JAL-653 (experimental) methods to resolve dummy to real sequence

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 9c642cf..d24593a 100644 (file)
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -461,4 +461,117 @@ public class AlignedCodonFrame
     }
     return result;
   }
+
+  /**
+   * Test whether the given sequence is substitutable for one or more dummy
+   * sequences in this mapping
+   * 
+   * @param map
+   * @param seq
+   * @return
+   */
+  public boolean isRealisableWith(SequenceI seq)
+  {
+    return realiseWith(seq, false) > 0;
+  }
+
+  /**
+   * Replace any matchable mapped dummy sequences with the given real one.
+   * Returns the count of sequence mappings instantiated.
+   * 
+   * @param seq
+   * @return
+   */
+  public int realiseWith(SequenceI seq)
+  {
+    return realiseWith(seq, true);
+  }
+
+  /**
+   * Returns the number of mapped dummy sequences that could be replaced with
+   * the given real sequence.
+   * 
+   * @param seq
+   *          a dataset sequence
+   * @param doUpdate
+   *          if true, performs replacements, else only counts
+   * @return
+   */
+  protected int realiseWith(SequenceI seq, boolean doUpdate)
+  {
+    SequenceI ds = seq.getDatasetSequence() != null ? seq
+            .getDatasetSequence() : seq;
+    int count = 0;
+
+    /*
+     * check for replaceable DNA ('map from') sequences
+     */
+    for (int i = 0; i < dnaSeqs.length; i++)
+    {
+      SequenceI dna = dnaSeqs[i];
+      if (dna instanceof SequenceDummy
+              && dna.getName().equals(ds.getName()))
+      {
+        Mapping mapping = dnaToProt[i];
+        int mapStart = mapping.getMap().getFromLowest();
+        int mapEnd = mapping.getMap().getFromHighest();
+        boolean mappable = couldReplaceSequence(dna, ds, mapStart, mapEnd);
+        if (mappable)
+        {
+          count++;
+          if (doUpdate)
+          {
+            dnaSeqs[i] = ds;
+          }
+        }
+      }
+
+      /*
+       * check for replaceable protein ('map to') sequences
+       */
+      SequenceI prot = dnaToProt[i].getTo();
+      Mapping mapping = dnaToProt[i];
+      int mapStart = mapping.getMap().getToLowest();
+      int mapEnd = mapping.getMap().getToHighest();
+      boolean mappable = couldReplaceSequence(prot, ds, mapStart, mapEnd);
+      if (mappable)
+      {
+        count++;
+        if (doUpdate)
+        {
+          dnaToProt[i].setTo(ds);
+        }
+      }
+    }
+    return count;
+  }
+
+  /**
+   * Helper method to test whether a 'real' sequence could replace a 'dummy'
+   * sequence in the map. The criteria are that they have the same name, and
+   * that the mapped region overlaps the candidate sequence.
+   * 
+   * @param existing
+   * @param replacement
+   * @param mapStart
+   * @param mapEnd
+   * @return
+   */
+  protected static boolean couldReplaceSequence(SequenceI existing,
+          SequenceI replacement, int mapStart, int mapEnd)
+  {
+    if (existing instanceof SequenceDummy
+            && existing.getName().equals(replacement.getName()))
+    {
+      int start = replacement.getStart();
+      int end = replacement.getEnd();
+      boolean mappingOverlapsSequence = (mapStart >= start && mapStart <= end)
+              || (mapEnd >= start && mapEnd <= end);
+      if (mappingOverlapsSequence)
+      {
+        return true;
+      }
+    }
+    return false;
+  }
 }

diff --git a/test/jalview/datamodel/AlignedCodonFrameTest.java b/test/jalview/datamodel/AlignedCodonFrameTest.java
index a0757cc..69e584a 100644 (file)
--- a/test/jalview/datamodel/AlignedCodonFrameTest.java
+++ b/test/jalview/datamodel/AlignedCodonFrameTest.java
@@ -21,7 +21,9 @@
 package jalview.datamodel;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.util.MapList;
 
@@ -176,4 +178,87 @@ public class AlignedCodonFrameTest
     assertEquals("[C, T, T]", Arrays.toString(acf.getMappedCodon(
             aseq1.getDatasetSequence(), 13)));
   }
+
+  @Test(groups = { "Functional" })
+  public void testCouldReplaceSequence()
+  {
+    SequenceI seq1 = new Sequence("Seq1/10-21", "aaacccgggttt");
+    SequenceI seq2 = new Sequence("Seq2", "PG");
+    SequenceI seq1proxy = new SequenceDummy("Seq1");
+
+    // map to region within sequence is ok
+    assertTrue(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 12,
+            17));
+    // map to region overlapping sequence is ok
+    assertTrue(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 5,
+            10));
+    assertTrue(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 21,
+            26));
+    // map to region before sequence is not ok
+    assertFalse(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 4,
+            9));
+    // map to region after sequence is not ok
+    assertFalse(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 22,
+            27));
+
+    /*
+     * test should fail if name doesn't match
+     */
+    seq1proxy.setName("Seq1a");
+    assertFalse(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 12,
+            17));
+    seq1proxy.setName("Seq1");
+    seq1.setName("Seq1a");
+    assertFalse(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 12,
+            17));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testIsRealisableWith()
+  {
+    SequenceI seq1 = new Sequence("Seq1", "tttaaaCCCGGGtttaaa");
+    SequenceI seq2 = new Sequence("Seq2", "PG");
+    SequenceI seq1proxy = new SequenceDummy("Seq1");
+    seq1.createDatasetSequence();
+    seq2.createDatasetSequence();
+    MapList mapList = new MapList(new int[] { 7, 12 }, new int[] { 2, 3 },
+            3, 1);
+    AlignedCodonFrame acf = new AlignedCodonFrame();
+    acf.addMap(seq1proxy, seq2, mapList);
+
+    /*
+     * Seq2 is mapped to SequenceDummy seq1proxy bases 4-9
+     * This is 'realisable' from real sequence Seq1
+     */
+    assertTrue(acf.isRealisableWith(seq1));
+
+    /*
+     * test should fail if name doesn't match
+     */
+    seq1proxy.setName("Seq1a");
+    assertFalse(acf.isRealisableWith(seq1));
+    seq1proxy.setName("Seq1");
+    seq1.setName("Seq1a");
+    assertFalse(acf.isRealisableWith(seq1));
+    seq1.setName("Seq1");
+
+    /*
+     * test should fail if no sequence overlap with mapping of bases 7-12
+     * use artificial start/end values to test this
+     */
+    seq1.setStart(1);
+    seq1.setEnd(6);
+    // seq1 precedes mapped region:
+    assertFalse(acf.isRealisableWith(seq1));
+    seq1.setEnd(7);
+    // seq1 includes first mapped base:
+    assertTrue(acf.isRealisableWith(seq1));
+    seq1.setStart(13);
+    seq1.setEnd(18);
+    // seq1 follows mapped region:
+    assertFalse(acf.isRealisableWith(seq1));
+    seq1.setStart(12);
+    // seq1 includes last mapped base:
+    assertTrue(acf.isRealisableWith(seq1));
+  }
 }