From d2b08d9048af25114cff8deabbd320471119d88d Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 7 Jul 2016 16:51:51 +0100
Subject: [PATCH] JAL-2110 added alignAsSameSequences to handle 'direct'
 (copy) case

---
 src/jalview/analysis/AlignmentUtils.java       |   59 ++++++++++++++++++++++++
 test/jalview/analysis/AlignmentUtilsTests.java |   49 ++++++++++++++++++++
 2 files changed, 108 insertions(+)

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 20fcf25..17aab15 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -2535,6 +2535,17 @@ 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<SequenceI>();
     Map<Integer, Map<SequenceI, Character>> columnMap = buildMappedColumnsMap(
             unaligned, aligned, unmapped);
@@ -2587,6 +2598,54 @@ public class AlignmentUtils
   }
 
   /**
+   * If unaligned and aligned sequences share the same dataset sequences, then
+   * simply copies the aligned sequences to the unaligned sequences and returns
+   * true; else returns false
+   * 
+   * @param unaligned
+   * @param aligned
+   * @return
+   */
+  static boolean alignAsSameSequences(AlignmentI unaligned,
+          AlignmentI aligned)
+  {
+    if (aligned.getDataset() == null || unaligned.getDataset() == null)
+    {
+      return false; // should only pass alignments with datasets here
+    }
+
+    Map<SequenceI, SequenceI> alignedDatasets = new HashMap<SequenceI, SequenceI>();
+    for (SequenceI seq : aligned.getSequences())
+    {
+      alignedDatasets.put(seq.getDatasetSequence(), seq);
+    }
+
+    /*
+     * first pass - check whether all sequences to be aligned share a dataset
+     * sequence with an aligned sequence
+     */
+    for (SequenceI seq : unaligned.getSequences())
+    {
+      if (!alignedDatasets.containsKey(seq.getDatasetSequence()))
+      {
+        return false;
+      }
+    }
+
+    /*
+     * second pass - copy aligned sequences
+     */
+    for (SequenceI seq : unaligned.getSequences())
+    {
+      SequenceI alignedSequence = alignedDatasets.get(seq
+              .getDatasetSequence());
+      seq.setSequence(alignedSequence.getSequenceAsString());
+    }
+
+    return true;
+  }
+
+  /**
    * Returns a map whose key is alignment column number (base 1), and whose
    * values are a map of sequence characters in that column.
    * 
diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 727cf22..5c75992 100644
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -2394,4 +2394,53 @@ public class AlignmentUtilsTests
     assertEquals(7, m.getStart());
     assertEquals(9, m.getEnd());
   }
+
+  /**
+   * Test the method that just copies aligned sequences, provided all sequences
+   * to be aligned share the aligned sequence's dataset
+   */
+  @Test(groups = "Functional")
+  public void testAlignAsSameSequences()
+  {
+    SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
+    SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
+    AlignmentI al1 = new Alignment(new SequenceI[] { dna1, dna2 });
+    ((Alignment) al1).createDatasetAlignment();
+
+    SequenceI dna3 = new Sequence(dna1);
+    SequenceI dna4 = new Sequence(dna2);
+    assertSame(dna3.getDatasetSequence(), dna1.getDatasetSequence());
+    assertSame(dna4.getDatasetSequence(), dna2.getDatasetSequence());
+    String seq1 = "-cc-GG-GT-TT--aaa";
+    dna3.setSequence(seq1);
+    String seq2 = "C--C-Cgg--gtt-tAA-A-";
+    dna4.setSequence(seq2);
+    AlignmentI al2 = new Alignment(new SequenceI[] { dna3, dna4 });
+    ((Alignment) al2).createDatasetAlignment();
+    
+    assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
+    assertEquals(seq1, al1.getSequenceAt(0).getSequenceAsString());
+    assertEquals(seq2, al1.getSequenceAt(1).getSequenceAsString());
+
+    /*
+     * add another sequence to 'aligned' - should still succeed, since
+     * unaligned sequences still share a dataset with aligned sequences
+     */
+    SequenceI dna5 = new Sequence("dna5", "CCCgggtttAAA");
+    dna5.createDatasetSequence();
+    al2.addSequence(dna5);
+    assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
+    assertEquals(seq1, al1.getSequenceAt(0).getSequenceAsString());
+    assertEquals(seq2, al1.getSequenceAt(1).getSequenceAsString());
+
+    /*
+     * add another sequence to 'unaligned' - should fail, since now not
+     * all unaligned sequences share a dataset with aligned sequences
+     */
+    SequenceI dna6 = new Sequence("dna6", "CCCgggtttAAA");
+    dna6.createDatasetSequence();
+    al1.addSequence(dna6);
+    assertFalse(AlignmentUtils.alignAsSameSequences(al1, al2));
+  }
+    
 }
-- 
1.7.10.2