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JAL-2674 tidy
author
kiramt
<k.mourao@dundee.ac.uk>
Wed, 4 Oct 2017 07:57:16 +0000
(08:57 +0100)
committer
kiramt
<k.mourao@dundee.ac.uk>
Wed, 4 Oct 2017 07:57:16 +0000
(08:57 +0100)
src/jalview/datamodel/HiddenColumns.java
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diff --git
a/src/jalview/datamodel/HiddenColumns.java
b/src/jalview/datamodel/HiddenColumns.java
index
839cee2
..
a6b4f82
100644
(file)
--- a/
src/jalview/datamodel/HiddenColumns.java
+++ b/
src/jalview/datamodel/HiddenColumns.java
@@
-701,21
+701,19
@@
public class HiddenColumns
try
{
LOCK.readLock().lock();
try
{
LOCK.readLock().lock();
- int fpos = seq.getStart();
- int lpos = seq.getEnd();
int start = 0;
if (hiddenColumns == null || hiddenColumns.size() == 0)
{
int start = 0;
if (hiddenColumns == null || hiddenColumns.size() == 0)
{
- int ifpos = seq.findIndex(fpos) - 1;
- int ilpos = seq.findIndex(lpos) - 1;
+ int ifpos = seq.findIndex(seq.getStart()) - 1;
+ int ilpos = seq.findIndex(seq.getEnd()) - 1;
return new int[] { ifpos, ifpos, ilpos };
}
// Simply walk along the sequence whilst watching for hidden column
// boundaries
Iterator<int[]> regions = iterator();
return new int[] { ifpos, ifpos, ilpos };
}
// Simply walk along the sequence whilst watching for hidden column
// boundaries
Iterator<int[]> regions = iterator();
- int spos = fpos;
+ int spos = seq.getStart();
int hideStart = seq.getLength();
int hideEnd = -1;
int visPrev = 0;
int hideStart = seq.getLength();
int hideEnd = -1;
int visPrev = 0;
@@
-723,8
+721,7
@@
public class HiddenColumns
int firstP = -1;
int lastP = -1;
boolean foundStart = false;
int firstP = -1;
int lastP = -1;
boolean foundStart = false;
- for (int p = 0, pLen = seq.getLength(); spos <= seq.getEnd()
- && p < pLen; p++)
+ for (int p = 0; spos <= seq.getEnd() && p < seq.getLength(); p++)
{
if (!Comparison.isGap(seq.getCharAt(p)))
{
{
if (!Comparison.isGap(seq.getCharAt(p)))
{
@@
-753,11
+750,9
@@
public class HiddenColumns
{
if (!foundStart)
{
{
if (!foundStart)
{
- fpos = spos;
start = p;
foundStart = true;
}
start = p;
foundStart = true;
}
- lpos = spos;
}
// look for next sequence position
spos++;
}
// look for next sequence position
spos++;