From 9a0e53e18ba1280658e1424c5e08b90e7beeebde Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 24 Aug 2016 16:47:35 +0100
Subject: [PATCH] JAL-2106 stricter check for 1:1 mapping (same numbering on
 both sides, and word size == 1)

---
 src/jalview/datamodel/DBRefEntry.java      |    9 +++++++
 test/jalview/datamodel/DBRefEntryTest.java |   37 ++++++++++++++++++++++------
 2 files changed, 38 insertions(+), 8 deletions(-)

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index e2ee195..11e77d8 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -297,6 +297,15 @@ public class DBRefEntry implements DBRefEntryI
       {
         return false;
       }
+      // check map is really 1:1, no shifts allowed.
+      if (map.getMap().getFromHighest() != map.getMap().getToHighest()
+              && map.getMap().getFromLowest() != map.getMap().getToLowest()
+              && !Arrays.equals(
+                      map.getMap().getFromRanges().toArray(new int[0][]),
+                      map.getMap().getToRanges().toArray(new int[0][])))
+      {
+        return false;
+      }
     }
     if (version == null)
     {
diff --git a/test/jalview/datamodel/DBRefEntryTest.java b/test/jalview/datamodel/DBRefEntryTest.java
index 8cc31e0..09d9df1 100644
--- a/test/jalview/datamodel/DBRefEntryTest.java
+++ b/test/jalview/datamodel/DBRefEntryTest.java
@@ -145,32 +145,53 @@ public class DBRefEntryTest
     DBRefEntry dbr = new DBRefEntry(DBRefSource.UNIPROT, "", "Q12345");
     assertTrue(dbr.isPrimary());
     /*
-     *  1:1 mapping with shift
+     *  1:1 mapping 
      */
-    dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 5, 9 }, 1,
+    dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 1, 3 }, 1,
             1));
     assertTrue(dbr.isPrimary());
+    /*
+     * Version string is prefixed with another dbref source string (fail)
+     */
+    dbr.setVersion(DBRefSource.EMBL + ":0");
+    assertFalse(dbr.isPrimary());
+
+    /*
+     * Version string is alphanumeric
+     */
+    dbr.setVersion("0.1.b");
+    assertTrue(dbr.isPrimary());
 
     /*
-     *  1:1 mapping with shift and sequenceRef
+     *  1:1 mapping with shift (fail)
+     */
+    dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 2, 4 }, 1,
+            1));
+    assertFalse(dbr.isPrimary());
+
+    /*
+     *  1:1 mapping and sequenceRef (fail)
      */
     dbr.setMap(new Mapping(new Sequence("foo", "ASDF"), new int[] { 1, 3 },
-            new int[] { 5, 9 }, 1, 1));
+            new int[] { 1, 3 }, 1, 1));
     assertFalse(dbr.isPrimary());
 
     /*
-     * 1:3 mapping with shift (fail)
+     * 1:3 mapping (fail)
      */
-    dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 5, 9 }, 1,
+    dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 1, 3 }, 1,
             3));
     assertFalse(dbr.isPrimary());
     /*
-     * 2:2 mapping with shift (expected fail, but maybe not realistic)
+     * 2:2 mapping with shift (expected fail, but maybe use case for a pass)
      */
-    dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 5, 9 }, 2,
+    dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 1, 3 }, 2,
             2));
     assertFalse(dbr.isPrimary());
 
+    /*
+     * Version string is prefixed with another dbref source string
+     */
     dbr.setVersion(DBRefSource.EMBL + ":0");
     assertFalse(dbr.isPrimary());
 
-- 
1.7.10.2