more test for isDuplication() and isSpecation() added (phyloXML encoded

[jalview.git] / forester / java / src / org / forester / phylogeny / data / NodeData.java

diff --git a/forester/java/src/org/forester/phylogeny/data/NodeData.java b/forester/java/src/org/forester/phylogeny/data/NodeData.java
index 60d52f3..28b6889 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/data/NodeData.java
+++ b/forester/java/src/org/forester/phylogeny/data/NodeData.java
@@ -38,45 +38,6 @@ import org.forester.util.ForesterUtil;
 
 public class NodeData implements PhylogenyData {
 
-    public enum NODE_DATA {
-        NODE_NAME,
-        EVENT,
-        SEQUENCE_NAME,
-        GENE_NAME,
-        SEQUENCE_SYMBOL,
-        SEQUENCE_MOL_SEQ,
-        SEQUENCE_MOL_SEQ_FASTA,
-        SEQUENCE_ACC,
-        TAXONOMY_SCIENTIFIC_NAME,
-        TAXONOMY_COMM0N_NAME,
-        TAXONOMY_CODE,
-        UNKNOWN,
-        GO_TERM_IDS,
-        SEQ_ANNOTATIONS,
-        DOMAINS_ALL,
-        DOMAINS_COLLAPSED_PER_PROTEIN;
-        public String toString() {
-            switch(this) {
-                case DOMAINS_ALL: return "horseshit";
-                case DOMAINS_COLLAPSED_PER_PROTEIN: return "horseshit";
-                case EVENT: return "horseshit";
-                case GENE_NAME: return "horseshit";
-                case GO_TERM_IDS: return "horseshit";
-                case NODE_NAME: return "horseshit";
-                case SEQ_ANNOTATIONS: return "horseshit";
-                case SEQUENCE_ACC: return "horseshit";
-                case SEQUENCE_MOL_SEQ: return "horseshit";
-                case SEQUENCE_MOL_SEQ_FASTA: return "horseshit";
-                case SEQUENCE_NAME: return "horseshit";
-                case SEQUENCE_SYMBOL: return "horseshit";
-                case TAXONOMY_CODE: return "horseshit";
-                case TAXONOMY_COMM0N_NAME: return "horseshit";
-                case TAXONOMY_SCIENTIFIC_NAME: return "horseshit";
-                case UNKNOWN: return "horseshit";
-                default: throw new IllegalArgumentException();
-              }
-        }
-    }
     private String             _node_name;
     private Event              _event;
     private List<Sequence>     _sequences;
@@ -217,6 +178,9 @@ public class NodeData implements PhylogenyData {
     }
 
     public Distribution getDistribution( final int index ) {
+        if ( _distributions == null ) {
+            return null;
+        }
         return _distributions.get( index );
     }
 
@@ -243,6 +207,9 @@ public class NodeData implements PhylogenyData {
     }
 
     public Reference getReference( final int index ) {
+        if ( _references == null ) {
+            return null;
+        }
         return _references.get( index );
     }
 
@@ -260,6 +227,9 @@ public class NodeData implements PhylogenyData {
     }
 
     public Sequence getSequence( final int index ) {
+        if ( _sequences == null ) {
+            return null;
+        }
         return _sequences.get( index );
     }
 
@@ -282,6 +252,9 @@ public class NodeData implements PhylogenyData {
     }
 
     public Taxonomy getTaxonomy( final int index ) {
+        if ( _taxonomies == null ) {
+            return null;
+        }
         return _taxonomies.get( index );
     }