JAL-845 applet colour by tree; translate as cDNA; pull up history list

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

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 7116af9..0441b1d 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -218,6 +218,11 @@ public class AlignmentUtils
           final AlignmentI proteinAlignment,
           final AlignmentI cdnaAlignment)
   {
+    if (proteinAlignment == null || cdnaAlignment == null)
+    {
+      return MappingResult.NotMapped;
+    }
+
     boolean mappingPossible = false;
     boolean mappingPerformed = false;
 
@@ -305,10 +310,15 @@ public class AlignmentUtils
   public static MapList mapProteinToCdna(SequenceI proteinSeq,
           SequenceI cdnaSeq)
   {
-    String aaSeqString = proteinSeq.getDatasetSequence()
-            .getSequenceAsString();
-    String cdnaSeqString = cdnaSeq.getDatasetSequence()
-            .getSequenceAsString();
+    /*
+     * Here we handle either dataset sequence set (desktop) or absent (applet)
+     */
+    final SequenceI proteinDataset = proteinSeq.getDatasetSequence();
+    String aaSeqString = proteinDataset != null ? proteinDataset
+            .getSequenceAsString() : proteinSeq.getSequenceAsString();
+    final SequenceI cdnaDataset = cdnaSeq.getDatasetSequence();
+    String cdnaSeqString = cdnaDataset != null ? cdnaDataset
+            .getSequenceAsString() : cdnaSeq.getSequenceAsString();
     if (aaSeqString == null || cdnaSeqString == null)
     {
       return null;