cleanup

diff --git a/forester/java/src/org/forester/application/gsdi.java b/forester/java/src/org/forester/application/gsdi.java
index e63c23a..0f77e5c 100644 (file)
--- a/forester/java/src/org/forester/application/gsdi.java
+++ b/forester/java/src/org/forester/application/gsdi.java
@@ -126,7 +126,6 @@ public final class gsdi {
     private static void execute( final CommandLineArguments cla ) throws IOException {
         BASE_ALGORITHM base_algorithm = BASE_ALGORITHM.GSDI;
         boolean most_parsimonous_duplication_model = false;
-        boolean species_tree_in_phyloxml = true;
         boolean allow_stripping_of_gene_tree = false;
         if ( cla.isOptionSet( gsdi.SDISE_OPTION ) ) {
             base_algorithm = BASE_ALGORITHM.SDI;
@@ -137,9 +136,6 @@ public final class gsdi {
             }
             most_parsimonous_duplication_model = true;
         }
-        if ( cla.isOptionSet( gsdi.GUESS_FORMAT_OF_SPECIES_TREE ) ) {
-            species_tree_in_phyloxml = false;
-        }
         if ( cla.isOptionSet( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION ) ) {
             if ( base_algorithm != BASE_ALGORITHM.GSDI ) {
                 ForesterUtil.fatalError( gsdi.PRG_NAME, "Can only allow stripping of gene tree with GSDI" );
@@ -195,11 +191,11 @@ public final class gsdi {
         }
         try {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            if ( species_tree_in_phyloxml ) {
-                species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ];
+            final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( species_tree_file, true );
+            if ( p instanceof PhyloXmlParser ) {
+                species_tree = factory.create( species_tree_file, p )[ 0 ];
             }
             else {
-                final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( species_tree_file, true );
                 if ( REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE && ( p instanceof NHXParser ) ) {
                     ( ( NHXParser ) p ).setReplaceUnderscores( true );
                 }
@@ -341,10 +337,11 @@ public final class gsdi {
             writer.toPhyloXML( out_file, gene_tree, 0 );
         }
         catch ( final IOException e ) {
-            ForesterUtil.fatalError( PRG_NAME, "Failed to write to [" + out_file + "]: " + e.getMessage() );
+            ForesterUtil.fatalError( PRG_NAME,
+                                     "Failed to write to [" + out_file.getCanonicalPath() + "]: " + e.getMessage() );
         }
-        System.out.println( "Wrote resulting gene tree to             : " + out_file );
-        log_writer.println( "Wrote resulting gene tree to             : " + out_file );
+        System.out.println( "Wrote resulting gene tree to             : " + out_file.getCanonicalPath() );
+        log_writer.println( "Wrote resulting gene tree to             : " + out_file.getCanonicalPath() );
         if ( base_algorithm == BASE_ALGORITHM.SDI ) {
             sdi.computeMappingCostL();
             System.out.println( "Mapping cost                             : " + sdi.computeMappingCostL() );
@@ -352,17 +349,20 @@ public final class gsdi {
         }
         else if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
             final GSDI gsdi = ( GSDI ) sdi;
-            final File species_tree_used_file = new File( out_file + SUFFIX_FOR_SPECIES_TREE_USED );
+            final File species_tree_used_file = new File( ForesterUtil.removeSuffix( out_file.toString() )
+                    + 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() );
+                ForesterUtil.fatalError( PRG_NAME, "Failed to write to [" + species_tree_used_file.getCanonicalPath()
+                        + "]: " + e.getMessage() );
             }
-            System.out.println( "Wrote (stripped) species tree to         : " + species_tree_used_file );
-            log_writer.println( "Wrote (stripped) species tree to         : " + species_tree_used_file );
+            System.out.println( "Wrote (stripped) species tree to         : "
+                    + species_tree_used_file.getCanonicalPath() );
+            log_writer.println( "Wrote (stripped) species tree to         : "
+                    + species_tree_used_file.getCanonicalPath() );
         }
         System.out.println( "Number of external nodes in gene tree    : " + gene_tree.getNumberOfExternalNodes() );
         log_writer.println( "Number of external nodes in gene tree    : " + gene_tree.getNumberOfExternalNodes() );
@@ -404,7 +404,7 @@ public final class gsdi {
             printStrippedSpeciesTreeNodesToLog( log_writer, gsdi );
         }
         System.out.println();
-        System.out.println( "Wrote log to                             : " + log_file );
+        System.out.println( "Wrote log to                             : " + log_file.getCanonicalPath() );
         System.out.println();
         log_writer.close();
     }

diff --git a/forester/java/src/org/forester/sdi/GSDI.java b/forester/java/src/org/forester/sdi/GSDI.java
index 0e48d32..a323ef7 100644 (file)
--- a/forester/java/src/org/forester/sdi/GSDI.java
+++ b/forester/java/src/org/forester/sdi/GSDI.java
@@ -88,8 +88,8 @@ public final class GSDI extends SDI {
         _stripped_gene_tree_nodes = new ArrayList<PhylogenyNode>();
         _stripped_species_tree_nodes = new ArrayList<PhylogenyNode>();
         _mapped_species_tree_nodes = new HashSet<PhylogenyNode>();
-        getSpeciesTree().preOrderReId();
         linkNodesOfG();
+        getSpeciesTree().preOrderReId();
         geneTreePostOrderTraversal();
     }
 
@@ -258,7 +258,11 @@ public final class GSDI extends SDI {
                     }
                 }
                 else {
-                    final PhylogenyNode s = species_to_node_map.get( tax_str );
+                    PhylogenyNode s = species_to_node_map.get( tax_str );
+                    if ( ( _tax_comp_base == TaxonomyComparisonBase.SCIENTIFIC_NAME ) && ( s == null )
+                            && ( ForesterUtil.countChars( tax_str, ' ' ) > 1 ) ) {
+                        s = tryMapByRemovingOverlySpecificData( species_to_node_map, tax_str, s );
+                    }
                     if ( s == null ) {
                         if ( _strip_gene_tree ) {
                             _stripped_gene_tree_nodes.add( g );
@@ -283,6 +287,37 @@ public final class GSDI extends SDI {
         }
     }
 
+    private final static PhylogenyNode tryMapByRemovingOverlySpecificData( final Map<String, PhylogenyNode> species_to_node_map,
+                                                                           final String tax_str,
+                                                                           PhylogenyNode s ) {
+        s = tryMapByRemovingOverlySpecificData( species_to_node_map, tax_str, " (" );
+        if ( s == null ) {
+            if ( ForesterUtil.countChars( tax_str, ' ' ) == 2 ) {
+                s = species_to_node_map.get( tax_str.substring( 0, tax_str.lastIndexOf( ' ' ) ).trim() );
+            }
+        }
+        if ( s == null ) {
+            for( final String t : new String[] { " subspecies ", " strain ", " variety ", " varietas ", " subvariety ",
+                    " form ", " subform ", " cultivar ", " section ", " subsection " } ) {
+                s = tryMapByRemovingOverlySpecificData( species_to_node_map, tax_str, t );
+                if ( s != null ) {
+                    break;
+                }
+            }
+        }
+        return s;
+    }
+
+    private final static PhylogenyNode tryMapByRemovingOverlySpecificData( final Map<String, PhylogenyNode> species_to_node_map,
+                                                                           final String tax_str,
+                                                                           final String term ) {
+        final int i = tax_str.indexOf( term );
+        if ( i > 4 ) {
+            return species_to_node_map.get( tax_str.substring( 0, i ).trim() );
+        }
+        return null;
+    }
+
     public TaxonomyComparisonBase getTaxCompBase() {
         return _tax_comp_base;
     }