JAL-2738 JAL-2154 add DBRef from transcript to synthesized CDS and vice

versa

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 6acac01..c88a462 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -1633,7 +1633,7 @@ public class AlignmentUtils
           AlignmentI dataset, SequenceI[] products)
   {
     if (dataset == null || dataset.getDataset() != null)
-    {
+  {
       throw new IllegalArgumentException(
               "IMPLEMENTATION ERROR: dataset.getDataset() must be null!");
     }
@@ -1645,10 +1645,10 @@ public class AlignmentUtils
     {
       productSeqs = new HashSet<SequenceI>();
       for (SequenceI seq : products)
-      {
-        productSeqs.add(seq.getDatasetSequence() == null ? seq
-                : seq.getDatasetSequence());
-      }
+    {
+        productSeqs.add(seq.getDatasetSequence() == null ? seq : seq
+                .getDatasetSequence());
+    }
     }
 
     /*
@@ -1670,15 +1670,15 @@ public class AlignmentUtils
       List<AlignedCodonFrame> seqMappings = MappingUtils
               .findMappingsForSequence(dnaSeq, mappings);
       for (AlignedCodonFrame mapping : seqMappings)
-      {
+    {
         List<Mapping> mappingsFromSequence = mapping
                 .getMappingsFromSequence(dnaSeq);
 
         for (Mapping aMapping : mappingsFromSequence)
-        {
+      {
           MapList mapList = aMapping.getMap();
           if (mapList.getFromRatio() == 1)
-          {
+        {
             /*
              * not a dna-to-protein mapping (likely dna-to-cds)
              */
@@ -1704,15 +1704,15 @@ public class AlignmentUtils
           if (cdsSeq != null)
           {
             if (!foundSeqs.contains(cdsSeq))
-            {
+          {
               foundSeqs.add(cdsSeq);
               SequenceI derivedSequence = cdsSeq.deriveSequence();
               cdsSeqs.add(derivedSequence);
               if (!dataset.getSequences().contains(cdsSeq))
-              {
+            {
                 dataset.addSequence(cdsSeq);
-              }
             }
+          }
             continue;
           }
 
@@ -1740,9 +1740,8 @@ public class AlignmentUtils
           /*
            * add a mapping from CDS to the (unchanged) mapped to range
            */
-          List<int[]> cdsRange = Collections
-                  .singletonList(new int[]
-                  { 1, cdsSeq.getLength() });
+          List<int[]> cdsRange = Collections.singletonList(new int[] { 1,
+              cdsSeq.getLength() });
           MapList cdsToProteinMap = new MapList(cdsRange,
                   mapList.getToRanges(), mapList.getFromRatio(),
                   mapList.getToRatio());
@@ -1792,40 +1791,46 @@ public class AlignmentUtils
 
           for (DBRefEntry primRef : dnaDss.getPrimaryDBRefs())
           {
-            // creates a complementary cross-reference to the source sequence's
-            // primary reference.
-
-            DBRefEntry cdsCrossRef = new DBRefEntry(primRef.getSource(),
-                    primRef.getSource() + ":" + primRef.getVersion(),
-                    primRef.getAccessionId());
-            cdsCrossRef
-                    .setMap(new Mapping(dnaDss, new MapList(dnaToCdsMap)));
+            /*
+             * create a cross-reference from CDS to the source sequence's
+             * primary reference and vice versa
+             */
+
+            String source = primRef.getSource();
+            String version = primRef.getVersion();
+            DBRefEntry cdsCrossRef = new DBRefEntry(source, source + ":"
+                    + version, primRef.getAccessionId());
+            cdsCrossRef.setMap(new Mapping(dnaDss, new MapList(dnaToCdsMap
+                    .getInverse())));
             cdsSeqDss.addDBRef(cdsCrossRef);
 
+            dnaSeq.addDBRef(new DBRefEntry(source, version, cdsSeq
+                    .getName(), new Mapping(cdsSeqDss, dnaToCdsMap)));
+
             // problem here is that the cross-reference is synthesized -
             // cdsSeq.getName() may be like 'CDS|dnaaccession' or
             // 'CDS|emblcdsacc'
             // assuming cds version same as dna ?!?
 
-            DBRefEntry proteinToCdsRef = new DBRefEntry(primRef.getSource(),
-                    primRef.getVersion(), cdsSeq.getName());
+            DBRefEntry proteinToCdsRef = new DBRefEntry(source, version,
+                    cdsSeq.getName());
             //
-            proteinToCdsRef.setMap(
-                    new Mapping(cdsSeqDss, cdsToProteinMap.getInverse()));
+            proteinToCdsRef.setMap(new Mapping(cdsSeqDss, cdsToProteinMap
+                    .getInverse()));
             proteinProduct.addDBRef(proteinToCdsRef);
-          }
+        }
 
           /*
            * transfer any features on dna that overlap the CDS
            */
           transferFeatures(dnaSeq, cdsSeq, dnaToCdsMap, null,
                   SequenceOntologyI.CDS);
-        }
       }
     }
+    }
 
-    AlignmentI cds = new Alignment(
-            cdsSeqs.toArray(new SequenceI[cdsSeqs.size()]));
+    AlignmentI cds = new Alignment(cdsSeqs.toArray(new SequenceI[cdsSeqs
+            .size()]));
     cds.setDataset(dataset);
 
     return cds;

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 4439bb9..7c64193 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -1044,14 +1044,18 @@ public class AlignmentUtilsTests
     dna.addCodonFrame(acf);
 
     /*
-     * In this case, mappings originally came from matching Uniprot accessions - so need an xref on dna involving those regions. These are normally constructed from CDS annotation
+     * In this case, mappings originally came from matching Uniprot accessions 
+     * - so need an xref on dna involving those regions. 
+     * These are normally constructed from CDS annotation
      */
     DBRefEntry dna1xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep1",
             new Mapping(mapfordna1));
-    dna1.getDatasetSequence().addDBRef(dna1xref);
+    dna1.addDBRef(dna1xref);
+    assertEquals(2, dna1.getDBRefs().length); // to self and to pep1
     DBRefEntry dna2xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep2",
             new Mapping(mapfordna2));
-    dna2.getDatasetSequence().addDBRef(dna2xref);
+    dna2.addDBRef(dna2xref);
+    assertEquals(2, dna2.getDBRefs().length); // to self and to pep2
 
     /*
      * execute method under test:
@@ -1106,6 +1110,38 @@ public class AlignmentUtilsTests
     assertEquals(cdsMapping.getInverse(), dbref.getMap().getMap());
 
     /*
+     * verify cDNA has added a dbref with mapping to CDS
+     */
+    assertEquals(3, dna1.getDBRefs().length);
+    DBRefEntry dbRefEntry = dna1.getDBRefs()[2];
+    assertSame(cds1Dss, dbRefEntry.getMap().getTo());
+    MapList dnaToCdsMapping = new MapList(new int[] { 4, 6, 10, 12 },
+            new int[] { 1, 6 }, 1, 1);
+    assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
+    assertEquals(3, dna2.getDBRefs().length);
+    dbRefEntry = dna2.getDBRefs()[2];
+    assertSame(cds2Dss, dbRefEntry.getMap().getTo());
+    dnaToCdsMapping = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
+            new int[] { 1, 9 }, 1, 1);
+    assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
+
+    /*
+     * verify CDS has added a dbref with mapping to cDNA
+     */
+    assertEquals(2, cds1Dss.getDBRefs().length);
+    dbRefEntry = cds1Dss.getDBRefs()[1];
+    assertSame(dna1.getDatasetSequence(), dbRefEntry.getMap().getTo());
+    MapList cdsToDnaMapping = new MapList(new int[] { 1, 6 }, new int[] {
+        4, 6, 10, 12 }, 1, 1);
+    assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap());
+    assertEquals(2, cds2Dss.getDBRefs().length);
+    dbRefEntry = cds2Dss.getDBRefs()[1];
+    assertSame(dna2.getDatasetSequence(), dbRefEntry.getMap().getTo());
+    cdsToDnaMapping = new MapList(new int[] { 1, 9 }, new int[] { 1, 3, 7,
+        9, 13, 15 }, 1, 1);
+    assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap());
+
+    /*
      * Verify mappings from CDS to peptide, cDNA to CDS, and cDNA to peptide
      * the mappings are on the shared alignment dataset
      * 6 mappings, 2*(DNA->CDS), 2*(DNA->Pep), 2*(CDS->Pep)