JAL-2110 bug fixing and tidying for get cross-refs

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

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index f94d393..9150d62 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -2347,13 +2347,13 @@ public class AlignmentUtils
   {
     /*
      * Map will hold, for each aligned column position, a map of
-     * {unalignedSequence, sequenceCharacter} at that position.
+     * {unalignedSequence, characterPerSequence} at that position.
      * TreeMap keeps the entries in ascending column order. 
      */
     Map<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
 
     /*
-     * r any sequences that have no mapping so can't be realigned
+     * record any sequences that have no mapping so can't be realigned
      */
     unmapped.addAll(unaligned.getSequences());
 
@@ -2402,6 +2402,15 @@ public class AlignmentUtils
       return false;
     }
 
+    /*
+     * invert mapping if it is from unaligned to aligned sequence
+     */
+    if (seqMap.getTo() == fromSeq.getDatasetSequence())
+    {
+      seqMap = new Mapping(seq.getDatasetSequence(), seqMap.getMap()
+              .getInverse());
+    }
+
     char[] fromChars = fromSeq.getSequence();
     int toStart = seq.getStart();
     char[] toChars = seq.getSequence();
@@ -2435,7 +2444,8 @@ public class AlignmentUtils
          * of the next character of the mapped-to sequence; stop when all
          * the characters of the range have been counted
          */
-        while (mappedCharPos <= range[1])
+        while (mappedCharPos <= range[1] && fromCol <= fromChars.length
+                && fromCol >= 0)
         {
           if (!Comparison.isGap(fromChars[fromCol - 1]))
           {