X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=6322243d9dede0ce4f3abd3156ccf0252e2d686a;hb=4d7fb8a093a3151363b0782dddb9598567de66e0;hp=eb686a4f3d361c71f1ecbafc50eb6f3c1e6d7129;hpb=0f5255080bd41820b3dcd934c499f68007fc5544;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index eb686a4..6322243 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -49,6 +49,7 @@ import jalview.structure.CommandListener;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.util.Comparison;
+import jalview.util.MapList;
 import jalview.util.MappingUtils;
 import jalview.viewmodel.styles.ViewStyle;
 import jalview.workers.AlignCalcManager;
@@ -65,7 +66,6 @@ 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 +837,28 @@ 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?
+      MapList[] mapLists = mapping.getdnaToProt();
+      // mapLists can be empty if project load has not finished resolving seqs
+      if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
       {
-        calculator.registerWorker(new ComplementConsensusThread(this, ap));
+        if (calculator
+                .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
+        {
+          calculator
+                  .registerWorker(new ComplementConsensusThread(this, ap));
+        }
       }
     }
   }
@@ -1424,7 +1437,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
     if (hiddenRepSequences == null)
     {
-      hiddenRepSequences = new Hashtable();
+      hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
     }
 
     hiddenRepSequences.put(repSequence, sg);
@@ -1780,14 +1793,22 @@ 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();
+        MapList[] mapLists = mapping.getdnaToProt();
+        // mapLists can be empty if project load has not finished resolving seqs
+        if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
+        {
+          complementConsensus = new AlignmentAnnotation("cDNA Consensus",
+                  "PID for cDNA", new Annotation[1], 0f, 100f,
+                  AlignmentAnnotation.BAR_GRAPH);
+          initConsensus(complementConsensus);
+        }
       }
     }
   }
@@ -2099,7 +2120,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public boolean areFeaturesDisplayed()
   {
     return featuresDisplayed != null
-            && featuresDisplayed.getRegisterdFeaturesCount() > 0;
+            && featuresDisplayed.getRegisteredFeaturesCount() > 0;
   }
 
   /**
@@ -2580,7 +2601,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     {
       return 0;
     }
-    final Set<AlignedCodonFrame> mappings = proteinAlignment
+    final List<AlignedCodonFrame> mappings = proteinAlignment
             .getCodonFrames();
 
     /*