappings, boolean allow_duplicates )
+            throws IOException {
         final BufferedReader reader = ForesterUtil.obtainReader( pfams_file );
         String line = "";
         int found_count = 0;
         int not_found_count = 0;
-        final Set<String> encountered_domains = new HashSet<String>();
+        Collection<String> encountered_domains = null;
+        if ( allow_duplicates ) {
+            encountered_domains = new ArrayList<String>();
+        }
+        else {
+            encountered_domains = new HashSet<String>();
+        }
         while ( ( line = reader.readLine() ) != null ) {
             line = line.trim();
             if ( ForesterUtil.isEmpty( line ) || line.startsWith( "##" ) ) {
@@ -65,7 +73,7 @@ public class pfam_go {
                 System.out.println( line );
             }
             else {
-                if ( !encountered_domains.contains( line ) ) {
+                if ( allow_duplicates || !encountered_domains.contains( line ) ) {
                     encountered_domains.add( line );
                     boolean found = false;
                     for( final PfamToGoMapping mapping : mappings ) {
@@ -104,7 +112,8 @@ public class pfam_go {
             System.exit( 0 );
         }
         final List<String> allowed_options = new ArrayList<String>();
-        if ( cla.getNumberOfNames() != 2 ) {
+        allowed_options.add( ALLOW_DUPLICATES_OPTION );
+        if ( cla.getNumberOfNames() != 2 && cla.getNumberOfNames() != 3 ) {
             printHelp();
             System.exit( -1 );
         }
@@ -114,6 +123,10 @@ public class pfam_go {
         }
         final File pfam2go_file = cla.getFile( 0 );
         final File pfams_file = cla.getFile( 1 );
+        boolean allow_duplicates = false;
+        if ( cla.isOptionSet( ALLOW_DUPLICATES_OPTION ) ) {
+            allow_duplicates = true;
+        }
         final PfamToGoParser pfam2go_parser = new PfamToGoParser( pfam2go_file );
         List<PfamToGoMapping> mappings = null;
         try {
@@ -123,7 +136,7 @@ public class pfam_go {
             e.printStackTrace();
         }
         try {
-            doit( pfams_file, mappings );
+            process( pfams_file, mappings, allow_duplicates );
         }
         catch ( final IOException e ) {
             e.printStackTrace();
@@ -135,7 +148,8 @@ public class pfam_go {
         ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
         System.out.println( "Usage:" );
         System.out.println();
-        System.out.println( PRG_NAME + " <pfam2go file> <file with pfams>" );
+        System.out.println( PRG_NAME + " [-" + ALLOW_DUPLICATES_OPTION
+                + " to allow duplicates] <pfam2go file> <file with pfams>" );
         System.out.println();
         System.out.println();
     }

diff --git a/forester/java/src/org/forester/application/simple_node_processor.java b/forester/java/src/org/forester/application/simple_node_processor.java
index 3f713dc..ac60660 100644 (file)
--- a/forester/java/src/org/forester/application/simple_node_processor.java
+++ b/forester/java/src/org/forester/application/simple_node_processor.java
@@ -28,7 +28,6 @@ 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.factories.ParserBasedPhylogenyFactory;
@@ -64,8 +63,8 @@ public class simple_node_processor {
                 processNode( node, i );
                 i++;
             }
-            final PhylogenyWriter writer = new PhylogenyWriter();
-            writer.toPhyloXML( out, phylogeny_0, 0 );
+            //  final PhylogenyWriter writer = new PhylogenyWriter();
+            //  writer.toPhyloXML( out, phylogeny_0, 0 );
         }
         catch ( final Exception e ) {
             System.out.println( e.getLocalizedMessage() );
@@ -74,12 +73,19 @@ public class simple_node_processor {
         }
     }
 
+    //    private static void processNode( final PhylogenyNode node, final int i ) {
+    //        node.setDistanceToParent( PhylogenyNode.DISTANCE_DEFAULT );
+    //        if ( !node.isExternal() ) {
+    //            if ( ( node.getName() == null ) || node.getName().isEmpty() ) {
+    //                node.setName( BASE + i );
+    //            }
+    //        }
+    //    }
     private static void processNode( final PhylogenyNode node, final int i ) {
-        node.setDistanceToParent( PhylogenyNode.DISTANCE_DEFAULT );
-        if ( !node.isExternal() ) {
-            if ( ( node.getName() == null ) || node.getName().isEmpty() ) {
-                node.setName( BASE + i );
-            }
+        if ( node.isExternal() ) {
+            String c = "" + node.getNodeData().getBinaryCharacters().getPresentCount();
+            String s = node.getNodeData().getTaxonomy().getScientificName();
+            System.out.println( s + "\t" + c );
         }
     }
 }

diff --git a/forester/java/src/org/forester/go/etc/MetaOntologizer.java b/forester/java/src/org/forester/go/etc/MetaOntologizer.java
index 10ac1fd..21b8dc8 100644 (file)
--- a/forester/java/src/org/forester/go/etc/MetaOntologizer.java
+++ b/forester/java/src/org/forester/go/etc/MetaOntologizer.java
@@ -66,7 +66,10 @@ public class MetaOntologizer {
     final static private String       PRG_NAME                         = "meta_ontologizer";
     private static final boolean      VERBOSE                          = true;
     //table-a_41_dollo_all_gains_d-Topology-Elim-Bonferroni.txt:
-    private final static Pattern      PATTERN_ONTOLOGIZER_TABLE_OUTPUT = Pattern.compile( ".*table-(.+)_dollo_.*",
+    //TODO change back
+    // private final static Pattern      PATTERN_ONTOLOGIZER_TABLE_OUTPUT = Pattern.compile( ".*table-(.+)_dollo_.*",
+    //                                                                                      Pattern.CASE_INSENSITIVE ); //TODO this might need some work...
+    private final static Pattern      PATTERN_ONTOLOGIZER_TABLE_OUTPUT = Pattern.compile( ".*table-(.+)\\.txt",
                                                                                           Pattern.CASE_INSENSITIVE ); //TODO this might need some work...
 
     private static boolean hasResultsForSpecies( final Map<GoId, GoTerm> go_id_to_terms,
@@ -146,6 +149,9 @@ public class MetaOntologizer {
                 else if ( line.startsWith( "#" ) ) {
                     current_species = new BasicSpecies( line.substring( 1 ) );
                     speciesto_to_domain_id.put( current_species, new TreeSet<DomainId>() );
+                    if ( VERBOSE ) {
+                        ForesterUtil.programMessage( PRG_NAME, "saw " + current_species );
+                    }
                 }
                 else {
                     if ( current_species == null ) {

diff --git a/forester/java/src/org/forester/phylogeny/data/NodeVisualization.java b/forester/java/src/org/forester/phylogeny/data/NodeVisualization.java
index 7b51574..5375526 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/data/NodeVisualization.java
+++ b/forester/java/src/org/forester/phylogeny/data/NodeVisualization.java
@@ -28,40 +28,36 @@ package org.forester.phylogeny.data;
 import java.awt.Color;
 import java.io.IOException;
 import java.io.Writer;
+import java.util.ArrayList;
+import java.util.List;
 
-public class NodeVisualization implements PhylogenyData {
+import org.forester.phylogeny.data.Property.AppliesTo;
 
-    public enum NodeFill {
-        NONE, GRADIENT, SOLID
-    }
+public class NodeVisualization implements PhylogenyData {
 
-    public enum NodeShape {
-        CIRCLE, RECTANGLE
-    }
     private NodeShape _shape;
     private NodeFill  _fill_type;
     private Color     _border_color;
     private Color     _fill_color;
     private double    _size;
+    private double    _transparancy;
 
     public NodeVisualization() {
-        _shape = NodeShape.CIRCLE;
-        _fill_type = NodeFill.SOLID;
-        _border_color = null;
-        _fill_color = null;
-        _size = 0;
+        init();
     }
 
     public NodeVisualization( final NodeShape shape,
                               final NodeFill fill_type,
                               final Color border_color,
                               final Color fill_color,
-                              final double size ) {
-        _shape = shape;
-        _fill_type = fill_type;
-        _border_color = border_color;
-        _fill_color = fill_color;
-        _size = size;
+                              final double size,
+                              final double transparancy ) {
+        setShape( shape );
+        setFillType( fill_type );
+        setBorderColor( border_color );
+        setFillColor( fill_color );
+        setSize( size );
+        setTransparancy( transparancy );
     }
 
     @Override
@@ -83,7 +79,8 @@ public class NodeVisualization implements PhylogenyData {
                                               .getGreen(), getBorderColor().getBlue() ) : null,
                                       getFillColor() != null ? new Color( getFillColor().getRed(), getFillColor()
                                               .getGreen(), getFillColor().getBlue() ) : null,
-                                      getSize() );
+                                      getSize(),
+                                      getTransparancy() );
     }
 
     public Color getBorderColor() {
@@ -106,6 +103,19 @@ public class NodeVisualization implements PhylogenyData {
         return _size;
     }
 
+    public double getTransparancy() {
+        return _transparancy;
+    }
+
+    private void init() {
+        setShape( NodeShape.CIRCLE );
+        setFillType( NodeFill.SOLID );
+        setBorderColor( null );
+        setFillColor( null );
+        setSize( 0 );
+        setTransparancy( 1 );
+    }
+
     @Override
     public boolean isEqual( final PhylogenyData data ) {
         throw new UnsupportedOperationException();
@@ -131,6 +141,10 @@ public class NodeVisualization implements PhylogenyData {
         _size = size;
     }
 
+    public void setTransparancy( final double transparancy ) {
+        _transparancy = transparancy;
+    }
+
     @Override
     public StringBuffer toNHX() {
         throw new UnsupportedOperationException();
@@ -145,4 +159,25 @@ public class NodeVisualization implements PhylogenyData {
     public String toString() {
         return asText().toString();
     }
+
+    public enum NodeFill {
+        NONE, GRADIENT, SOLID
+    }
+
+    public enum NodeShape {
+        CIRCLE, RECTANGLE
+    }
+
+    private List<Property> toProperties() {
+        final List<Property> properties = new ArrayList<Property>();
+        properties.add( new Property( SIZE_REF, String.valueOf( getSize() ), "", SIZE_TYPE, AppliesTo.NODE ) );
+        properties.add( new Property( SIZE_REF, String.valueOf( getShape() ), "", SIZE_TYPE, AppliesTo.NODE ) );
+        properties.add( new Property( SIZE_REF, String.valueOf( getFillType() ), "", SIZE_TYPE, AppliesTo.NODE ) );
+        properties.add( new Property( SIZE_REF, String.valueOf( getTransparancy() ), "", SIZE_TYPE, AppliesTo.NODE ) );
+        properties.add( new Property( SIZE_REF, String.valueOf( getFillColor() ), "", SIZE_TYPE, AppliesTo.NODE ) );
+        properties.add( new Property( SIZE_REF, String.valueOf( getBorderColor() ), "", SIZE_TYPE, AppliesTo.NODE ) );
+        return properties;
+    }
+    public static final String SIZE_REF  = "aptx_visualiation:node_sise";
+    public static final String SIZE_TYPE = "xsd:decimal";
 }