From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 20 Jul 2016 09:00:57 +0000 (+0100)
Subject: JAL-2023 stronger check for whether to start cdna consensus
X-Git-Tag: Release_2_10_0~125^2~10
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1811f4469c23e9cce0a72649e17b634f60f9fbe0;p=jalview.git

JAL-2023 stronger check for whether to start cdna consensus
---

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index d3df56c..19ebf45 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -844,14 +844,22 @@ public abstract class AlignmentViewport implements AlignViewportI,
             && !al.getCodonFrames().isEmpty())
     {
       /*
-       * fudge - check first mapping is protein-to-nucleotide
+       * fudge - check first for protein-to-nucleotide mappings
        * (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)
+      boolean doConsensus = false;
+      for (AlignedCodonFrame mapping : al.getCodonFrames())
+      {
+        // 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)
+        {
+          doConsensus = true;
+          break;
+        }
+      }
+      if (doConsensus)
       {
         if (calculator
                 .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
@@ -1872,12 +1880,20 @@ public abstract class AlignmentViewport implements AlignViewportI,
               .getCodonFrames();
       if (codonMappings != null && !codonMappings.isEmpty())
       {
-        // 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)
+        boolean doConsensus = false;
+        for (AlignedCodonFrame mapping : codonMappings)
+        {
+          // 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)
+          {
+            doConsensus = true;
+            break;
+          }
+        }
+        if (doConsensus)
         {
           complementConsensus = new AlignmentAnnotation("cDNA Consensus",
                   "PID for cDNA", new Annotation[1], 0f, 100f,