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Pad gaps removes excess gaps
author
amwaterhouse
<Andrew Waterhouse>
Tue, 4 Apr 2006 09:37:12 +0000
(09:37 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Tue, 4 Apr 2006 09:37:12 +0000
(09:37 +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
00d1be8
..
b0b04ca
100755
(executable)
--- a/
src/jalview/datamodel/Alignment.java
+++ b/
src/jalview/datamodel/Alignment.java
@@
-810,18
+810,41
@@
public class Alignment implements AlignmentI
\r
public boolean padGaps() {
\r
boolean modified=false;
\r
\r
public boolean padGaps() {
\r
boolean modified=false;
\r
- int Width = getWidth();
\r
+
\r
+ //Remove excess gaps from the end of alignment
\r
+ int maxLength = -1;
\r
+
\r
SequenceI current;
\r
SequenceI current;
\r
+ for (int i = 0; i < sequences.size(); i++)
\r
+ {
\r
+ current = getSequenceAt(i);
\r
+ for (int j = current.getLength(); j > maxLength; j--)
\r
+ {
\r
+ if (j > maxLength && !jalview.util.Comparison.isGap(
\r
+ current.getCharAt(j)))
\r
+ {
\r
+ maxLength = j;
\r
+ break;
\r
+ }
\r
+ }
\r
+ }
\r
+
\r
+ maxLength++;
\r
+
\r
for (int i = 0; i < sequences.size();
\r
i++)
\r
{
\r
current = getSequenceAt(i);
\r
\r
for (int i = 0; i < sequences.size();
\r
i++)
\r
{
\r
current = getSequenceAt(i);
\r
\r
- if (current.getLength() < Width)
\r
+ if (current.getLength() < maxLength)
\r
{
\r
{
\r
- current.insertCharAt(Width - 1, gapCharacter);
\r
+ current.insertCharAt(maxLength - 1, gapCharacter);
\r
modified=true;
\r
}
\r
modified=true;
\r
}
\r
+ else if(current.getLength() > maxLength)
\r
+ {
\r
+ current.deleteChars(maxLength, current.getLength());
\r
+ }
\r
}
\r
return modified;
\r
}
\r
}
\r
return modified;
\r
}
\r