From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 24 Apr 2019 15:05:56 +0000 (+0100)
Subject: JAL-3010 TEMPORARY patch for BioJava bug to save all synonyms
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=fefafff8f5082392f6dc59307738dc8b2be103d5;p=jalview.git

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
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);
+	}
+}