JAL-2110 add 'products' parameter to filter results in madeCdsAlignment

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 74066d7..f94d393 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -1407,11 +1407,14 @@ public class AlignmentUtils
    *          aligned dna sequences
    * @param dataset
    *          - throws error if not given a dataset
+   * @param products
+   *          (optional) to restrict results to CDS that map to specified
+   *          protein products
    * @return an alignment whose sequences are the cds-only parts of the dna
    *         sequences (or null if no mappings are found)
    */
   public static AlignmentI makeCdsAlignment(SequenceI[] dna,
-          AlignmentI dataset)
+          AlignmentI dataset, AlignmentI products)
   {
     if (dataset.getDataset() != null)
     {
@@ -1420,7 +1423,16 @@ public class AlignmentUtils
     }
     List<SequenceI> cdsSeqs = new ArrayList<SequenceI>();
     List<AlignedCodonFrame> mappings = dataset.getCodonFrames();
-    
+    HashSet<SequenceI> productSeqs = null;
+    if (products != null)
+    {
+      productSeqs = new HashSet<SequenceI>();
+      for (SequenceI seq : products.getSequences())
+      {
+        productSeqs.add(seq.getDatasetSequence() == null ? seq : seq
+                .getDatasetSequence());
+      }
+    }
 
     /*
      * construct CDS sequences from the (cds-to-protein) mappings made earlier;
@@ -1453,9 +1465,20 @@ public class AlignmentUtils
            * the dna mapping's product
            */
           SequenceI cdsSeq = null;
+
           // TODO better mappings collection data model so we can do
-          // a table lookup instead of double loops to find mappings
+          // a direct lookup instead of double loops to find mappings
+
           SequenceI proteinProduct = aMapping.getTo();
+
+          /*
+           * skip if not mapped to one of a specified set of proteins
+           */
+          if (productSeqs != null && !productSeqs.contains(proteinProduct))
+          {
+            continue;
+          }
+
           for (AlignedCodonFrame acf : MappingUtils
                   .findMappingsForSequence(proteinProduct, mappings))
           {
@@ -1544,7 +1567,7 @@ public class AlignmentUtils
 
     AlignmentI cds = new Alignment(cdsSeqs.toArray(new SequenceI[cdsSeqs
             .size()]));
-    cds.setDataset((Alignment) dataset);
+    cds.setDataset(dataset);
 
     return cds;
   }

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 54b1cb6..64bdf44 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -4768,7 +4768,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           if (dna)
           {
             copyAlignment = AlignmentUtils.makeCdsAlignment(
-                    sequenceSelection, dataset);
+                    sequenceSelection, dataset, xrefsAlignment);
             if (copyAlignment.getHeight() == 0)
             {
               System.err.println("Failed to make CDS alignment");

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 3de2ce4..d704ec6 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -981,16 +981,6 @@ public class AlignmentUtilsTests
     dna2.createDatasetSequence();
     pep1.createDatasetSequence();
     pep2.createDatasetSequence();
-    dna1.addSequenceFeature(new SequenceFeature("CDS", "cds1", 4, 6, 0f,
-            null));
-    dna1.addSequenceFeature(new SequenceFeature("CDS", "cds2", 10, 12, 0f,
-            null));
-    dna2.addSequenceFeature(new SequenceFeature("CDS", "cds3", 1, 3, 0f,
-            null));
-    dna2.addSequenceFeature(new SequenceFeature("CDS", "cds4", 7, 9, 0f,
-            null));
-    dna2.addSequenceFeature(new SequenceFeature("CDS", "cds5", 13, 15, 0f,
-            null));
     AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
     dna.setDataset(null);
 
@@ -1009,7 +999,7 @@ public class AlignmentUtilsTests
      * execute method under test:
      */
     AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
-        dna1, dna2 }, dna.getDataset());
+        dna1, dna2 }, dna.getDataset(), null);
 
     assertEquals(2, cds.getSequences().size());
     assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
@@ -1115,18 +1105,6 @@ public class AlignmentUtilsTests
     pep1.createDatasetSequence();
     pep2.createDatasetSequence();
     pep3.createDatasetSequence();
-    dna1.addSequenceFeature(new SequenceFeature("CDS", "cds1", 4, 6, 0f,
-            null));
-    dna1.addSequenceFeature(new SequenceFeature("CDS", "cds2", 10, 12, 0f,
-            null));
-    dna1.addSequenceFeature(new SequenceFeature("CDS", "cds3", 1, 3, 0f,
-            null));
-    dna1.addSequenceFeature(new SequenceFeature("CDS", "cds4", 7, 9, 0f,
-            null));
-    dna1.addSequenceFeature(new SequenceFeature("CDS", "cds5", 1, 3, 0f,
-            null));
-    dna1.addSequenceFeature(new SequenceFeature("CDS", "cds6", 10, 12, 0f,
-            null));
     pep1.getDatasetSequence().addDBRef(
             new DBRefEntry("EMBLCDS", "2", "A12345"));
     pep2.getDatasetSequence().addDBRef(
@@ -1166,7 +1144,7 @@ public class AlignmentUtilsTests
      * execute method under test
      */
     AlignmentI cdsal = AlignmentUtils.makeCdsAlignment(
-            new SequenceI[] { dna1 }, dna.getDataset());
+            new SequenceI[] { dna1 }, dna.getDataset(), null);
 
     /*
      * Verify we have 3 cds sequences, mapped to pep1/2/3 respectively
@@ -1538,18 +1516,6 @@ public class AlignmentUtilsTests
     dna3.createDatasetSequence();
     pep1.createDatasetSequence();
     pep2.createDatasetSequence();
-    dna1.addSequenceFeature(new SequenceFeature("CDS", "cds1", 4, 8, 0f,
-            null));
-    dna1.addSequenceFeature(new SequenceFeature("CDS", "cds2", 9, 12, 0f,
-            null));
-    dna1.addSequenceFeature(new SequenceFeature("CDS", "cds3", 16, 18, 0f,
-            null));
-    dna2.addSequenceFeature(new SequenceFeature("CDS", "cds", 4, 8, 0f,
-            null));
-    dna2.addSequenceFeature(new SequenceFeature("CDS", "cds", 12, 12, 0f,
-            null));
-    dna2.addSequenceFeature(new SequenceFeature("CDS", "cds", 16, 18, 0f,
-            null));
 
     AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
     dna.setDataset(null);
@@ -1567,7 +1533,7 @@ public class AlignmentUtilsTests
     dna.addCodonFrame(acf);
   
     AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
-        dna1, dna2, dna3 }, dna.getDataset());
+        dna1, dna2, dna3 }, dna.getDataset(), null);
     List<SequenceI> cdsSeqs = cds.getSequences();
     assertEquals(2, cdsSeqs.size());
     assertEquals("GGGCCCTTTGGG", cdsSeqs.get(0).getSequenceAsString());
@@ -2244,4 +2210,138 @@ public class AlignmentUtilsTests
     assertEquals('T', map.get(11).get(seq1).charValue());
     assertEquals('T', map.get(12).get(seq1).charValue());
   }
+
+  /**
+   * Test for the case where the products for which we want CDS are specified.
+   * This is to represent the case where EMBL has CDS mappings to both Uniprot
+   * and EMBLCDSPROTEIN. makeCdsAlignment() should only return the mappings for
+   * the protein sequences specified.
+   */
+  @Test(groups = { "Functional" })
+  public void testMakeCdsAlignment_filterProducts()
+  {
+    SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
+    SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC");
+    SequenceI pep1 = new Sequence("Uniprot|pep1", "GF");
+    SequenceI pep2 = new Sequence("Uniprot|pep2", "GFP");
+    SequenceI pep3 = new Sequence("EMBL|pep3", "GF");
+    SequenceI pep4 = new Sequence("EMBL|pep4", "GFP");
+    dna1.createDatasetSequence();
+    dna2.createDatasetSequence();
+    pep1.createDatasetSequence();
+    pep2.createDatasetSequence();
+    pep3.createDatasetSequence();
+    pep4.createDatasetSequence();
+    AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
+    dna.setDataset(null);
+    AlignmentI emblPeptides = new Alignment(new SequenceI[] { pep3, pep4 });
+    emblPeptides.setDataset(null);
+  
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+    MapList map = new MapList(new int[] { 4, 6, 10, 12 },
+            new int[] { 1, 2 }, 3, 1);
+    acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
+    acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
+    dna.addCodonFrame(acf);
+
+    acf = new AlignedCodonFrame();
+    map = new MapList(new int[] { 1, 3, 7, 9, 13, 15 }, new int[] { 1, 3 },
+            3, 1);
+    acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
+    acf.addMap(dna2.getDatasetSequence(), pep4.getDatasetSequence(), map);
+    dna.addCodonFrame(acf);
+  
+    /*
+     * execute method under test to find CDS for EMBL peptides only
+     */
+    AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
+        dna1, dna2 }, dna.getDataset(), emblPeptides);
+  
+    assertEquals(2, cds.getSequences().size());
+    assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
+    assertEquals("GGGTTTCCC", cds.getSequenceAt(1).getSequenceAsString());
+  
+    /*
+     * verify shared, extended alignment dataset
+     */
+    assertSame(dna.getDataset(), cds.getDataset());
+    assertTrue(dna.getDataset().getSequences()
+            .contains(cds.getSequenceAt(0).getDatasetSequence()));
+    assertTrue(dna.getDataset().getSequences()
+            .contains(cds.getSequenceAt(1).getDatasetSequence()));
+  
+    /*
+     * Verify mappings from CDS to peptide, cDNA to CDS, and cDNA to peptide
+     * the mappings are on the shared alignment dataset
+     */
+    List<AlignedCodonFrame> cdsMappings = cds.getDataset().getCodonFrames();
+    /*
+     * 6 mappings, 2*(DNA->CDS), 2*(DNA->Pep), 2*(CDS->Pep) 
+     */
+    assertEquals(6, cdsMappings.size());
+  
+    /*
+     * verify that mapping sets for dna and cds alignments are different
+     * [not current behaviour - all mappings are on the alignment dataset]  
+     */
+    // select -> subselect type to test.
+    // Assert.assertNotSame(dna.getCodonFrames(), cds.getCodonFrames());
+    // assertEquals(4, dna.getCodonFrames().size());
+    // assertEquals(4, cds.getCodonFrames().size());
+  
+    /*
+     * Two mappings involve pep3 (dna to pep3, cds to pep3)
+     * Mapping from pep3 to GGGTTT in first new exon sequence
+     */
+    List<AlignedCodonFrame> pep3Mappings = MappingUtils
+            .findMappingsForSequence(pep3, cdsMappings);
+    assertEquals(2, pep3Mappings.size());
+    List<AlignedCodonFrame> mappings = MappingUtils
+            .findMappingsForSequence(cds.getSequenceAt(0), pep3Mappings);
+    assertEquals(1, mappings.size());
+  
+    // map G to GGG
+    SearchResults sr = MappingUtils.buildSearchResults(pep3, 1, mappings);
+    assertEquals(1, sr.getResults().size());
+    Match m = sr.getResults().get(0);
+    assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
+    assertEquals(1, m.getStart());
+    assertEquals(3, m.getEnd());
+    // map F to TTT
+    sr = MappingUtils.buildSearchResults(pep3, 2, mappings);
+    m = sr.getResults().get(0);
+    assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
+    assertEquals(4, m.getStart());
+    assertEquals(6, m.getEnd());
+  
+    /*
+     * Two mappings involve pep4 (dna to pep4, cds to pep4)
+     * Verify mapping from pep4 to GGGTTTCCC in second new exon sequence
+     */
+    List<AlignedCodonFrame> pep4Mappings = MappingUtils
+            .findMappingsForSequence(pep4, cdsMappings);
+    assertEquals(2, pep4Mappings.size());
+    mappings = MappingUtils.findMappingsForSequence(cds.getSequenceAt(1),
+            pep4Mappings);
+    assertEquals(1, mappings.size());
+    // map G to GGG
+    sr = MappingUtils.buildSearchResults(pep4, 1, mappings);
+    assertEquals(1, sr.getResults().size());
+    m = sr.getResults().get(0);
+    assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
+    assertEquals(1, m.getStart());
+    assertEquals(3, m.getEnd());
+    // map F to TTT
+    sr = MappingUtils.buildSearchResults(pep4, 2, mappings);
+    m = sr.getResults().get(0);
+    assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
+    assertEquals(4, m.getStart());
+    assertEquals(6, m.getEnd());
+    // map P to CCC
+    sr = MappingUtils.buildSearchResults(pep4, 3, mappings);
+    m = sr.getResults().get(0);
+    assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
+    assertEquals(7, m.getStart());
+    assertEquals(9, m.getEnd());
+  }
 }