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:
bcfc087
)
fix for unicode char labels causing arrayOutOfBoundsException bug spotted by cameron...
author
jprocter
<Jim Procter>
Thu, 1 May 2008 09:22:43 +0000
(09:22 +0000)
committer
jprocter
<Jim Procter>
Thu, 1 May 2008 09:22:43 +0000
(09:22 +0000)
src/jalview/datamodel/AlignmentAnnotation.java
patch
|
blob
|
history
diff --git
a/src/jalview/datamodel/AlignmentAnnotation.java
b/src/jalview/datamodel/AlignmentAnnotation.java
index
f68786b
..
40d2b7e
100755
(executable)
--- a/
src/jalview/datamodel/AlignmentAnnotation.java
+++ b/
src/jalview/datamodel/AlignmentAnnotation.java
@@
-118,10
+118,9
@@
public class AlignmentAnnotation
/**
* Creates a new AlignmentAnnotation object.
*
/**
* Creates a new AlignmentAnnotation object.
*
- * @param label DOCUMENT ME!
- * @param description DOCUMENT ME!
- * @param annotations DOCUMENT ME!about:blank
-Loading...
+ * @param label short label shown under sequence labels
+ * @param description text displayed on mouseover
+ * @param annotations set of positional annotation elements
*/
public AlignmentAnnotation(String label, String description,
Annotation[] annotations)
*/
public AlignmentAnnotation(String label, String description,
Annotation[] annotations)
@@
-138,6
+137,7
@@
Loading...
void areLabelsSecondaryStructure()
{
boolean nonSSLabel = false;
void areLabelsSecondaryStructure()
{
boolean nonSSLabel = false;
+ char firstChar=0;
for (int i = 0; i < annotations.length; i++)
{
if (annotations[i] == null)
for (int i = 0; i < annotations.length; i++)
{
if (annotations[i] == null)
@@
-154,28
+154,32
@@
Loading...
{
continue;
}
{
continue;
}
-
- if (annotations[i].displayCharacter.length() == 1
- // Uncomment to only catch case where displayCharacter==secondary Structure
+ if (annotations[i].displayCharacter.length() == 1)
+ {
+ firstChar = annotations[i].displayCharacter.charAt(0);
+ // check to see if it looks like a sequence or is secondary structure labelling.
+ if (
+ // Uncomment to only catch case where displayCharacter==secondary Structure
// to correctly redisplay SS annotation imported from Stockholm, exported to JalviewXML and read back in again.
// && annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
// to correctly redisplay SS annotation imported from Stockholm, exported to JalviewXML and read back in again.
// && annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
- && !annotations[i].displayCharacter.equals("H")
- && !annotations[i].displayCharacter.equals("E")
- && !annotations[i].displayCharacter.equals("-")
- && !annotations[i].displayCharacter.equals("."))
+ firstChar!='H'
+ && firstChar!='E'
+ && firstChar!='-'
+ && firstChar!='-' && firstChar<jalview.schemes.ResidueProperties.aaIndex.length)
{
if (jalview.schemes.ResidueProperties.aaIndex
{
if (jalview.schemes.ResidueProperties.aaIndex
- [annotations[i].displayCharacter.charAt(0)] < 23)
+ [firstChar] < 23)
{
nonSSLabel = true;
}
}
{
nonSSLabel = true;
}
}
+ }
- if (annotations[i].displayCharacter.length() > 0)
- {
- hasText = true;
- }
+ if (annotations[i].displayCharacter.length() > 0)
+ {
+ hasText = true;
}
}
+ }
if (nonSSLabel)
{
if (nonSSLabel)
{