JAL-3010 TEMPORARY patch for BioJava bug to save all synonyms

diff --git a/src/org/biojava/nbio/ontology/Synonym.java b/src/org/biojava/nbio/ontology/Synonym.java
new file mode 100644 (file)
index 0000000..3902026
--- /dev/null
+++ b/src/org/biojava/nbio/ontology/Synonym.java
@@ -0,0 +1,128 @@
+/*
+ *                  BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ *
+ * Created on Jan 24, 2008
+ *
+ */
+
+package org.biojava.nbio.ontology;
+
+import java.util.Comparator;
+
+
+public class Synonym implements Comparable<Synonym>{
+
+
+       public final static int UNKNOWN_SCOPE = -1;
+       public final static int RELATED_SYNONYM = 0;
+       public final static int EXACT_SYNONYM = 1;
+       public final static int NARROW_SYNONYM = 2;
+       public final static int BROAD_SYNONYM = 3;
+
+       int scope;
+       String category;
+       String name;
+
+       @Override
+       public String toString(){
+               String txt = "Synonym: name:"+name+ " category:" + category + " scope: " +scope;
+               return txt;
+       }
+
+  @Override
+  public int hashCode()
+  {
+    return toString().hashCode();
+  }
+
+  @Override
+        public boolean equals(Object obj)
+        {
+    return obj instanceof Synonym
+            && ((Synonym) obj).toString().equals(this.toString());
+        }
+
+  public final static Comparator<Synonym> COMPARATOR = new Comparator<Synonym>()
+  {
+               @Override
+               public int compare(Synonym a, Synonym b) {
+                       if (a == null && b == null)
+      {
+        return 0;
+      }
+      if (a == null)
+      {
+        return -1;
+      }
+      if (b == null)
+      {
+        return 1;
+      }
+      if (a.equals(b))
+      {
+        return 0;
+      }
+      String catA = a.getCategory();
+      String catB = b.getCategory();
+      if (catA == null && catB != null)
+      {
+        return 1;
+      }
+      if (catA != null && catB == null)
+      {
+        return -1;
+      }
+      if (catA != null && catB != null)
+      {
+        int comp = catA.compareToIgnoreCase(catB);
+        if (comp != 0)
+        {
+          return comp;
+        }
+      }
+      // todo check for null name
+      return a.getName().compareToIgnoreCase(b.getName());
+    }
+       };
+
+       public Synonym() {
+       }
+       public String getName() {
+               return name;
+       }
+       public void setName(String name) {
+               this.name = name;
+       }
+       public String getCategory() {
+               return category;
+       }
+       public void setCategory(String category) {
+               this.category = category;
+       }
+       public int getScope() {
+               return scope;
+       }
+       public void setScope(int scope) {
+               this.scope = scope;
+       }
+       @Override
+       public int compareTo(Synonym o) {
+               return COMPARATOR.compare(this, o);
+       }
+}