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JAL-2986 corrected findIndex for out of range residue value
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Fri, 11 May 2018 11:19:52 +0000
(12:19 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Fri, 11 May 2018 11:19:52 +0000
(12:19 +0100)
src/jalview/datamodel/Sequence.java
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diff --git
a/src/jalview/datamodel/Sequence.java
b/src/jalview/datamodel/Sequence.java
index
59c3fb1
..
33de452
100755
(executable)
--- a/
src/jalview/datamodel/Sequence.java
+++ b/
src/jalview/datamodel/Sequence.java
@@
-445,7
+445,7
@@
public class Sequence extends ASequence implements SequenceI
@Override
public Vector<PDBEntry> getAllPDBEntries()
{
@Override
public Vector<PDBEntry> getAllPDBEntries()
{
- return pdbIds == null ? new Vector<PDBEntry>() : pdbIds;
+ return pdbIds == null ? new Vector<>() : pdbIds;
}
/**
}
/**
@@
-815,7
+815,7
@@
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))
{
@@
-841,10
+841,15
@@
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;
@@
-852,7
+857,14
@@
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;
}