Merge branch 'develop' into JAL-1705_trialMerge

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index c4ae76d..ab9740c 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -65,7 +65,6 @@ import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
-import java.util.Set;
 
 /**
  * base class holding visualization and analysis attributes and common logic for
@@ -837,15 +836,26 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
     /*
      * A separate thread to compute cDNA consensus for a protein alignment
+     * which has mapping to cDNA
      */
     final AlignmentI al = this.getAlignment();
     if (!al.isNucleotide() && al.getCodonFrames() != null
             && !al.getCodonFrames().isEmpty())
     {
-      if (calculator
-              .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
+      /*
+       * fudge - check first mapping is protein-to-nucleotide
+       * (we don't want to do this for protein-to-protein)
+       */
+      AlignedCodonFrame mapping = al.getCodonFrames().iterator().next();
+      // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
+      if (mapping.getdnaToProt()[0].getFromRatio() == 3)
       {
-        calculator.registerWorker(new ComplementConsensusThread(this, ap));
+        if (calculator
+                .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
+        {
+          calculator
+                  .registerWorker(new ComplementConsensusThread(this, ap));
+        }
       }
     }
   }
@@ -1424,7 +1434,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
     if (hiddenRepSequences == null)
     {
-      hiddenRepSequences = new Hashtable();
+      hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
     }
 
     hiddenRepSequences.put(repSequence, sg);
@@ -1769,14 +1779,20 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     if (!alignment.isNucleotide())
     {
-      final Set<AlignedCodonFrame> codonMappings = alignment
+      final List<AlignedCodonFrame> codonMappings = alignment
               .getCodonFrames();
       if (codonMappings != null && !codonMappings.isEmpty())
       {
-        complementConsensus = new AlignmentAnnotation("cDNA Consensus",
-                "PID for cDNA", new Annotation[1], 0f, 100f,
-                AlignmentAnnotation.BAR_GRAPH);
-        initConsensus(complementConsensus);
+        // fudge: check mappings are not protein-to-protein
+        // TODO: nicer
+        AlignedCodonFrame mapping = codonMappings.iterator().next();
+        if (mapping.getdnaToProt()[0].getFromRatio() == 3)
+        {
+          complementConsensus = new AlignmentAnnotation("cDNA Consensus",
+                  "PID for cDNA", new Annotation[1], 0f, 100f,
+                  AlignmentAnnotation.BAR_GRAPH);
+          initConsensus(complementConsensus);
+        }
       }
     }
   }
@@ -2569,7 +2585,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     {
       return 0;
     }
-    final Set<AlignedCodonFrame> mappings = proteinAlignment
+    final List<AlignedCodonFrame> mappings = proteinAlignment
             .getCodonFrames();
 
     /*