improving GSDI, under construction...

diff --git a/forester/java/src/org/forester/application/gsdi.java b/forester/java/src/org/forester/application/gsdi.java
index 3df2a74..de949a8 100644 (file)
--- a/forester/java/src/org/forester/application/gsdi.java
+++ b/forester/java/src/org/forester/application/gsdi.java
@@ -27,7 +27,6 @@ package org.forester.application;
 
 import java.io.File;
 import java.io.IOException;
-import java.io.Writer;
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
 import java.util.Date;
@@ -49,6 +48,7 @@ import org.forester.sdi.SDI.TaxonomyComparisonBase;
 import org.forester.sdi.SDIse;
 import org.forester.sdi.SdiException;
 import org.forester.util.CommandLineArguments;
+import org.forester.util.EasyWriter;
 import org.forester.util.ForesterConstants;
 import org.forester.util.ForesterUtil;
 
@@ -58,15 +58,15 @@ public final class gsdi {
         GSDI, SDI
     }
     final static public boolean REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE     = true;
-    final static private String STRIP_OPTION                               = "s";
     final static private String ALLOW_STRIPPING_OF_GENE_TREE_OPTION        = "g";
     final static private String SDI_OPTION                                 = "b";
     final static private String MOST_PARSIMONIOUS_OPTION                   = "m";
     final static private String GUESS_FORMAT_OF_SPECIES_TREE               = "q";
     final static private String HELP_OPTION_1                              = "help";
     final static private String HELP_OPTION_2                              = "h";
-    final static private String DEFAULT_OUTFILE_SUFFIX                     = "_gsdi_out.phylo.xml";
+    final static private String DEFAULT_OUTFILE_SUFFIX                     = "_gsdi_out.xml";
     final static private String SUFFIX_FOR_LIST_OF_STIPPED_GENE_TREE_NODES = "_stripped_gene_tree_nodes.txt";
+    final static private String SUFFIX_FOR_SPECIES_TREE_USED               = "_species_tree_used.xml";
     final static private String LOGFILE_SUFFIX                             = "_gsdi_log.txt";
     final static private String PRG_NAME                                   = "gsdi";
     final static private String PRG_VERSION                                = "0.901";
@@ -104,7 +104,6 @@ public final class gsdi {
                 System.exit( -1 );
             }
             final List<String> allowed_options = new ArrayList<String>();
-            allowed_options.add( gsdi.STRIP_OPTION );
             allowed_options.add( gsdi.SDI_OPTION );
             allowed_options.add( gsdi.GUESS_FORMAT_OF_SPECIES_TREE );
             allowed_options.add( gsdi.MOST_PARSIMONIOUS_OPTION );
@@ -122,13 +121,9 @@ public final class gsdi {
 
     private static void execute( final CommandLineArguments cla ) throws IOException {
         BASE_ALGORITHM base_algorithm = BASE_ALGORITHM.GSDI;
-        boolean strip_species_tree = false;
         boolean most_parsimonous_duplication_model = false;
         boolean species_tree_in_phyloxml = true;
         boolean allow_stripping_of_gene_tree = false;
-        if ( cla.isOptionSet( gsdi.STRIP_OPTION ) ) {
-            strip_species_tree = true;
-        }
         if ( cla.isOptionSet( gsdi.SDI_OPTION ) ) {
             base_algorithm = BASE_ALGORITHM.SDI;
         }
@@ -153,7 +148,7 @@ public final class gsdi {
         File species_tree_file = null;
         File out_file = null;
         File log_file = null;
-        Writer log_writer = null;
+        EasyWriter log_writer = null;
         try {
             gene_tree_file = cla.getFile( 0 );
             species_tree_file = cla.getFile( 1 );
@@ -181,7 +176,7 @@ public final class gsdi {
             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( log_file ) );
         }
         try {
-            log_writer = ForesterUtil.createBufferedWriter( log_file );
+            log_writer = ForesterUtil.createEasyWriter( log_file );
         }
         catch ( final IOException e ) {
             ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to create [" + log_file + "]: " + e.getMessage() );
@@ -232,15 +227,13 @@ public final class gsdi {
         gene_tree.setRooted( true );
         species_tree.setRooted( true );
         if ( !gene_tree.isCompletelyBinary() ) {
-            log_writer.write( "User Error: gene tree is not completely binary" );
-            log_writer.write( ForesterUtil.LINE_SEPARATOR );
+            log_writer.println( "User Error: gene tree is not completely binary" );
             log_writer.close();
             ForesterUtil.fatalError( gsdi.PRG_NAME, "gene tree is not completely binary" );
         }
         if ( base_algorithm != BASE_ALGORITHM.GSDI ) {
             if ( !species_tree.isCompletelyBinary() ) {
-                log_writer.write( "User Error: species tree is not completely binary, use GSDI instead" );
-                log_writer.write( ForesterUtil.LINE_SEPARATOR );
+                log_writer.println( "User Error: species tree is not completely binary, use GSDI instead" );
                 log_writer.close();
                 ForesterUtil.fatalError( gsdi.PRG_NAME, "species tree is not completely binary, use GSDI instead" );
             }
@@ -257,31 +250,18 @@ public final class gsdi {
         // Helper.randomizeSpecies( 1, 8192, gene_tree );
         // Helper.intervalNumberSpecies( gene_tree, 4096 );
         // Helper.numberSpeciesInDescOrder( gene_tree );
-        log_writer.write( PRG_NAME + " - " + PRG_DESC );
-        log_writer.write( ForesterUtil.LINE_SEPARATOR );
-        log_writer.write( "  version         : " + PRG_VERSION );
-        log_writer.write( ForesterUtil.LINE_SEPARATOR );
-        log_writer.write( "  date            : " + PRG_DATE );
-        log_writer.write( ForesterUtil.LINE_SEPARATOR );
-        log_writer.write( "  forester version: " + ForesterConstants.FORESTER_VERSION );
-        log_writer.write( ForesterUtil.LINE_SEPARATOR );
-        log_writer.write( ForesterUtil.LINE_SEPARATOR );
-        log_writer.write( "Start time: " + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
-        log_writer.write( ForesterUtil.LINE_SEPARATOR );
-        log_writer.write( "Gene tree file: " + gene_tree_file.getCanonicalPath() );
-        log_writer.write( ForesterUtil.LINE_SEPARATOR );
-        log_writer.write( "Gene tree name: "
+        log_writer.println( PRG_NAME + " - " + PRG_DESC );
+        log_writer.println( "  version         : " + PRG_VERSION );
+        log_writer.println( "  date            : " + PRG_DATE );
+        log_writer.println( "  forester version: " + ForesterConstants.FORESTER_VERSION );
+        log_writer.println( "Start time: " + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
+        log_writer.println( "Gene tree file: " + gene_tree_file.getCanonicalPath() );
+        log_writer.println( "Gene tree name: "
                 + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
-        log_writer.write( ForesterUtil.LINE_SEPARATOR );
-        log_writer.write( "Species tree file: " + species_tree_file.getCanonicalPath() );
-        log_writer.write( ForesterUtil.LINE_SEPARATOR );
-        log_writer.write( "Species tree name: "
+        log_writer.println( "Species tree file: " + species_tree_file.getCanonicalPath() );
+        log_writer.println( "Species tree name: "
                 + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) );
-        log_writer.write( ForesterUtil.LINE_SEPARATOR );
         System.out.println();
-        System.out.println( "Strip species tree: " + strip_species_tree );
-        log_writer.write( "Strip species tree: " + strip_species_tree );
-        log_writer.write( ForesterUtil.LINE_SEPARATOR );
         SDI sdi = null;
         final long start_time = new Date().getTime();
         try {
@@ -289,49 +269,42 @@ public final class gsdi {
                 System.out.println();
                 System.out.println( "Use most parsimonous duplication model: " + most_parsimonous_duplication_model );
                 System.out.println( "Allow stripping of gene tree nodes    : " + allow_stripping_of_gene_tree );
-                log_writer.write( "Use most parsimonous duplication model: " + most_parsimonous_duplication_model );
-                log_writer.write( ForesterUtil.LINE_SEPARATOR );
+                log_writer.println( "Use most parsimonous duplication model: " + most_parsimonous_duplication_model );
                 log_writer.write( "Allow stripping of gene tree nodes    : " + allow_stripping_of_gene_tree );
-                log_writer.write( ForesterUtil.LINE_SEPARATOR );
                 log_writer.flush();
                 sdi = new GSDI( gene_tree,
                                 species_tree,
                                 most_parsimonous_duplication_model,
                                 allow_stripping_of_gene_tree,
-                                strip_species_tree );
+                                true );
             }
             else {
                 System.out.println();
                 System.out.println( "Using SDIse algorithm" );
-                log_writer.write( "Using SDIse algorithm" );
-                log_writer.write( ForesterUtil.LINE_SEPARATOR );
+                log_writer.println( "Using SDIse algorithm" );
                 log_writer.flush();
                 sdi = new SDIse( gene_tree, species_tree );
             }
         }
         catch ( final SdiException e ) {
-            log_writer.write( "User Error: " + e.getLocalizedMessage() );
-            log_writer.write( ForesterUtil.LINE_SEPARATOR );
+            log_writer.println( "User Error: " + e.getLocalizedMessage() );
             log_writer.close();
             ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
         }
         catch ( final IOException e ) {
-            log_writer.write( "Error: " + e );
-            log_writer.write( ForesterUtil.LINE_SEPARATOR );
+            log_writer.println( "Error: " + e );
             log_writer.close();
             ForesterUtil.fatalError( PRG_NAME, e.toString() );
         }
         catch ( final Exception e ) {
-            log_writer.write( "Error: " + e );
-            log_writer.write( ForesterUtil.LINE_SEPARATOR );
+            log_writer.println( "Error: " + e );
             log_writer.close();
             e.printStackTrace();
             System.exit( -1 );
         }
         System.out.println();
         System.out.println( "Running time (excluding I/O): " + ( new Date().getTime() - start_time ) + "ms" );
-        log_writer.write( "Running time (excluding I/O): " + ( new Date().getTime() - start_time ) + "ms" );
-        log_writer.write( ForesterUtil.LINE_SEPARATOR );
+        log_writer.println( "Running time (excluding I/O): " + ( new Date().getTime() - start_time ) + "ms" );
         try {
             final PhylogenyWriter writer = new PhylogenyWriter();
             writer.toPhyloXML( out_file, gene_tree, 0 );
@@ -340,31 +313,39 @@ public final class gsdi {
             ForesterUtil.fatalError( PRG_NAME, "Failed to write to [" + out_file + "]: " + e.getMessage() );
         }
         System.out.println();
-        System.out.println( "Successfully wrote resulting gene tree to: " + out_file );
+        System.out.println( "Wrote resulting gene tree to: " + out_file );
         System.out.println();
-        log_writer.write( "Wrote resulting gene tree to: " + out_file );
-        log_writer.write( ForesterUtil.LINE_SEPARATOR );
+        log_writer.println( "Wrote resulting gene tree to: " + out_file );
         if ( base_algorithm == BASE_ALGORITHM.SDI ) {
             sdi.computeMappingCostL();
             System.out.println( "Mapping cost                    : " + sdi.computeMappingCostL() );
-            log_writer.write( "Mapping cost                    : " + sdi.computeMappingCostL() );
-            log_writer.write( ForesterUtil.LINE_SEPARATOR );
+            log_writer.println( "Mapping cost                    : " + sdi.computeMappingCostL() );
         }
         System.out.println( "Number of duplications          : " + sdi.getDuplicationsSum() );
-        log_writer.write( "Number of duplications          : " + sdi.getDuplicationsSum() );
-        log_writer.write( ForesterUtil.LINE_SEPARATOR );
+        log_writer.println( "Number of duplications          : " + sdi.getDuplicationsSum() );
         if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
             final GSDI gsdi = ( GSDI ) sdi;
+            File species_tree_used_file = new File( out_file + SUFFIX_FOR_SPECIES_TREE_USED );
+            try {
+                final PhylogenyWriter writer = new PhylogenyWriter();
+                writer.toPhyloXML( species_tree_used_file, gsdi.getSpeciesTree(), 0 );
+            }
+            catch ( final IOException e ) {
+                ForesterUtil.fatalError( PRG_NAME,
+                                         "Failed to write to [" + species_tree_used_file + "]: " + e.getMessage() );
+            }
+            System.out.println();
+            System.out.println( "Wrote used species tree to: " + species_tree_used_file );
+            System.out.println();
+            log_writer.println( "Wrote used species tree to: " + species_tree_used_file );
             if ( !most_parsimonous_duplication_model ) {
                 final int duplications = gsdi.getSpeciationOrDuplicationEventsSum();
                 System.out.println( "Number of potential duplications: " + duplications );
-                log_writer.write( "Number of potential duplications: " + duplications );
-                log_writer.write( ForesterUtil.LINE_SEPARATOR );
+                log_writer.println( "Number of potential duplications: " + duplications );
             }
             final int spec = gsdi.getSpeciationsSum();
             System.out.println( "Number of speciations            : " + spec );
-            log_writer.write( "Number of speciations            : " + spec );
-            log_writer.write( ForesterUtil.LINE_SEPARATOR );
+            log_writer.println( "Number of speciations            : " + spec );
             for( PhylogenyNode n : gsdi.getMappedExternalSpeciesTreeNodes() ) {
                 System.out.println( n.toString() );
             }
@@ -390,8 +371,6 @@ public final class gsdi {
         System.out.println();
         System.out.println( "Options:" );
         //    System.out.println( " -" + gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION + ": to allow stripping of gene tree nodes without a matching species in the species tree (writes list of stripped nodes to " + );
-        System.out.println( " -" + gsdi.STRIP_OPTION
-                + ": to strip the species tree of unneeded species prior to duplication inference" );
         System.out.println( " -" + gsdi.SDI_OPTION + ": to use SDI algorithm instead of GSDI algorithm" );//TODO gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION not allowed
         System.out.println( " -" + gsdi.MOST_PARSIMONIOUS_OPTION
                 + ": use most parimonious duplication model for GSDI: " );

diff --git a/forester/java/src/org/forester/phylogeny/Phylogeny.java b/forester/java/src/org/forester/phylogeny/Phylogeny.java
index 44851b2..42470ba 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/Phylogeny.java
+++ b/forester/java/src/org/forester/phylogeny/Phylogeny.java
@@ -268,7 +268,7 @@ public class Phylogeny {
                 }
             }
         }
-        remove_us.reset();
+        remove_us.removeConnections();
         setIdHash( null );
         externalNodesHaveChanged();
     }

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
index 8dedcd2..033eceb 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
@@ -70,12 +70,10 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
         setSumExtNodes( 1 ); // For ext node, this number is 1 (not 0!!)
     }
 
-    public void reset() {
+    public void removeConnections() {
         _parent = null;
         _link = null;
         _descendants = null;
-        _node_data = null;
-        _branch_data = null;
     }
 
     /**
@@ -173,6 +171,7 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
      * 
      */
     final public boolean equals( final Object o ) {
+        System.out.print( " PN___e___ " );
         if ( this == o ) {
             return true;
         }
@@ -195,12 +194,12 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
                 return ( this_data.getTaxonomy().isEqual( other_data.getTaxonomy() ) && this_data.getSequence()
                         .isEqual( other_data.getSequence() ) );
             }
-            else if ( this_data.isHasSequence() && other_data.isHasSequence() ) {
-                return ( this_data.getSequence().isEqual( other_data.getSequence() ) );
-            }
             else if ( this_data.isHasTaxonomy() && other_data.isHasTaxonomy() ) {
                 return ( this_data.getTaxonomy().isEqual( other_data.getTaxonomy() ) );
             }
+            else if ( this_data.isHasSequence() && other_data.isHasSequence() ) {
+                return ( this_data.getSequence().isEqual( other_data.getSequence() ) );
+            }
             else if ( getName().length() > 0 ) {
                 // Node name is not empty, and equal.
                 return true;
@@ -577,6 +576,7 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
 
     @Override
     final public int hashCode() {
+        System.out.print( " PNh " );
         final NodeData data = getNodeData();
         if ( ( getName().length() < 1 ) && !data.isHasSequence() && !data.isHasTaxonomy() ) {
             return super.hashCode();

diff --git a/forester/java/src/org/forester/phylogeny/data/Identifier.java b/forester/java/src/org/forester/phylogeny/data/Identifier.java
index d3b4437..f56a023 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/data/Identifier.java
+++ b/forester/java/src/org/forester/phylogeny/data/Identifier.java
@@ -34,14 +34,11 @@ import org.forester.util.ForesterUtil;
 
 public final class Identifier implements PhylogenyData {
 
-    final public static String NCBI = "ncbi";
+    final public static String NCBI   = "ncbi";
     final public static String REFSEQ = "refseq";
-    
-    final private String _value;
-    final private String _provider;
-    final private String _value_provider;
-    
-   
+    final private String       _value;
+    final private String       _provider;
+    final private String       _value_provider;
 
     public Identifier() {
         _value = "";

diff --git a/forester/java/src/org/forester/sdi/GSDI.java b/forester/java/src/org/forester/sdi/GSDI.java
index 06db0a9..6947910 100644 (file)
--- a/forester/java/src/org/forester/sdi/GSDI.java
+++ b/forester/java/src/org/forester/sdi/GSDI.java
@@ -27,10 +27,8 @@ package org.forester.sdi;
 
 import java.util.ArrayList;
 import java.util.HashMap;
-import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
-import java.util.Set;
 import java.util.SortedSet;
 import java.util.TreeSet;
 
@@ -304,7 +302,7 @@ public final class GSDI extends SDI {
     //    }
     final void linkNodesOfG() throws SdiException {
         final Map<String, PhylogenyNode> species_to_node_map = new HashMap<String, PhylogenyNode>();
-        final Set<PhylogenyNode> species_tree_ext_nodes = new HashSet<PhylogenyNode>();
+        final List<PhylogenyNode> species_tree_ext_nodes = new ArrayList<PhylogenyNode>();
         final TaxonomyComparisonBase tax_comp_base = determineTaxonomyComparisonBase( _gene_tree );
         System.out.println( "comp base is: " + tax_comp_base );
         // Stringyfied taxonomy is the key, node is the value.
@@ -365,11 +363,22 @@ public final class GSDI extends SDI {
             }
         }
         if ( _strip_species_tree ) {
+            for( PhylogenyNode x : _mapped_species_tree_nodes ) {
+                System.out.println( ">>" + x );
+            }
             for( final PhylogenyNode s : species_tree_ext_nodes ) {
+                System.out.print( ">>>>>>>>>" + s );
                 if ( !_mapped_species_tree_nodes.contains( s ) ) {
                     _species_tree.deleteSubtree( s, true );
+                    System.out.println( " DELETING" );
+                }
+                else {
+                    System.out.println();
                 }
             }
+            for( PhylogenyNode x : _mapped_species_tree_nodes ) {
+                System.out.println( ">>" + x );
+            }
         }
     }
 

diff --git a/forester/java/src/org/forester/util/EasyWriter.java b/forester/java/src/org/forester/util/EasyWriter.java
new file mode 100644 (file)
index 0000000..5fc907d
--- /dev/null
+++ b/forester/java/src/org/forester/util/EasyWriter.java
@@ -0,0 +1,23 @@
+
+package org.forester.util;
+
+import java.io.BufferedWriter;
+import java.io.IOException;
+
+public final class EasyWriter extends BufferedWriter {
+
+    private final static String LINE_SEPARATOR = ForesterUtil.LINE_SEPARATOR;
+
+    public EasyWriter( BufferedWriter out ) {
+        super( out );
+    }
+
+    public void println( final String s ) throws IOException {
+        write( s );
+        write( LINE_SEPARATOR );
+    }
+
+    public void print( final String s ) throws IOException {
+        write( s );
+    }
+}

diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java
index 36355ac..c344a0d 100644 (file)
--- a/forester/java/src/org/forester/util/ForesterUtil.java
+++ b/forester/java/src/org/forester/util/ForesterUtil.java
@@ -304,6 +304,14 @@ public final class ForesterUtil {
         return new BufferedWriter( new FileWriter( file ) );
     }
 
+    final public static EasyWriter createEasyWriter( final File file ) throws IOException {
+        return new EasyWriter( createBufferedWriter( file ) );
+    }
+
+    final public static BufferedWriter createEasyWriter( final String name ) throws IOException {
+        return createEasyWriter( createFileForWriting( name ) );
+    }
+
     final public static BufferedWriter createBufferedWriter( final String name ) throws IOException {
         return new BufferedWriter( new FileWriter( createFileForWriting( name ) ) );
     }