From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 1 May 2020 11:41:00 +0000 (+0100)
Subject: Merge branch 'bug/JAL-3613emblCDSTracking' into releases/Release_2_11_1_Branch
X-Git-Tag: Release_2_11_1_1~22^2~26
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6885ffda83ffb3bf1f3053f67e131bbf263b3b74;hp=-c;p=jalview.git

Merge branch 'bug/JAL-3613emblCDSTracking' into releases/Release_2_11_1_Branch
---

6885ffda83ffb3bf1f3053f67e131bbf263b3b74
diff --combined src/jalview/gui/SeqPanel.java
index cd974a4,d7d4af0..def4be1
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@@ -862,8 -862,7 +862,8 @@@ public class SeqPanel extends JPane
      {
        setStatusMessage(results);
      }
 -    return results.isEmpty() ? null : getHighlightInfo(results);
 +    // JAL-3303 feature suppressed for now pending review
 +    return null; // results.isEmpty() ? null : getHighlightInfo(results);
    }
  
    /**
@@@ -1200,7 -1199,7 +1200,7 @@@
    {
      char sequenceChar = sequence.getCharAt(column);
      int pos = sequence.findPosition(column);
-     setStatusMessage(sequence, seqIndex, sequenceChar, pos);
+     setStatusMessage(sequence.getName(), seqIndex, sequenceChar, pos);
  
      return pos;
    }
@@@ -1216,7 -1215,7 +1216,7 @@@
     * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
     * </pre>
     * 
-    * @param sequence
+    * @param seqName
     * @param seqIndex
     *          sequence position in the alignment (1..)
     * @param sequenceChar
@@@ -1224,7 -1223,7 +1224,7 @@@
     * @param residuePos
     *          the sequence residue position (if not over a gap)
     */
-   protected void setStatusMessage(SequenceI sequence, int seqIndex,
+   protected void setStatusMessage(String seqName, int seqIndex,
            char sequenceChar, int residuePos)
    {
      StringBuilder text = new StringBuilder(32);
@@@ -1234,7 -1233,7 +1234,7 @@@
       */
      String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
      text.append("Sequence").append(seqno).append(" ID: ")
-             .append(sequence.getName());
+             .append(seqName);
  
      String residue = null;
  
@@@ -1279,7 -1278,8 +1279,8 @@@
      {
        return;
      }
-     SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
+     SequenceI alignedSeq = al.getSequenceAt(sequenceIndex);
+     SequenceI ds = alignedSeq.getDatasetSequence();
      for (SearchResultMatchI m : results.getResults())
      {
        SequenceI seq = m.getSequence();
@@@ -1291,8 -1291,8 +1292,8 @@@
        if (seq == ds)
        {
          int start = m.getStart();
-         setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
-                 start);
+         setStatusMessage(alignedSeq.getName(), sequenceIndex,
+                 seq.getCharAt(start - 1), start);
          return;
        }
      }