JAL-2154 always compare canonicalised DBRefEntry source strings!

diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index a1f06e5..405f6e6 100755 (executable)
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -248,7 +248,8 @@ public class DBRefUtils
     public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
       if (refa.getSource() == null
-              || refb.getSource().equals(refa.getSource()))
+              || DBRefUtils.getCanonicalName(refb.getSource()).equals(
+                      DBRefUtils.getCanonicalName(refa.getSource())))
       {
         if (refa.getVersion() == null
                 || refb.getVersion().equals(refa.getVersion()))
@@ -279,7 +280,7 @@ public class DBRefUtils
     @Override
     public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
-      if (nullOrEqual(refa.getSource(), refb.getSource())
+      if (nullOrEqualSource(refa.getSource(), refb.getSource())
               && nullOrEqual(refa.getVersion(), refb.getVersion())
               && nullOrEqual(refa.getAccessionId(), refb.getAccessionId())
               && nullOrEqual(refa.getMap(), refb.getMap()))
@@ -301,7 +302,8 @@ public class DBRefUtils
     public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
       if (refa.getSource() != null && refb.getSource() != null
-              && refb.getSource().equals(refa.getSource()))
+              && DBRefUtils.getCanonicalName(refb.getSource()).equals(
+                      DBRefUtils.getCanonicalName(refa.getSource())))
       {
         // We dont care about version
         if (refa.getAccessionId() != null && refb.getAccessionId() != null
@@ -332,7 +334,8 @@ public class DBRefUtils
     public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
       if (refa.getSource() != null && refb.getSource() != null
-              && refb.getSource().equals(refa.getSource()))
+              && DBRefUtils.getCanonicalName(refb.getSource()).equals(
+                      DBRefUtils.getCanonicalName(refa.getSource())))
       {
         // We dont care about version
         if (refa.getAccessionId() != null && refb.getAccessionId() != null
@@ -368,7 +371,8 @@ public class DBRefUtils
     public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
       if (refa.getSource() != null && refb.getSource() != null
-              && refb.getSource().equals(refa.getSource()))
+              && DBRefUtils.getCanonicalName(refb.getSource()).equals(
+                      DBRefUtils.getCanonicalName(refa.getSource())))
       {
         // We dont care about version
         // if ((refa.getVersion()==null || refb.getVersion()==null)
@@ -407,7 +411,8 @@ public class DBRefUtils
     public boolean matches(DBRefEntry refa, DBRefEntry refb)
     {
       if (refa.getSource() != null && refb.getSource() != null
-              && refb.getSource().equals(refa.getSource()))
+              && DBRefUtils.getCanonicalName(refb.getSource()).equals(
+                      DBRefUtils.getCanonicalName(refa.getSource())))
       {
         // We dont care about version
 
@@ -538,6 +543,27 @@ public class DBRefUtils
   }
 
   /**
+   * canonicalise source string before comparing. null is always wildcard
+   * 
+   * @param o1
+   *          - null or source string to compare
+   * @param o2
+   *          - null or source string to compare
+   * @return true if either o1 or o2 are null, or o1 equals o2 under
+   *         DBRefUtils.getCanonicalName
+   *         (o1).equals(DBRefUtils.getCanonicalName(o2))
+   */
+  public static boolean nullOrEqualSource(String o1, String o2)
+  {
+    if (o1 == null || o2 == null)
+    {
+      return true;
+    }
+    return DBRefUtils.getCanonicalName(o1).equals(
+            DBRefUtils.getCanonicalName(o2));
+  }
+
+  /**
    * Selects just the DNA or protein references from a set of references
    * 
    * @param selectDna