JAL-3187 update alignAs code and unit tests for 'shared dataset' case

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 77cc4d6..8e0335f 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -22,6 +22,7 @@ package jalview.analysis;
 
 import static jalview.io.gff.GffConstants.CLINICAL_SIGNIFICANCE;
 
+import jalview.commands.RemoveGapColCommand;
 import jalview.datamodel.AlignedCodon;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
@@ -2440,17 +2441,17 @@ public class AlignmentUtils
   }
 
   /**
-   * Computes non-synonymous peptide variants from codon variants and adds them
-   * as sequence_variant features on the protein sequence (one feature per
-   * allele variant). Selected attributes (variant id, clinical significance)
-   * are copied over to the new features.
+   * Computes non-synonymous peptide variants from codon variants and adds them as
+   * sequence_variant features on the protein sequence (one feature per allele
+   * variant). Selected attributes (variant id, clinical significance) are copied
+   * over to the new features.
    * 
    * @param peptide
-   *          the protein sequence
+   *                        the protein dataset (ungapped) sequence
    * @param peptidePos
-   *          the position to compute peptide variants for
+   *                        the position to compute peptide variants for
    * @param codonVariants
-   *          a list of dna variants per codon position
+   *                        a list of dna variants per codon position
    * @return the number of features added
    */
   static int computePeptideVariants(SequenceI peptide, int peptidePos,
@@ -2837,6 +2838,17 @@ public class AlignmentUtils
    */
   public static int alignAs(AlignmentI unaligned, AlignmentI aligned)
   {
+    /*
+     * easy case - aligning a copy of aligned sequences
+     */
+    if (alignAsSameSequences(unaligned, aligned))
+    {
+      return unaligned.getHeight();
+    }
+
+    /*
+     * fancy case - aligning via mappings between sequences
+     */
     List<SequenceI> unmapped = new ArrayList<>();
     Map<Integer, Map<SequenceI, Character>> columnMap = buildMappedColumnsMap(
             unaligned, aligned, unmapped);
@@ -2902,9 +2914,7 @@ public class AlignmentUtils
    *                    - 'guide' alignment containing sequences derived from same
    *                    dataset as unaligned
    * @return
-   * @deprecated probably obsolete and incomplete
    */
-  @Deprecated
   static boolean alignAsSameSequences(AlignmentI unaligned,
           AlignmentI aligned)
   {
@@ -2975,6 +2985,12 @@ public class AlignmentUtils
       }
     }
 
+    /*
+     * finally remove gapped columns (e.g. introns)
+     */
+    new RemoveGapColCommand("", unaligned.getSequencesArray(), 0,
+            unaligned.getWidth() - 1, unaligned);
+
     return true;
   }
 

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 14559dd..dabd3ee 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -2044,41 +2044,48 @@ public class AlignmentUtilsTests
      * NB setting "id" (as returned by Ensembl for features in JSON format);
      * previously "ID" (as returned for GFF3 format)
      */
-    SequenceFeature sf1 = new SequenceFeature("sequence_variant", "", 1, 1,
+    SequenceFeature sf1 = new SequenceFeature("sequence_variant", "", 10,
+            10,
             0f, ensembl);
     sf1.setValue("alleles", "A,G"); // AAA -> GAA -> K/E
     sf1.setValue("id", "var1.125A>G");
 
-    SequenceFeature sf2 = new SequenceFeature("sequence_variant", "", 1, 1,
+    SequenceFeature sf2 = new SequenceFeature("sequence_variant", "", 10,
+            10,
             0f, dbSnp);
     sf2.setValue("alleles", "A,C"); // AAA -> CAA -> K/Q
     sf2.setValue("id", "var2");
     sf2.setValue("clinical_significance", "Dodgy");
 
-    SequenceFeature sf3 = new SequenceFeature("sequence_variant", "", 1, 1,
+    SequenceFeature sf3 = new SequenceFeature("sequence_variant", "", 11,
+            11,
             0f, dbSnp);
     sf3.setValue("alleles", "A,T"); // AAA -> TAA -> stop codon
     sf3.setValue("id", "var3");
     sf3.setValue("clinical_significance", "Bad");
 
-    SequenceFeature sf4 = new SequenceFeature("sequence_variant", "", 3, 3,
+    SequenceFeature sf4 = new SequenceFeature("sequence_variant", "", 12,
+            12,
             0f, cosmic);
     sf4.setValue("alleles", "A,G"); // AAA -> AAG synonymous
     sf4.setValue("id", "var4");
     sf4.setValue("clinical_significance", "None");
 
-    SequenceFeature sf5 = new SequenceFeature("sequence_variant", "", 3, 3,
+    SequenceFeature sf5 = new SequenceFeature("sequence_variant", "", 12,
+            12,
             0f, ensembl);
     sf5.setValue("alleles", "A,T"); // AAA -> AAT -> K/N
     sf5.setValue("id", "sequence_variant:var5"); // prefix gets stripped off
     sf5.setValue("clinical_significance", "Benign");
 
-    SequenceFeature sf6 = new SequenceFeature("sequence_variant", "", 6, 6,
+    SequenceFeature sf6 = new SequenceFeature("sequence_variant", "", 15,
+            15,
             0f, dbSnp);
     sf6.setValue("alleles", "T,C"); // TTT -> TTC synonymous
     sf6.setValue("id", "var6");
 
-    SequenceFeature sf7 = new SequenceFeature("sequence_variant", "", 8, 8,
+    SequenceFeature sf7 = new SequenceFeature("sequence_variant", "", 17,
+            17,
             0f, cosmic);
     sf7.setValue("alleles", "C,A,G"); // CCC -> CAC,CGC -> P/H/R
     sf7.setValue("id", "var7");
@@ -2103,7 +2110,7 @@ public class AlignmentUtilsTests
     // codon2Variants.add(new DnaVariant("A"));
     codon3Variants.add(new DnaVariant("A", sf4));
     codon3Variants.add(new DnaVariant("A", sf5));
-    AlignmentUtils.computePeptideVariants(peptide, 1, codonVariants);
+    AlignmentUtils.computePeptideVariants(peptide, 10, codonVariants);
 
     /*
      * compute variants for protein position 2
@@ -2114,7 +2121,7 @@ public class AlignmentUtilsTests
     codon1Variants.add(new DnaVariant("T"));
     codon2Variants.add(new DnaVariant("T"));
     codon3Variants.add(new DnaVariant("T", sf6));
-    AlignmentUtils.computePeptideVariants(peptide, 2, codonVariants);
+    AlignmentUtils.computePeptideVariants(peptide, 11, codonVariants);
 
     /*
      * compute variants for protein position 3
@@ -2125,7 +2132,7 @@ public class AlignmentUtilsTests
     codon1Variants.add(new DnaVariant("C"));
     codon2Variants.add(new DnaVariant("C", sf7));
     codon3Variants.add(new DnaVariant("C"));
-    AlignmentUtils.computePeptideVariants(peptide, 3, codonVariants);
+    AlignmentUtils.computePeptideVariants(peptide, 12, codonVariants);
 
     /*
      * verify added sequence features for
@@ -2149,55 +2156,55 @@ public class AlignmentUtilsTests
      */
     // AAA -> AAT -> K/N
     SequenceFeature sf = sfs.get(0);
-    assertEquals(1, sf.getBegin());
-    assertEquals(1, sf.getEnd());
+    assertEquals(10, sf.getBegin());
+    assertEquals(10, sf.getEnd());
     assertEquals("nonsynonymous_variant", sf.getType());
-    assertEquals("p.Lys1Asn", sf.getDescription());
+    assertEquals("p.Lys10Asn", sf.getDescription());
     assertEquals("var5", sf.getValue("id"));
     assertEquals("Benign", sf.getValue("clinical_significance"));
     assertEquals("id=var5;clinical_significance=Benign",
             sf.getAttributes());
     assertEquals(1, sf.links.size());
     assertEquals(
-            "p.Lys1Asn var5|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var5",
+            "p.Lys10Asn var5|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var5",
             sf.links.get(0));
     assertEquals(ensembl, sf.getFeatureGroup());
 
     // AAA -> CAA -> K/Q
     sf = sfs.get(1);
-    assertEquals(1, sf.getBegin());
-    assertEquals(1, sf.getEnd());
+    assertEquals(10, sf.getBegin());
+    assertEquals(10, sf.getEnd());
     assertEquals("nonsynonymous_variant", sf.getType());
-    assertEquals("p.Lys1Gln", sf.getDescription());
+    assertEquals("p.Lys10Gln", sf.getDescription());
     assertEquals("var2", sf.getValue("id"));
     assertEquals("Dodgy", sf.getValue("clinical_significance"));
     assertEquals("id=var2;clinical_significance=Dodgy", sf.getAttributes());
     assertEquals(1, sf.links.size());
     assertEquals(
-            "p.Lys1Gln var2|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var2",
+            "p.Lys10Gln var2|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var2",
             sf.links.get(0));
     assertEquals(dbSnp, sf.getFeatureGroup());
 
     // AAA -> GAA -> K/E
     sf = sfs.get(2);
-    assertEquals(1, sf.getBegin());
-    assertEquals(1, sf.getEnd());
+    assertEquals(10, sf.getBegin());
+    assertEquals(10, sf.getEnd());
     assertEquals("nonsynonymous_variant", sf.getType());
-    assertEquals("p.Lys1Glu", sf.getDescription());
+    assertEquals("p.Lys10Glu", sf.getDescription());
     assertEquals("var1.125A>G", sf.getValue("id"));
     assertNull(sf.getValue("clinical_significance"));
     assertEquals("id=var1.125A>G", sf.getAttributes());
     assertEquals(1, sf.links.size());
     // link to variation is urlencoded
     assertEquals(
-            "p.Lys1Glu var1.125A>G|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var1.125A%3EG",
+            "p.Lys10Glu var1.125A>G|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var1.125A%3EG",
             sf.links.get(0));
     assertEquals(ensembl, sf.getFeatureGroup());
 
     // AAA -> TAA -> stop codon
     sf = sfs.get(3);
-    assertEquals(1, sf.getBegin());
-    assertEquals(1, sf.getEnd());
+    assertEquals(10, sf.getBegin());
+    assertEquals(10, sf.getEnd());
     assertEquals("stop_gained", sf.getType());
     assertEquals("Aaa/Taa", sf.getDescription());
     assertEquals("var3", sf.getValue("id"));
@@ -2211,8 +2218,8 @@ public class AlignmentUtilsTests
 
     // AAA -> AAG synonymous
     sf = sfs.get(4);
-    assertEquals(1, sf.getBegin());
-    assertEquals(1, sf.getEnd());
+    assertEquals(10, sf.getBegin());
+    assertEquals(10, sf.getEnd());
     assertEquals("synonymous_variant", sf.getType());
     assertEquals("aaA/aaG", sf.getDescription());
     assertEquals("var4", sf.getValue("id"));
@@ -2226,8 +2233,8 @@ public class AlignmentUtilsTests
 
     // TTT -> TTC synonymous
     sf = sfs.get(5);
-    assertEquals(2, sf.getBegin());
-    assertEquals(2, sf.getEnd());
+    assertEquals(11, sf.getBegin());
+    assertEquals(11, sf.getEnd());
     assertEquals("synonymous_variant", sf.getType());
     assertEquals("ttT/ttC", sf.getDescription());
     assertEquals("var6", sf.getValue("id"));
@@ -2242,31 +2249,31 @@ public class AlignmentUtilsTests
     // var7 generates two distinct protein variant features (two alleles)
     // CCC -> CGC -> P/R
     sf = sfs.get(6);
-    assertEquals(3, sf.getBegin());
-    assertEquals(3, sf.getEnd());
+    assertEquals(12, sf.getBegin());
+    assertEquals(12, sf.getEnd());
     assertEquals("nonsynonymous_variant", sf.getType());
-    assertEquals("p.Pro3Arg", sf.getDescription());
+    assertEquals("p.Pro12Arg", sf.getDescription());
     assertEquals("var7", sf.getValue("id"));
     assertEquals("Good", sf.getValue("clinical_significance"));
     assertEquals("id=var7;clinical_significance=Good", sf.getAttributes());
     assertEquals(1, sf.links.size());
     assertEquals(
-            "p.Pro3Arg var7|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var7",
+            "p.Pro12Arg var7|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var7",
             sf.links.get(0));
     assertEquals(cosmic, sf.getFeatureGroup());
 
     // CCC -> CAC -> P/H
     sf = sfs.get(7);
-    assertEquals(3, sf.getBegin());
-    assertEquals(3, sf.getEnd());
+    assertEquals(12, sf.getBegin());
+    assertEquals(12, sf.getEnd());
     assertEquals("nonsynonymous_variant", sf.getType());
-    assertEquals("p.Pro3His", sf.getDescription());
+    assertEquals("p.Pro12His", sf.getDescription());
     assertEquals("var7", sf.getValue("id"));
     assertEquals("Good", sf.getValue("clinical_significance"));
     assertEquals("id=var7;clinical_significance=Good", sf.getAttributes());
     assertEquals(1, sf.links.size());
     assertEquals(
-            "p.Pro3His var7|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var7",
+            "p.Pro12His var7|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var7",
             sf.links.get(0));
     assertEquals(cosmic, sf.getFeatureGroup());
   }
@@ -2591,9 +2598,16 @@ public class AlignmentUtilsTests
     AlignmentI al2 = new Alignment(new SequenceI[] { dna3, dna4 });
     ((Alignment) al2).createDatasetAlignment();
 
+    /*
+     * alignment removes gapped columns (two internal, two trailing)
+     */
     assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
-    assertEquals(seq1, al1.getSequenceAt(0).getSequenceAsString());
-    assertEquals(seq2, al1.getSequenceAt(1).getSequenceAsString());
+    String aligned1 = "-cc-GG-GTTT-aaa";
+    assertEquals(aligned1,
+            al1.getSequenceAt(0).getSequenceAsString());
+    String aligned2 = "C--C-Cgg-gtttAAA";
+    assertEquals(aligned2,
+            al1.getSequenceAt(1).getSequenceAsString());
 
     /*
      * add another sequence to 'aligned' - should still succeed, since
@@ -2603,8 +2617,8 @@ public class AlignmentUtilsTests
     dna5.createDatasetSequence();
     al2.addSequence(dna5);
     assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
-    assertEquals(seq1, al1.getSequenceAt(0).getSequenceAsString());
-    assertEquals(seq2, al1.getSequenceAt(1).getSequenceAsString());
+    assertEquals(aligned1, al1.getSequenceAt(0).getSequenceAsString());
+    assertEquals(aligned2, al1.getSequenceAt(1).getSequenceAsString());
 
     /*
      * add another sequence to 'unaligned' - should fail, since now not
@@ -2622,15 +2636,15 @@ public class AlignmentUtilsTests
   {
     SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
     SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
-    SequenceI as1 = dna1.deriveSequence();
-    SequenceI as2 = dna1.deriveSequence().getSubSequence(3, 7);
-    SequenceI as3 = dna2.deriveSequence();
+    SequenceI as1 = dna1.deriveSequence(); // cccGGGTTTaaa/1-12
+    SequenceI as2 = dna1.deriveSequence().getSubSequence(3, 7); // GGGT/4-7
+    SequenceI as3 = dna2.deriveSequence(); // CCCgggtttAAA/1-12
     as1.insertCharAt(6, 5, '-');
-    String s_as1 = as1.getSequenceAsString();
+    assertEquals("cccGGG-----TTTaaa", as1.getSequenceAsString());
     as2.insertCharAt(6, 5, '-');
-    String s_as2 = as2.getSequenceAsString();
-    as3.insertCharAt(6, 5, '-');
-    String s_as3 = as3.getSequenceAsString();
+    assertEquals("GGGT-----", as2.getSequenceAsString());
+    as3.insertCharAt(3, 5, '-');
+    assertEquals("CCC-----gggtttAAA", as3.getSequenceAsString());
     AlignmentI aligned = new Alignment(new SequenceI[] { as1, as2, as3 });
 
     // why do we need to cast this still ?
@@ -2642,10 +2656,13 @@ public class AlignmentUtilsTests
         uas3 });
     ((Alignment) tobealigned).createDatasetAlignment();
 
+    /*
+     * alignAs lines up dataset sequences and removes empty columns (two)
+     */
     assertTrue(AlignmentUtils.alignAsSameSequences(tobealigned, aligned));
-    assertEquals(s_as1, uas1.getSequenceAsString());
-    assertEquals(s_as2, uas2.getSequenceAsString());
-    assertEquals(s_as3, uas3.getSequenceAsString());
+    assertEquals("cccGGG---TTTaaa", uas1.getSequenceAsString());
+    assertEquals("GGGT", uas2.getSequenceAsString());
+    assertEquals("CCC---gggtttAAA", uas3.getSequenceAsString());
   }
 
   @Test(groups = { "Functional" })