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JAL-2674 Rewrote propagateInsertions
[jalview.git]
/
src
/
jalview
/
io
/
ClustalFile.java
diff --git
a/src/jalview/io/ClustalFile.java
b/src/jalview/io/ClustalFile.java
index
6c35ca1
..
c21b02c
100755
(executable)
--- a/
src/jalview/io/ClustalFile.java
+++ b/
src/jalview/io/ClustalFile.java
@@
-209,10
+209,7
@@
public class ClustalFile extends AlignFile
{
String tmp = printId(s[i], jvsuffix);
{
String tmp = printId(s[i], jvsuffix);
- if (s[i].getSequence().length > max)
- {
- max = s[i].getSequence().length;
- }
+ max = Math.max(max, s[i].getLength());
if (tmp.length() > maxid)
{
if (tmp.length() > maxid)
{
@@
-244,14
+241,14
@@
public class ClustalFile extends AlignFile
int start = i * len;
int end = start + len;
int start = i * len;
int end = start + len;
- if ((end < s[j].getSequence().length)
- && (start < s[j].getSequence().length))
+ int length = s[j].getLength();
+ if ((end < length) && (start < length))
{
out.append(s[j].getSequenceAsString(start, end));
}
else
{
{
out.append(s[j].getSequenceAsString(start, end));
}
else
{
- if (start < s[j].getSequence().length)
+ if (start < length)
{
out.append(s[j].getSequenceAsString().substring(start));
}
{
out.append(s[j].getSequenceAsString().substring(start));
}