X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsdi%2FSDI.java;h=b1258f0820f58c05707179be26936e4045ac8de7;hb=b1a74bd076c917d428002284a53a2c6f390226fb;hp=c783ce095332f7f9a899367dc059d45142518c1f;hpb=4cefcbf8c547e86e56ed503f0a3d1a06e462e60e;p=jalview.git

diff --git a/forester/java/src/org/forester/sdi/SDI.java b/forester/java/src/org/forester/sdi/SDI.java
index c783ce0..b1258f0 100644
--- a/forester/java/src/org/forester/sdi/SDI.java
+++ b/forester/java/src/org/forester/sdi/SDI.java
@@ -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;
@@ -214,8 +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.
@@ -287,20 +289,43 @@ public abstract class SDI {
     }
 
     static String taxonomyToString( final PhylogenyNode n, final TaxonomyComparisonBase base ) {
-        final Taxonomy tax = n.getNodeData().getTaxonomy();
         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();
+                return n.getNodeData().getTaxonomy().getScientificName();
             default:
                 throw new IllegalArgumentException( "unknown comparison base for taxonomies: " + base );
         }
     }
 
     public enum TaxonomyComparisonBase {
-        ID, CODE, SCIENTIFIC_NAME
+        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";
+            }
+        }
     }
 }