git://source.jalview.org
/
jalview.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (parent:
2d68099
)
Correction for sequences with start not equal to 1
author
amwaterhouse
<Andrew Waterhouse>
Wed, 10 May 2006 13:30:10 +0000
(13:30 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Wed, 10 May 2006 13:30:10 +0000
(13:30 +0000)
src/jalview/datamodel/AlignmentAnnotation.java
patch
|
blob
|
history
diff --git
a/src/jalview/datamodel/AlignmentAnnotation.java
b/src/jalview/datamodel/AlignmentAnnotation.java
index
d75683c
..
ae3c5f9
100755
(executable)
--- a/
src/jalview/datamodel/AlignmentAnnotation.java
+++ b/
src/jalview/datamodel/AlignmentAnnotation.java
@@
-254,7
+254,7
@@
public class AlignmentAnnotation
if(startRes < sequenceRef.getStart())
\r
startRes = sequenceRef.getStart();
\r
\r
if(startRes < sequenceRef.getStart())
\r
startRes = sequenceRef.getStart();
\r
\r
- int seqPos, seqIndex;
\r
+ int seqPos;
\r
\r
int fileOffset = 0;
\r
if(startRes > sequenceRef.getStart())
\r
\r
int fileOffset = 0;
\r
if(startRes > sequenceRef.getStart())
\r
@@
-264,16
+264,13
@@
public class AlignmentAnnotation
\r
for(int i = 0; i < annotations.length; i++)
\r
{
\r
\r
for(int i = 0; i < annotations.length; i++)
\r
{
\r
- seqPos = sequenceRef.findPosition(i - fileOffset)-1;
\r
+ seqPos = sequenceRef.findPosition(i + fileOffset);
\r
if(seqPos<annotations.length)
\r
{
\r
if(seqPos<annotations.length)
\r
{
\r
- if (annotations[seqPos] != null)
\r
+ if (annotations[i] != null)
\r
{
\r
{
\r
- seqIndex = sequenceRef.findIndex(i) + 1;
\r
-
\r
- if(seqIndex>=startRes)
\r
- sequenceMapping.put(new Integer(seqIndex),
\r
- annotations[seqPos]);
\r
+ sequenceMapping.put(new Integer(seqPos),
\r
+ annotations[i]);
\r
}
\r
}
\r
}
\r
}
\r
}
\r
}
\r