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Watch for trim left/right null widths
author
amwaterhouse
<Andrew Waterhouse>
Thu, 22 Dec 2005 15:59:21 +0000
(15:59 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Thu, 22 Dec 2005 15:59:21 +0000
(15:59 +0000)
src/jalview/datamodel/Alignment.java
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diff --git
a/src/jalview/datamodel/Alignment.java
b/src/jalview/datamodel/Alignment.java
index
338294b
..
f0aeed9
100755
(executable)
--- a/
src/jalview/datamodel/Alignment.java
+++ b/
src/jalview/datamodel/Alignment.java
@@
-205,13
+205,23
@@
public class Alignment implements AlignmentI
*/
\r
public void trimLeft(int i)
\r
{
\r
*/
\r
public void trimLeft(int i)
\r
{
\r
- for (int j = 0; j < getHeight(); j++)
\r
+ int j, jSize = getHeight();
\r
+ for (j = 0; j < jSize; j++)
\r
{
\r
SequenceI s = getSequenceAt(j);
\r
int newstart = s.findPosition(i);
\r
\r
{
\r
SequenceI s = getSequenceAt(j);
\r
int newstart = s.findPosition(i);
\r
\r
- s.setStart(newstart);
\r
- s.setSequence(s.getSequence().substring(i));
\r
+ if(i>s.getLength())
\r
+ {
\r
+ sequences.removeElement(s);
\r
+ j--;
\r
+ jSize--;
\r
+ }
\r
+ else
\r
+ {
\r
+ s.setStart(newstart);
\r
+ s.setSequence(s.getSequence().substring(i));
\r
+ }
\r
}
\r
}
\r
\r
}
\r
}
\r
\r
@@
-228,7
+238,8
@@
public class Alignment implements AlignmentI
int newend = s.findPosition(i);
\r
\r
s.setEnd(newend);
\r
int newend = s.findPosition(i);
\r
\r
s.setEnd(newend);
\r
- s.setSequence(s.getSequence().substring(0, i + 1));
\r
+ if(s.getLength()>i)
\r
+ s.setSequence(s.getSequence().substring(0, i + 1));
\r
}
\r
}
\r
\r
}
\r
}
\r
\r