git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-4223 - test and patch to ensure numbering matches sequence data from RNAML file
[jalview.git]
/
src
/
jalview
/
io
/
RnamlFile.java
diff --git
a/src/jalview/io/RnamlFile.java
b/src/jalview/io/RnamlFile.java
index
4d3ddc1
..
3041a23
100644
(file)
--- a/
src/jalview/io/RnamlFile.java
+++ b/
src/jalview/io/RnamlFile.java
@@
-160,8
+160,10
@@
public class RnamlFile extends AlignFile
}
}
sqs[i] = new Sequence(id, seq, begin, end);
}
}
sqs[i] = new Sequence(id, seq, begin, end);
-
- sqs[i].setEnd(sqs[i].findPosition(sqs[i].getLength()));
+ if (seq.length()!=(end-begin+1))
+ {
+ sqs[i].setEnd(sqs[i].findPosition(sqs[i].getLength()));
+ }
String[] annot = new String[rna.length()];
Annotation[] ann = new Annotation[rna.length()];
String[] annot = new String[rna.length()];
Annotation[] ann = new Annotation[rna.length()];