JAL-2023 CDS sequences added to / share alignment dataset

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 07cb689..6322243 100644 (file)
--- 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;
@@ -848,7 +849,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
        */
       AlignedCodonFrame mapping = al.getCodonFrames().iterator().next();
       // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
-      if (mapping.getdnaToProt()[0].getFromRatio() == 3)
+      MapList[] mapLists = mapping.getdnaToProt();
+      // mapLists can be empty if project load has not finished resolving seqs
+      if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
       {
         if (calculator
                 .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
@@ -1797,7 +1800,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
         // fudge: check mappings are not protein-to-protein
         // TODO: nicer
         AlignedCodonFrame mapping = codonMappings.iterator().next();
-        if (mapping.getdnaToProt()[0].getFromRatio() == 3)
+        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,