X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsdi%2FGSDI.java;h=2419d131d03bde83142298d10323a85038230aea;hb=e9ca0dc1764303d53fc6b9b087f33cdee53726ea;hp=0e48d32a2ae83d1551d1fe26fecd469a07bc68a0;hpb=d30f8d155dee1fbfa17946cf80a203cc886ffdd6;p=jalview.git

diff --git a/forester/java/src/org/forester/sdi/GSDI.java b/forester/java/src/org/forester/sdi/GSDI.java
index 0e48d32..2419d13 100644
--- a/forester/java/src/org/forester/sdi/GSDI.java
+++ b/forester/java/src/org/forester/sdi/GSDI.java
@@ -31,8 +31,11 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.SortedSet;
+import java.util.TreeSet;
 
 import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.data.Event;
 import org.forester.phylogeny.data.Taxonomy;
@@ -72,6 +75,7 @@ public final class GSDI extends SDI {
     private final List<PhylogenyNode> _stripped_species_tree_nodes;
     private final Set<PhylogenyNode>  _mapped_species_tree_nodes;
     private TaxonomyComparisonBase    _tax_comp_base;
+    private final SortedSet<String>   _scientific_names_mapped_to_reduced_specificity;
 
     public GSDI( final Phylogeny gene_tree,
                  final Phylogeny species_tree,
@@ -88,8 +92,9 @@ 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();
+        _scientific_names_mapped_to_reduced_specificity = new TreeSet<String>();
         linkNodesOfG();
+        PhylogenyMethods.preOrderReId( getSpeciesTree() );
         geneTreePostOrderTraversal();
     }
 
@@ -228,12 +233,14 @@ public final class GSDI extends SDI {
         for( final PhylogenyNodeIterator iter = _species_tree.iteratorExternalForward(); iter.hasNext(); ) {
             final PhylogenyNode s = iter.next();
             species_tree_ext_nodes.add( s );
-            final String tax_str = taxonomyToString( s, _tax_comp_base );
-            if ( !ForesterUtil.isEmpty( tax_str ) ) {
-                if ( species_to_node_map.containsKey( tax_str ) ) {
-                    throw new SDIException( "taxonomy \"" + s + "\" is not unique in species tree" );
+            if ( s.getNodeData().isHasTaxonomy() ) {
+                final String tax_str = taxonomyToString( s, _tax_comp_base );
+                if ( !ForesterUtil.isEmpty( tax_str ) ) {
+                    if ( species_to_node_map.containsKey( tax_str ) ) {
+                        throw new SDIException( "taxonomy \"" + s + "\" is not unique in species tree" );
+                    }
+                    species_to_node_map.put( tax_str, s );
                 }
-                species_to_node_map.put( tax_str, s );
             }
         }
         // Retrieve the reference to the node with a matching stringyfied taxonomy.
@@ -258,7 +265,11 @@ 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 );
+                    }
                     if ( s == null ) {
                         if ( _strip_gene_tree ) {
                             _stripped_gene_tree_nodes.add( g );
@@ -277,12 +288,62 @@ public final class GSDI extends SDI {
         } // for loop
         if ( _strip_gene_tree ) {
             stripGeneTree();
+            if ( getGeneTree().isEmpty() || ( getGeneTree().getNumberOfExternalNodes() < 2 ) ) {
+                throw new SDIException( "species could not be mapped between gene tree and species tree" );
+            }
         }
         if ( _strip_species_tree ) {
             stripSpeciesTree( species_tree_ext_nodes );
         }
     }
 
+    private final PhylogenyNode tryMapByRemovingOverlySpecificData( final Map<String, PhylogenyNode> species_to_node_map,
+                                                                    final String tax_str ) {
+        PhylogenyNode s = tryMapByRemovingOverlySpecificData( species_to_node_map, tax_str, " (" );
+        if ( s == null ) {
+            if ( ForesterUtil.countChars( tax_str, ' ' ) == 2 ) {
+                final String new_tax_str = tax_str.substring( 0, tax_str.lastIndexOf( ' ' ) ).trim();
+                s = species_to_node_map.get( new_tax_str );
+                if ( s != null ) {
+                    addScientificNamesMappedToReducedSpecificity( tax_str, new_tax_str );
+                }
+            }
+        }
+        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 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 ) {
+            final String new_tax_str = tax_str.substring( 0, i ).trim();
+            final PhylogenyNode s = species_to_node_map.get( new_tax_str );
+            if ( s != null ) {
+                addScientificNamesMappedToReducedSpecificity( tax_str, new_tax_str );
+            }
+            return s;
+        }
+        return null;
+    }
+
+    private final void addScientificNamesMappedToReducedSpecificity( final String s1, final String s2 ) {
+        _scientific_names_mapped_to_reduced_specificity.add( s1 + " -> " + s2 );
+    }
+
+    public final SortedSet<String> getReMappedScientificNamesFromGeneTree() {
+        return _scientific_names_mapped_to_reduced_specificity;
+    }
+
     public TaxonomyComparisonBase getTaxCompBase() {
         return _tax_comp_base;
     }
@@ -294,6 +355,8 @@ public final class GSDI extends SDI {
                 _stripped_species_tree_nodes.add( s );
             }
         }
+        _species_tree.clearHashIdToNodeMap();
+        _species_tree.externalNodesHaveChanged();
     }
 
     public List<PhylogenyNode> getStrippedSpeciesTreeNodes() {
@@ -304,6 +367,8 @@ public final class GSDI extends SDI {
         for( final PhylogenyNode g : _stripped_gene_tree_nodes ) {
             _gene_tree.deleteSubtree( g, true );
         }
+        _gene_tree.clearHashIdToNodeMap();
+        _gene_tree.externalNodesHaveChanged();
     }
 
     public Set<PhylogenyNode> getMappedExternalSpeciesTreeNodes() {
@@ -342,12 +407,12 @@ public final class GSDI extends SDI {
         else if ( max == 1 ) {
             throw new IllegalArgumentException( "gene tree has only one node with taxonomic data" );
         }
-        else if ( max == with_sn_count ) {
-            return SDI.TaxonomyComparisonBase.SCIENTIFIC_NAME;
-        }
         else if ( max == with_id_count ) {
             return SDI.TaxonomyComparisonBase.ID;
         }
+        else if ( max == with_sn_count ) {
+            return SDI.TaxonomyComparisonBase.SCIENTIFIC_NAME;
+        }
         else {
             return SDI.TaxonomyComparisonBase.CODE;
         }