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JAL-4386 Added further checks for sequences that have no secondary structure.
[jalview.git]
/
src
/
jalview
/
analysis
/
scoremodels
/
SecondaryStructureDistanceModel.java
diff --git
a/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
b/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
index
7fcee35
..
0aac7fa
100644
(file)
--- a/
src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
+++ b/
src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
@@
-255,14
+255,19
@@
public class SecondaryStructureDistanceModel extends DistanceScoreModel
int seqPosition = seq.findPosition(columnPosition);
AlignmentAnnotation[] aa = seq.getRefSeq().getAnnotation("Secondary Structure");
if (aa != null) {
int seqPosition = seq.findPosition(columnPosition);
AlignmentAnnotation[] aa = seq.getRefSeq().getAnnotation("Secondary Structure");
if (aa != null) {
+ if (aa[0].getAnnotationForPosition(seqPosition) != null) {
Annotation a = aa[0].getAnnotationForPosition(seqPosition);
ss = a.secondaryStructure;
if (ss == ' ') {
Annotation a = aa[0].getAnnotationForPosition(seqPosition);
ss = a.secondaryStructure;
if (ss == ' ') {
- ss = 'C'; // In JalView, 'C' is represented as ' '
- }
- if (ss != '\0') { // Check if ss is not the default null character
- secondaryStructure.add(String.valueOf(ss));
+ ss = 'C'; // In JalView, 'C' is represented as ' '
}
}
+ }
+ else {
+ ss = 'C';
+ }
+ if (ss != '\0') { // Check if ss is not the default null character
+ secondaryStructure.add(String.valueOf(ss));
+ }
}
return secondaryStructure;
}
}
return secondaryStructure;
}