JAL-2106 DBRefEntry.isPrimary() renamed isPrimaryCandidate()

diff --git a/src/jalview/api/DBRefEntryI.java b/src/jalview/api/DBRefEntryI.java
index a4ec575..52ee381 100644 (file)
--- a/src/jalview/api/DBRefEntryI.java
+++ b/src/jalview/api/DBRefEntryI.java
@@ -72,7 +72,10 @@ public interface DBRefEntryI
   public boolean updateFrom(DBRefEntryI otherEntry);
 
   /**
-   * Method to distinguish between direct and indirect database references. <br>
+   * Answers true if the ref looks like a primary (direct) database reference. <br>
+   * The only way a dbref's mappings can be fully verified is via the local
+   * sequence frame, so rather than use isPrimaryCandidate directly, please use
+   * SequenceI.getPrimaryDbRefs(). <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
@@ -82,13 +85,10 @@ public interface DBRefEntryI
    * 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. <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().
+   * non-contiguous) 1:1 mapping.
    *
    * @return true if this reference provides a primary accession for the
    *         associated sequence object
    */
-  public boolean isPrimary();
+  public boolean isPrimaryCandidate();
 }

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 143a4d2..ec6dcf8 100755 (executable)
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -282,7 +282,7 @@ public class DBRefEntry implements DBRefEntryI
   }
 
   @Override
-  public boolean isPrimary()
+  public boolean isPrimaryCandidate()
   {
     /*
      * if a map is present, unless it is 1:1 and has no SequenceI mate, it cannot be a primary reference.  
@@ -298,7 +298,7 @@ public class DBRefEntry implements DBRefEntryI
       {
         return false;
       }
-      // check map is really 1:1, between identical single ranges
+      // check map is between identical single contiguous ranges
       List<int[]> fromRanges = map.getMap().getFromRanges();
       List<int[]> toRanges = map.getMap().getToRanges();
       if (fromRanges.size() != 1 || toRanges.size() != 1)

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index b50e5af..5886ae0 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1431,7 +1431,7 @@ public class Sequence extends ASequence implements SequenceI
       DBRefEntry[] tmp = new DBRefEntry[1];
       for (DBRefEntry ref : dbrefs)
       {
-        if (!ref.isPrimary())
+        if (!ref.isPrimaryCandidate())
         {
           continue;
         }

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index e08b8cb..f20954e 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -338,11 +338,10 @@ public class SiftsClient implements SiftsClientI
       {
         continue;
       }
+      String canonicalSource = DBRefUtils.getCanonicalName(dbRef
+              .getSource());
       if (isValidDBRefEntry(dbRef)
-              && dbRef.isPrimary()
-              && (DBRefUtils.getCanonicalName(dbRef.getSource())
-                      .equalsIgnoreCase(DBRefSource.UNIPROT) || DBRefUtils
-                      .getCanonicalName(dbRef.getSource())
+              && (canonicalSource.equalsIgnoreCase(DBRefSource.UNIPROT) || canonicalSource
                       .equalsIgnoreCase(DBRefSource.PDB)))
       {
         return dbRef;

diff --git a/test/jalview/datamodel/DBRefEntryTest.java b/test/jalview/datamodel/DBRefEntryTest.java
index ee0bd41..7b1ab57 100644 (file)
--- a/test/jalview/datamodel/DBRefEntryTest.java
+++ b/test/jalview/datamodel/DBRefEntryTest.java
@@ -140,80 +140,80 @@ public class DBRefEntryTest
   }
 
   @Test(groups = { "Functional" })
-  public void testIsPrimary()
+  public void testIsPrimaryCandidate()
   {
     DBRefEntry dbr = new DBRefEntry(DBRefSource.UNIPROT, "", "Q12345");
-    assertTrue(dbr.isPrimary());
+    assertTrue(dbr.isPrimaryCandidate());
 
     /*
      *  1:1 mapping - ok
      */
     dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 1, 3 }, 1,
             1));
-    assertTrue(dbr.isPrimary());
+    assertTrue(dbr.isPrimaryCandidate());
 
     /*
      *  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());
+    assertFalse(dbr.isPrimaryCandidate());
 
     /*
      *  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());
+    assertFalse(dbr.isPrimaryCandidate());
 
     /*
      *  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());
+    assertFalse(dbr.isPrimaryCandidate());
     dbr.setMap(null);
-    assertTrue(dbr.isPrimary());
+    assertTrue(dbr.isPrimaryCandidate());
 
     /*
      * Version string is prefixed with another dbref source string (fail)
      */
     dbr.setVersion(DBRefSource.EMBL + ":0");
-    assertFalse(dbr.isPrimary());
+    assertFalse(dbr.isPrimaryCandidate());
 
     /*
      * Version string is alphanumeric
      */
     dbr.setVersion("0.1.b");
-    assertTrue(dbr.isPrimary());
+    assertTrue(dbr.isPrimaryCandidate());
 
     /*
      * null version string can't be primary ref
      */
     dbr.setVersion(null);
-    assertFalse(dbr.isPrimary());
+    assertFalse(dbr.isPrimaryCandidate());
     dbr.setVersion("");
-    assertTrue(dbr.isPrimary());
+    assertTrue(dbr.isPrimaryCandidate());
 
     /*
      *  1:1 mapping and sequenceRef (fail)
      */
     dbr.setMap(new Mapping(new Sequence("foo", "ASDF"), new int[] { 1, 3 },
             new int[] { 1, 3 }, 1, 1));
-    assertFalse(dbr.isPrimary());
+    assertFalse(dbr.isPrimaryCandidate());
 
     /*
      * 1:3 mapping (fail)
      */
     dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 1, 3 }, 1,
             3));
-    assertFalse(dbr.isPrimary());
+    assertFalse(dbr.isPrimaryCandidate());
 
     /*
      * 2:2 mapping with shift (expected fail, but maybe use case for a pass)
      */
     dbr.setMap(new Mapping(null, new int[] { 1, 4 }, new int[] { 1, 4 }, 2,
             2));
-    assertFalse(dbr.isPrimary());
+    assertFalse(dbr.isPrimaryCandidate());
   }
 }

diff --git a/test/jalview/ext/ensembl/EnsemblXrefTest.java b/test/jalview/ext/ensembl/EnsemblXrefTest.java
index 4dc8ab2..df1c1ad 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblXrefTest.java
+++ b/test/jalview/ext/ensembl/EnsemblXrefTest.java
@@ -44,12 +44,12 @@ public class EnsemblXrefTest
     assertEquals(2, dbrefs.size());
     assertEquals("CCDS", dbrefs.get(0).getSource());
     assertEquals("CCDS5863", dbrefs.get(0).getAccessionId());
-    assertFalse(dbrefs.get(0).isPrimary());
+    assertFalse(dbrefs.get(0).isPrimaryCandidate());
     assertEquals(dbName + ":" + dbVers, dbrefs.get(0).getVersion());
     // Uniprot name should get converted to Jalview canonical form
     assertEquals("UNIPROT", dbrefs.get(1).getSource());
     assertEquals("P15056", dbrefs.get(1).getAccessionId());
     assertEquals(dbName + ":" + dbVers, dbrefs.get(1).getVersion());
-    assertFalse(dbrefs.get(1).isPrimary());
+    assertFalse(dbrefs.get(1).isPrimaryCandidate());
   }
 }