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-3181 simplified code and test
[jalview.git]
/
src
/
jalview
/
analysis
/
scoremodels
/
FeatureDistanceModel.java
diff --git
a/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
b/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
index
c20d4f1
..
e506be2
100644
(file)
--- a/
src/jalview/analysis/scoremodels/FeatureDistanceModel.java
+++ b/
src/jalview/analysis/scoremodels/FeatureDistanceModel.java
@@
-177,10
+177,12
@@
public class FeatureDistanceModel extends DistanceScoreModel
/**
* Builds and returns a map containing a (possibly empty) list (one per
* SeqCigar) of visible feature types at the given column position. The map
/**
* Builds and returns a map containing a (possibly empty) list (one per
* SeqCigar) of visible feature types at the given column position. The map
- * has no entry for sequences which are gapped at the column position.
+ * does not include entries for features which straddle a gapped column
+ * positions.
*
* @param seqs
* @param columnPosition
*
* @param seqs
* @param columnPosition
+ * (0..)
* @return
*/
protected Map<SeqCigar, Set<String>> findFeatureTypesAtColumn(
* @return
*/
protected Map<SeqCigar, Set<String>> findFeatureTypesAtColumn(
@@
-192,9
+194,12
@@
public class FeatureDistanceModel extends DistanceScoreModel
int spos = seq.findPosition(columnPosition);
if (spos != -1)
{
int spos = seq.findPosition(columnPosition);
if (spos != -1)
{
+ /*
+ * position is not a gap
+ */
Set<String> types = new HashSet<String>();
Set<String> types = new HashSet<String>();
- List<SequenceFeature> sfs = fr.findFeaturesAtRes(seq.getRefSeq(),
- spos);
+ List<SequenceFeature> sfs = fr.findFeaturesAtResidue(
+ seq.getRefSeq(), spos);
for (SequenceFeature sf : sfs)
{
types.add(sf.getType());
for (SequenceFeature sf : sfs)
{
types.add(sf.getType());