JAL-2110 work in progress

[jalview.git] / src / jalview / analysis / AlignmentUtils.java

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index fba023f..949c47a 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -1411,6 +1411,12 @@ public class AlignmentUtils
   {
     List<SequenceI> cdsSeqs = new ArrayList<SequenceI>();
     
+    /*
+     * construct CDS sequences from the (cds-to-protein) mappings made earlier;
+     * this makes it possible to model multiple products from dna (e.g. EMBL); 
+     * however it does mean we don't have the EMBL protein_id (a property on 
+     * the CDS features) in order to make the CDS sequence name :-( 
+     */
     for (SequenceI seq : dna)
     {
       AlignedCodonFrame cdsMappings = new AlignedCodonFrame();
@@ -1795,17 +1801,20 @@ public class AlignmentUtils
      * sort to get sequence features in start position order
      * - would be better to store in Sequence as a TreeSet or NCList?
      */
-    Arrays.sort(peptide.getSequenceFeatures(),
-            new Comparator<SequenceFeature>()
-            {
-              @Override
-              public int compare(SequenceFeature o1, SequenceFeature o2)
+    if (peptide.getSequenceFeatures() != null)
+    {
+      Arrays.sort(peptide.getSequenceFeatures(),
+              new Comparator<SequenceFeature>()
               {
-                int c = Integer.compare(o1.getBegin(), o2.getBegin());
-                return c == 0 ? Integer.compare(o1.getEnd(), o2.getEnd())
-                        : c;
-              }
-            });
+                @Override
+                public int compare(SequenceFeature o1, SequenceFeature o2)
+                {
+                  int c = Integer.compare(o1.getBegin(), o2.getBegin());
+                  return c == 0 ? Integer.compare(o1.getEnd(), o2.getEnd())
+                          : c;
+                }
+              });
+    }
     return count;
   }
 
@@ -2114,6 +2123,26 @@ public class AlignmentUtils
   {
     AlignmentI copy = new Alignment(new Alignment(seqs));
 
+    /*
+     * add mappings between sequences to the new alignment
+     */
+    AlignedCodonFrame mappings = new AlignedCodonFrame();
+    copy.addCodonFrame(mappings);
+    for (int i = 0; i < copy.getHeight(); i++)
+    {
+      SequenceI from = seqs[i];
+      SequenceI to = copy.getSequenceAt(i);
+      if (to.getDatasetSequence() != null)
+      {
+        to = to.getDatasetSequence();
+      }
+      int start = from.getStart();
+      int end = from.getEnd();
+      MapList map = new MapList(new int[] { start, end }, new int[] {
+          start, end }, 1, 1);
+      mappings.addMap(to, from, map);
+    }
+
     SequenceIdMatcher matcher = new SequenceIdMatcher(seqs);
     if (xrefs != null)
     {