JAL-3700 mapped sequence group includes short (or all gapped) sequences

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 6294ca1..177c54d 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -343,26 +343,23 @@ public final class MappingUtils
         firstUngappedPos++;
       }
 
-      /*
-       * If this sequence is only gaps in the selected range, skip it
-       */
-      if (firstUngappedPos > selectionEndRes)
-      {
-        continue;
-      }
+      boolean allGapped = (firstUngappedPos > selectionEndRes);
 
       int lastUngappedPos = selectionEndRes;
-      while (lastUngappedPos >= selectionStartRes
-              && Comparison.isGap(selected.getCharAt(lastUngappedPos)))
+      if (!allGapped)
       {
-        lastUngappedPos--;
+        while (lastUngappedPos >= selectionStartRes
+                && Comparison.isGap(selected.getCharAt(lastUngappedPos)))
+        {
+          lastUngappedPos--;
+        }
       }
 
       /*
        * Find the selected start/end residue positions in sequence
        */
-      int startResiduePos = selected.findPosition(firstUngappedPos);
-      int endResiduePos = selected.findPosition(lastUngappedPos);
+      int startResiduePos = allGapped ? 0 : selected.findPosition(firstUngappedPos);
+      int endResiduePos = allGapped ? 0 : selected.findPosition(lastUngappedPos);
 
       for (AlignedCodonFrame acf : codonFrames)
       {
@@ -376,6 +373,14 @@ public final class MappingUtils
           {
             continue;
           }
+          mappedGroup.addSequence(seq, false);
+          if (allGapped)
+          {
+            /*
+             * sequence is mapped but includes no mapped residues
+             */
+            continue;
+          }
           int mappedStartResidue = 0;
           int mappedEndResidue = 0;
           List<AlignedCodonFrame> mapping = Arrays.asList(acf);
@@ -403,7 +408,6 @@ public final class MappingUtils
           int mappedEndCol = seq.findIndex(mappedEndResidue) - 1;
           maxEndCol = maxEndCol == -1 ? mappedEndCol
                   : Math.max(maxEndCol, mappedEndCol);
-          mappedGroup.addSequence(seq, false);
           break;
         }
       }

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index 0997fec..08673ae 100644 (file)
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -26,7 +26,6 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.AssertJUnit.fail;
-
 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
 import java.awt.Color;
@@ -241,8 +240,8 @@ public class MappingUtilsTest
             .asList(new AlignedCodonFrame[]
             { acf });
 
-    AlignViewportI dnaView = new AlignViewport(cdna);
-    AlignViewportI proteinView = new AlignViewport(protein);
+    AlignViewportI theDnaView = new AlignViewport(cdna);
+    AlignViewportI theProteinView = new AlignViewport(protein);
     protein.setCodonFrames(acfList);
 
     /*
@@ -260,7 +259,7 @@ public class MappingUtilsTest
      * Verify the mapped sequence group in dna
      */
     SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg,
-            proteinView, dnaView);
+            theProteinView, theDnaView);
     assertTrue(mappedGroup.getColourText());
     assertSame(sg.getIdColour(), mappedGroup.getIdColour());
     assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
@@ -278,7 +277,7 @@ public class MappingUtilsTest
     sg.addSequence(cdna.getSequenceAt(0), false);
     sg.setStartRes(0);
     sg.setEndRes(2);
-    mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView);
+    mappedGroup = MappingUtils.mapSequenceGroup(sg, theDnaView, theProteinView);
     assertTrue(mappedGroup.getColourText());
     assertSame(sg.getIdColour(), mappedGroup.getIdColour());
     assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
@@ -532,8 +531,8 @@ public class MappingUtilsTest
             .asList(new AlignedCodonFrame[]
             { acf });
 
-    AlignViewportI dnaView = new AlignViewport(cdna);
-    AlignViewportI proteinView = new AlignViewport(protein);
+    AlignViewportI theDnaView = new AlignViewport(cdna);
+    AlignViewportI theProteinView = new AlignViewport(protein);
     protein.setCodonFrames(acfList);
 
     /*
@@ -553,7 +552,7 @@ public class MappingUtilsTest
      * Verify the mapped sequence group in dna
      */
     SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg,
-            proteinView, dnaView);
+            theProteinView, theDnaView);
     assertTrue(mappedGroup.getColourText());
     assertSame(sg.getIdColour(), mappedGroup.getIdColour());
     assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
@@ -574,7 +573,7 @@ public class MappingUtilsTest
     // select columns 2 and 3 in DNA which span protein columns 0 and 1
     sg.setStartRes(2);
     sg.setEndRes(3);
-    mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView);
+    mappedGroup = MappingUtils.mapSequenceGroup(sg, theDnaView, theProteinView);
     assertTrue(mappedGroup.getColourText());
     assertSame(sg.getIdColour(), mappedGroup.getIdColour());
     assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
@@ -599,11 +598,11 @@ public class MappingUtilsTest
      * viewport).
      */
     AlignmentI cdna = loadAlignment(
-            ">Seq1\nA-CG-GC--AT-CA\n>Seq2\n-TG-AC-AG-T-AT\n>Seq3\n-T--ACG-TAAT-G\n",
+            ">Cds11\nA-CG-GC--AT-CA\n>Cds2\n-TG-AC-AG-T-AT\n>Cds3\n-T--ACG-TAAT-G\n",
             FileFormat.Fasta);
     cdna.setDataset(null);
     AlignmentI protein = loadAlignment(
-            ">Seq1\n-KA-S\n>Seq2\n--L-QY\n>Seq3\nQ-V-M\n",
+            ">Pep1\n-KA-S\n>Pep2\n--L-QY\n>Pep3\nQ-V-M\n",
             FileFormat.Fasta);
     protein.setDataset(null);
     AlignedCodonFrame acf = new AlignedCodonFrame();
@@ -617,15 +616,14 @@ public class MappingUtilsTest
             .asList(new AlignedCodonFrame[]
             { acf });
 
-    AlignViewportI dnaView = new AlignViewport(cdna);
-    AlignViewportI proteinView = new AlignViewport(protein);
+    AlignViewportI theDnaView = new AlignViewport(cdna);
+    AlignViewportI theProteinView = new AlignViewport(protein);
     protein.setCodonFrames(acfList);
 
     /*
-     * Select Seq1 and Seq2 in the protein, column 1 (K/-). Expect mapped
-     * sequence group to cover Seq1, columns 0-3 (ACG). Because the selection
-     * only includes a gap in Seq2 there is no mappable selection region in the
-     * corresponding DNA.
+     * Select Pep1 and Pep2 in the protein, column 1 (K/-). Expect mapped
+     * sequence group to cover Cds1, columns 0-3 (ACG). Although the selection
+     * only includes a gap in Cds2, mapped Cds2 is included with 'no columns'
      */
     SequenceGroup sg = new SequenceGroup();
     sg.setColourText(true);
@@ -640,14 +638,15 @@ public class MappingUtilsTest
      * Verify the mapped sequence group in dna
      */
     SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg,
-            proteinView, dnaView);
+            theProteinView, theDnaView);
     assertTrue(mappedGroup.getColourText());
     assertSame(sg.getIdColour(), mappedGroup.getIdColour());
     assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
-    assertEquals(1, mappedGroup.getSequences().size());
+    assertEquals(2, mappedGroup.getSequences().size());
     assertSame(cdna.getSequenceAt(0), mappedGroup.getSequences().get(0));
-    // Seq2 in protein has a gap in column 1 - ignored
-    // Seq1 has K which should map to columns 0-3 in Seq1
+    assertSame(cdna.getSequenceAt(1), mappedGroup.getSequences().get(1));
+    // Pep2 in protein has a gap in column 1 - doesn't map to any column
+    // Pep1 has K which should map to columns 0-3 in Cds1
     assertEquals(0, mappedGroup.getStartRes());
     assertEquals(3, mappedGroup.getEndRes());
 
@@ -657,7 +656,7 @@ public class MappingUtilsTest
      */
     sg.setStartRes(2);
     sg.setEndRes(4);
-    mappedGroup = MappingUtils.mapSequenceGroup(sg, proteinView, dnaView);
+    mappedGroup = MappingUtils.mapSequenceGroup(sg, theProteinView, theDnaView);
     assertEquals(1, mappedGroup.getStartRes());
     assertEquals(13, mappedGroup.getEndRes());
 
@@ -670,19 +669,19 @@ public class MappingUtilsTest
     // select columns 4,5 - includes Seq1:codon2 (A) only
     sg.setStartRes(4);
     sg.setEndRes(5);
-    mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView);
+    mappedGroup = MappingUtils.mapSequenceGroup(sg, theDnaView, theProteinView);
     assertEquals(2, mappedGroup.getStartRes());
     assertEquals(2, mappedGroup.getEndRes());
 
     // add Seq2 to dna selection cols 4-5 include codons 1 and 2 (LQ)
     sg.addSequence(cdna.getSequenceAt(1), false);
-    mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView);
+    mappedGroup = MappingUtils.mapSequenceGroup(sg, theDnaView, theProteinView);
     assertEquals(2, mappedGroup.getStartRes());
     assertEquals(4, mappedGroup.getEndRes());
 
     // add Seq3 to dna selection cols 4-5 include codon 1 (Q)
     sg.addSequence(cdna.getSequenceAt(2), false);
-    mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView);
+    mappedGroup = MappingUtils.mapSequenceGroup(sg, theDnaView, theProteinView);
     assertEquals(0, mappedGroup.getStartRes());
     assertEquals(4, mappedGroup.getEndRes());
   }