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Merge branch 'bug/JAL-3613emblCDSTracking' into releases/Release_2_11_1_Branch
[jalview.git]
/
src
/
jalview
/
gui
/
SeqPanel.java
diff --git
a/src/jalview/gui/SeqPanel.java
b/src/jalview/gui/SeqPanel.java
index
cd974a4
..
def4be1
100644
(file)
--- a/
src/jalview/gui/SeqPanel.java
+++ b/
src/jalview/gui/SeqPanel.java
@@
-1200,7
+1200,7
@@
public class SeqPanel extends JPanel
{
char sequenceChar = sequence.getCharAt(column);
int pos = sequence.findPosition(column);
{
char sequenceChar = sequence.getCharAt(column);
int pos = sequence.findPosition(column);
- setStatusMessage(sequence, seqIndex, sequenceChar, pos);
+ setStatusMessage(sequence.getName(), seqIndex, sequenceChar, pos);
return pos;
}
return pos;
}
@@
-1216,7
+1216,7
@@
public class SeqPanel extends JPanel
* Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
* </pre>
*
* Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
* </pre>
*
- * @param sequence
+ * @param seqName
* @param seqIndex
* sequence position in the alignment (1..)
* @param sequenceChar
* @param seqIndex
* sequence position in the alignment (1..)
* @param sequenceChar
@@
-1224,7
+1224,7
@@
public class SeqPanel extends JPanel
* @param residuePos
* the sequence residue position (if not over a gap)
*/
* @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);
char sequenceChar, int residuePos)
{
StringBuilder text = new StringBuilder(32);
@@
-1234,7
+1234,7
@@
public class SeqPanel extends JPanel
*/
String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
text.append("Sequence").append(seqno).append(" ID: ")
*/
String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
text.append("Sequence").append(seqno).append(" ID: ")
- .append(sequence.getName());
+ .append(seqName);
String residue = null;
String residue = null;
@@
-1279,7
+1279,8
@@
public class SeqPanel extends JPanel
{
return;
}
{
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();
for (SearchResultMatchI m : results.getResults())
{
SequenceI seq = m.getSequence();
@@
-1291,8
+1292,8
@@
public class SeqPanel extends JPanel
if (seq == ds)
{
int start = m.getStart();
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;
}
}
return;
}
}