in progress

[jalview.git] / forester / java / src / org / forester / sdi / SDI.java

diff --git a/forester/java/src/org/forester/sdi/SDI.java b/forester/java/src/org/forester/sdi/SDI.java
index b21b9b5..b1258f0 100644 (file)
--- a/forester/java/src/org/forester/sdi/SDI.java
+++ b/forester/java/src/org/forester/sdi/SDI.java
@@ -7,7 +7,7 @@
 // Copyright (C) 2000-2001 Washington University School of Medicine
 // and Howard Hughes Medical Institute
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -17,7 +17,7 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
@@ -32,6 +32,7 @@ import java.util.Map;
 
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Identifier;
 import org.forester.phylogeny.data.Taxonomy;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.util.ForesterUtil;
@@ -131,7 +132,6 @@ public abstract class SDI {
         boolean all_have_id = true;
         boolean all_have_code = true;
         boolean all_have_sn = true;
-        boolean all_have_cn = true;
         for( final PhylogenyNodeIterator iter = _species_tree.iteratorExternalForward(); iter.hasNext(); ) {
             final PhylogenyNode n = iter.next();
             if ( n.getNodeData().isHasTaxonomy() ) {
@@ -145,9 +145,6 @@ public abstract class SDI {
                 if ( ForesterUtil.isEmpty( tax.getScientificName() ) ) {
                     all_have_sn = false;
                 }
-                if ( ForesterUtil.isEmpty( tax.getCommonName() ) ) {
-                    all_have_cn = false;
-                }
             }
             else {
                 throw new IllegalArgumentException( "species tree node [" + n + "] has no taxonomic data" );
@@ -166,9 +163,6 @@ public abstract class SDI {
                 if ( ForesterUtil.isEmpty( tax.getScientificName() ) ) {
                     all_have_sn = false;
                 }
-                if ( ForesterUtil.isEmpty( tax.getCommonName() ) ) {
-                    all_have_cn = false;
-                }
             }
             else {
                 throw new IllegalArgumentException( "gene tree node [" + n + "] has no taxonomic data" );
@@ -183,9 +177,6 @@ public abstract class SDI {
         else if ( all_have_sn ) {
             base = TaxonomyComparisonBase.SCIENTIFIC_NAME;
         }
-        else if ( all_have_cn ) {
-            base = TaxonomyComparisonBase.COMMON_NAME;
-        }
         else {
             throw new IllegalArgumentException( "gene tree and species tree have incomparable taxonomies" );
         }
@@ -224,8 +215,9 @@ public abstract class SDI {
      * links (sets the field "link" of PhylogenyNode) each external
      * PhylogenyNode of gene_tree to the external PhylogenyNode of species_tree
      * which has the same species name.
+     * @throws SDIException 
      */
-    void linkNodesOfG() {
+    void linkNodesOfG() throws SDIException {
         final Map<String, PhylogenyNode> speciestree_ext_nodes = new HashMap<String, PhylogenyNode>();
         final TaxonomyComparisonBase tax_comp_base = determineTaxonomyComparisonBase();
         // Put references to all external nodes of the species tree into a map.
@@ -296,23 +288,44 @@ public abstract class SDI {
         return sb.toString();
     }
 
-    private static String taxonomyToString( final PhylogenyNode n, final TaxonomyComparisonBase base ) {
-        final Taxonomy tax = n.getNodeData().getTaxonomy();
+    static String taxonomyToString( final PhylogenyNode n, final TaxonomyComparisonBase base ) {
         switch ( base ) {
             case ID:
-                return tax.getIdentifier().getValue();
+                final Identifier id = n.getNodeData().getTaxonomy().getIdentifier();
+                if ( id == null ) {
+                    return null;
+                }
+                return id.getValuePlusProvider();
             case CODE:
-                return tax.getTaxonomyCode();
+                return n.getNodeData().getTaxonomy().getTaxonomyCode();
             case SCIENTIFIC_NAME:
-                return tax.getScientificName();
-            case COMMON_NAME:
-                return tax.getCommonName();
+                return n.getNodeData().getTaxonomy().getScientificName();
             default:
                 throw new IllegalArgumentException( "unknown comparison base for taxonomies: " + base );
         }
     }
 
-    enum TaxonomyComparisonBase {
-        ID, CODE, SCIENTIFIC_NAME, COMMON_NAME;
+    public enum TaxonomyComparisonBase {
+        ID {
+
+            @Override
+            public String toString() {
+                return "taxonomy id";
+            }
+        },
+        CODE {
+
+            @Override
+            public String toString() {
+                return "taxonomy code/mnemonic";
+            }
+        },
+        SCIENTIFIC_NAME {
+
+            @Override
+            public String toString() {
+                return "scientific name";
+            }
+        }
     }
 }