From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 5 Sep 2016 14:07:52 +0000 (+0100)
Subject: JAL-2106 corrections to DBRefEntry.isPrimary code and tests
X-Git-Tag: Release_2_10_0~47^2~4^2~13
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d240900df4c81bd7b054afc0f569c7a75d4e1751;p=jalview.git

JAL-2106 corrections to DBRefEntry.isPrimary code and tests
---

diff --git a/src/jalview/api/DBRefEntryI.java b/src/jalview/api/DBRefEntryI.java
index 701acb6..a4ec575 100644
--- a/src/jalview/api/DBRefEntryI.java
+++ b/src/jalview/api/DBRefEntryI.java
@@ -72,23 +72,20 @@ public interface DBRefEntryI
   public boolean updateFrom(DBRefEntryI otherEntry);
 
   /**
-   * Method to distinguish between direct and indirect database references
-   * 
-   * primary references indicate the local sequence data directly corresponds
-   * with the database record. All other references are secondary. direct
+   * Method to distinguish between direct and indirect database references. <br>
+   * Primary references indicate the local sequence data directly corresponds
+   * with the database record. All other references are secondary. Direct
    * references indicate that part or all of the local sequence data can be
    * mapped with another sequence, enabling annotation transfer.
-   * cross-references indicate the local sequence data can be corresponded to
-   * some other linear coordinate system via a transformation.
-   * 
+   * Cross-references indicate the local sequence data can be corresponded to
+   * some other linear coordinate system via a transformation. <br>
    * This method is also sufficient to distinguish direct DBRefEntry mappings
    * from other relationships - e.g. coding relationships (imply a 1:3/3:1
    * mapping), but not transcript relationships, which imply a (possibly
-   * non-contiguous) 1:1 mapping
-   * 
+   * non-contiguous) 1:1 mapping. <br>
    * The only way a dbref's mappings can be fully verified is via the local
    * sequence frame, so rather than use isPrimary directly, please use
-   * SequenceI.getPrimaryDbRefs()
+   * SequenceI.getPrimaryDbRefs().
    *
    * @return true if this reference provides a primary accession for the
    *         associated sequence object
diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 11e77d8..143a4d2 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -23,6 +23,7 @@ package jalview.datamodel;
 import jalview.api.DBRefEntryI;
 
 import java.util.Arrays;
+import java.util.List;
 
 public class DBRefEntry implements DBRefEntryI
 {
@@ -297,12 +298,15 @@ 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][])))
+      // check map is really 1:1, between identical single ranges
+      List<int[]> fromRanges = map.getMap().getFromRanges();
+      List<int[]> toRanges = map.getMap().getToRanges();
+      if (fromRanges.size() != 1 || toRanges.size() != 1)
+      {
+        return false;
+      }
+      if (fromRanges.get(0)[0] != toRanges.get(0)[0]
+              || fromRanges.get(0)[1] != toRanges.get(0)[1])
       {
         return false;
       }
diff --git a/test/jalview/datamodel/DBRefEntryTest.java b/test/jalview/datamodel/DBRefEntryTest.java
index 09d9df1..ee0bd41 100644
--- a/test/jalview/datamodel/DBRefEntryTest.java
+++ b/test/jalview/datamodel/DBRefEntryTest.java
@@ -144,12 +144,37 @@ public class DBRefEntryTest
   {
     DBRefEntry dbr = new DBRefEntry(DBRefSource.UNIPROT, "", "Q12345");
     assertTrue(dbr.isPrimary());
+
     /*
-     *  1:1 mapping 
+     *  1:1 mapping - ok
      */
     dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 1, 3 }, 1,
             1));
     assertTrue(dbr.isPrimary());
+
+    /*
+     *  1:1 mapping of identical split ranges - not ok
+     */
+    dbr.setMap(new Mapping(null, new int[] { 1, 3, 6, 9 }, new int[] { 1,
+        3, 6, 9 }, 1, 1));
+    assertFalse(dbr.isPrimary());
+
+    /*
+     *  1:1 mapping of different ranges - not ok
+     */
+    dbr.setMap(new Mapping(null, new int[] { 1, 4 }, new int[] { 2, 5 }, 1,
+            1));
+    assertFalse(dbr.isPrimary());
+
+    /*
+     *  1:1 mapping of 'isoform' ranges - not ok
+     */
+    dbr.setMap(new Mapping(null, new int[] { 1, 2, 6, 9 }, new int[] { 1,
+        3, 7, 9 }, 1, 1));
+    assertFalse(dbr.isPrimary());
+    dbr.setMap(null);
+    assertTrue(dbr.isPrimary());
+
     /*
      * Version string is prefixed with another dbref source string (fail)
      */
@@ -163,11 +188,12 @@ public class DBRefEntryTest
     assertTrue(dbr.isPrimary());
 
     /*
-     *  1:1 mapping with shift (fail)
+     * null version string can't be primary ref
      */
-    dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 2, 4 }, 1,
-            1));
+    dbr.setVersion(null);
     assertFalse(dbr.isPrimary());
+    dbr.setVersion("");
+    assertTrue(dbr.isPrimary());
 
     /*
      *  1:1 mapping and sequenceRef (fail)
@@ -182,18 +208,12 @@ public class DBRefEntryTest
     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 use case for a pass)
      */
-    dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 1, 3 }, 2,
+    dbr.setMap(new Mapping(null, new int[] { 1, 4 }, new int[] { 1, 4 }, 2,
             2));
     assertFalse(dbr.isPrimary());
-
-    /*
-     * Version string is prefixed with another dbref source string
-     */
-    dbr.setVersion(DBRefSource.EMBL + ":0");
-    assertFalse(dbr.isPrimary());
-
   }
 }