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JAL-2629 update spike branch to latest
[jalview.git]
/
src
/
jalview
/
datamodel
/
Sequence.java
diff --git
a/src/jalview/datamodel/Sequence.java
b/src/jalview/datamodel/Sequence.java
index
9464c74
..
7972626
100755
(executable)
--- a/
src/jalview/datamodel/Sequence.java
+++ b/
src/jalview/datamodel/Sequence.java
@@
-825,7
+825,7
@@
public class Sequence extends ASequence implements SequenceI
* @param curs
* @return
*/
* @param curs
* @return
*/
- protected int findIndex(int pos, SequenceCursor curs)
+ protected int findIndex(final int pos, SequenceCursor curs)
{
if (!isValidCursor(curs))
{
{
if (!isValidCursor(curs))
{
@@
-851,10
+851,15
@@
public class Sequence extends ASequence implements SequenceI
while (newPos != pos)
{
col += delta; // shift one column left or right
while (newPos != pos)
{
col += delta; // shift one column left or right
- if (col < 0 || col == sequence.length)
+ if (col < 0)
{
break;
}
{
break;
}
+ if (col == sequence.length)
+ {
+ col--; // return last column if we failed to reach pos
+ break;
+ }
if (!Comparison.isGap(sequence[col]))
{
newPos += delta;
if (!Comparison.isGap(sequence[col]))
{
newPos += delta;
@@
-862,7
+867,14
@@
public class Sequence extends ASequence implements SequenceI
}
col++; // convert back to base 1
}
col++; // convert back to base 1
- updateCursor(pos, col, curs.firstColumnPosition);
+
+ /*
+ * only update cursor if we found the target position
+ */
+ if (newPos == pos)
+ {
+ updateCursor(pos, col, curs.firstColumnPosition);
+ }
return col;
}
return col;
}