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Merge branch 'develop' into features/JAL-2446NCList
[jalview.git]
/
src
/
jalview
/
datamodel
/
AlignmentAnnotation.java
diff --git
a/src/jalview/datamodel/AlignmentAnnotation.java
b/src/jalview/datamodel/AlignmentAnnotation.java
index
6bbd566
..
c464af2
100755
(executable)
--- a/
src/jalview/datamodel/AlignmentAnnotation.java
+++ b/
src/jalview/datamodel/AlignmentAnnotation.java
@@
-96,14
+96,13
@@
public class AlignmentAnnotation
* Updates the _rnasecstr field Determines the positions that base pair and
* the positions of helices based on secondary structure from a Stockholm file
*
* Updates the _rnasecstr field Determines the positions that base pair and
* the positions of helices based on secondary structure from a Stockholm file
*
- * @param RNAannot
+ * @param rnaAnnotation
*/
*/
- private void _updateRnaSecStr(CharSequence RNAannot)
+ private void _updateRnaSecStr(CharSequence rnaAnnotation)
{
try
{
{
try
{
- bps = Rna.getModeleBP(RNAannot);
- _rnasecstr = Rna.getBasePairs(bps);
+ _rnasecstr = Rna.getHelixMap(rnaAnnotation);
invalidrnastruc = -1;
} catch (WUSSParseException px)
{
invalidrnastruc = -1;
} catch (WUSSParseException px)
{
@@
-114,8
+113,6
@@
public class AlignmentAnnotation
{
return;
}
{
return;
}
- Rna.HelixMap(_rnasecstr);
- // setRNAStruc(RNAannot);
if (_rnasecstr != null && _rnasecstr.length > 0)
{
if (_rnasecstr != null && _rnasecstr.length > 0)
{
@@
-273,12
+270,6
@@
public class AlignmentAnnotation
}
}
}
}
- // JBPNote: what does this do ?
- public void ConcenStru(CharSequence RNAannot) throws WUSSParseException
- {
- bps = Rna.getModeleBP(RNAannot);
- }
-
/**
* Creates a new AlignmentAnnotation object.
*
/**
* Creates a new AlignmentAnnotation object.
*