From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 4 Aug 2016 19:57:33 +0000 (+0100)
Subject: JAL-2154 make sure all sequences referenced via DBRefEntry->getMap()->getTo() are... 
X-Git-Tag: Release_2_10_0~47^2~4^2~43^2~59
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=eb481110f91c590e971499bbae5f6dd65f7f83ea;p=jalview.git

JAL-2154 make sure all sequences referenced via DBRefEntry->getMap()->getTo() are added to dataset when it is created
---

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 32bb761..e9c0b4c 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -21,6 +21,7 @@
 package jalview.datamodel;
 
 import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
 import jalview.io.FastaFile;
 import jalview.util.Comparison;
 import jalview.util.MessageManager;
@@ -1029,6 +1030,62 @@ public class Alignment implements AlignmentI
   }
 
   /**
+   * add dataset sequences to seq for currentSeq and any sequences it references
+   */
+  private void resolveAndAddDatasetSeq(SequenceI currentSeq,
+          Set<SequenceI> seqs, boolean createDatasetSequence)
+  {
+    if (currentSeq.getDatasetSequence() != null)
+    {
+      currentSeq = currentSeq.getDatasetSequence();
+    }
+    else
+    {
+      if (createDatasetSequence)
+      {
+        currentSeq = currentSeq.createDatasetSequence();
+      }
+    }
+    if (seqs.contains(currentSeq))
+    {
+      return;
+    }
+    List<SequenceI> toProcess = new ArrayList<SequenceI>();
+    toProcess.add(currentSeq);
+    while (toProcess.size() > 0)
+    {
+      // use a queue ?
+      SequenceI curDs = toProcess.remove(0);
+      if (seqs.contains(curDs))
+      {
+        continue;
+      }
+      seqs.add(curDs);
+      // iterate over database references, making sure we add forward referenced
+      // sequences
+      if (curDs.getDBRefs() != null)
+      {
+        for (DBRefEntry dbr : curDs.getDBRefs())
+        {
+          if (dbr.getMap() != null && dbr.getMap().getTo() != null)
+          {
+            if (dbr.getMap().getTo().getDatasetSequence() != null)
+            {
+              throw new Error("Implementation error: Map.getTo() for dbref"
+                      + dbr + " is not a dataset sequence.");
+              // TODO: if this happens, could also rewrite the reference to
+              // point to new dataset sequence
+            }
+            // we recurse to add all forward references to dataset sequences via
+            // DBRefs/etc
+            toProcess.add(dbr.getMap().getTo());
+          }
+        }
+      }
+    }
+  }
+
+  /**
    * Creates a new dataset for this alignment. Can only be done once - if
    * dataset is not null this will not be performed.
    */
@@ -1038,22 +1095,32 @@ public class Alignment implements AlignmentI
     {
       return;
     }
-    SequenceI[] seqs = new SequenceI[getHeight()];
-    SequenceI currentSeq;
+    // try to avoid using equals at this stage, it will be expensive
+    Set<SequenceI> seqs = new jalview.util.LinkedIdentityHashSet<SequenceI>();
+
     for (int i = 0; i < getHeight(); i++)
     {
-      currentSeq = getSequenceAt(i);
-      if (currentSeq.getDatasetSequence() != null)
-      {
-        seqs[i] = currentSeq.getDatasetSequence();
-      }
-      else
+      SequenceI currentSeq = getSequenceAt(i);
+      resolveAndAddDatasetSeq(currentSeq, seqs, true);
+    }
+
+    // verify all mappings are in dataset
+    for (AlignedCodonFrame cf : codonFrameList)
+    {
+      for (SequenceToSequenceMapping ssm : cf.getMappings())
       {
-        seqs[i] = currentSeq.createDatasetSequence();
+        if (!seqs.contains(ssm.getFromSeq()))
+        {
+          resolveAndAddDatasetSeq(ssm.getFromSeq(), seqs, false);
+        }
+        if (!seqs.contains(ssm.getMapping().getTo()))
+        {
+          resolveAndAddDatasetSeq(ssm.getMapping().getTo(), seqs, false);
+        }
       }
     }
-
-    dataset = new Alignment(seqs);
+    // finally construct dataset
+    dataset = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
     // move mappings to the dataset alignment
     dataset.codonFrameList = this.codonFrameList;
     this.codonFrameList = null;
diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index b75ef50..90090d3 100644
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -460,6 +460,60 @@ public class AlignmentTest
     assertTrue(ds.getCodonFrames().contains(acf));
   }
 
+  /**
+   * tests the addition of *all* sequences referred to by a sequence being added
+   * to the dataset
+   */
+  @Test(groups = "Functional")
+  public void testCreateDatasetAlignmentWithMappedToSeqs()
+  {
+    // Alignment with two sequences, gapped.
+    SequenceI sq1 = new Sequence("sq1", "A--SDF");
+    SequenceI sq2 = new Sequence("sq2", "G--TRQ");
+
+    // cross-references to two more sequences.
+    DBRefEntry dbr = new DBRefEntry("SQ1", "", "sq3");
+    SequenceI sq3 = new Sequence("sq3", "VWANG");
+    dbr.setMap(new Mapping(sq3, new MapList(new int[] { 1, 4 }, new int[] {
+        2, 5 }, 1, 1)));
+    sq1.addDBRef(dbr);
+
+    SequenceI sq4 = new Sequence("sq4", "ERKWI");
+    DBRefEntry dbr2 = new DBRefEntry("SQ2", "", "sq4");
+    dbr2.setMap(new Mapping(sq4, new MapList(new int[] { 1, 4 }, new int[] {
+        2, 5 }, 1, 1)));
+    sq2.addDBRef(dbr2);
+    // and a 1:1 codonframe mapping between them.
+    AlignedCodonFrame alc = new AlignedCodonFrame();
+    alc.addMap(sq1, sq2, new MapList(new int[] { 1, 4 },
+            new int[] { 1, 4 }, 1, 1));
+
+    AlignmentI protein = new Alignment(new SequenceI[] { sq1, sq2 });
+
+    /*
+     * create the alignment dataset
+     * note this creates sequence datasets where missing
+     * as a side-effect (in this case, on seq2
+     */
+
+    // TODO promote this method to AlignmentI
+    ((Alignment) protein).createDatasetAlignment();
+
+    AlignmentI ds = protein.getDataset();
+
+    // should be 4 sequences in dataset - two materialised, and two propagated
+    // from dbref
+    assertEquals(4, ds.getHeight());
+    assertTrue(ds.getSequences().contains(sq1.getDatasetSequence()));
+    assertTrue(ds.getSequences().contains(sq2.getDatasetSequence()));
+    assertTrue(ds.getSequences().contains(sq3));
+    assertTrue(ds.getSequences().contains(sq4));
+    // Should have one codon frame mapping between sq1 and sq2 via dataset
+    // sequences
+    assertEquals(ds.getCodonFrame(sq1.getDatasetSequence()),
+            ds.getCodonFrame(sq2.getDatasetSequence()));
+  }
+
   @Test(groups = "Functional")
   public void testAddCodonFrame()
   {