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Merge branch 'develop' into trialMerge
[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
ddbaf73
..
0aa77fa
100644
(file)
--- a/
src/jalview/analysis/scoremodels/FeatureDistanceModel.java
+++ b/
src/jalview/analysis/scoremodels/FeatureDistanceModel.java
@@
-58,7
+58,7
@@
public class FeatureDistanceModel extends DistanceScoreModel
FeatureDistanceModel instance;
try
{
FeatureDistanceModel instance;
try
{
- instance = this.getClass().newInstance();
+ instance = this.getClass().getDeclaredConstructor().newInstance();
instance.configureFromAlignmentView(view);
return instance;
} catch (InstantiationException | IllegalAccessException e)
instance.configureFromAlignmentView(view);
return instance;
} catch (InstantiationException | IllegalAccessException e)
@@
-66,6
+66,9
@@
public class FeatureDistanceModel extends DistanceScoreModel
System.err.println("Error in " + getClass().getName()
+ ".getInstance(): " + e.getMessage());
return null;
System.err.println("Error in " + getClass().getName()
+ ".getInstance(): " + e.getMessage());
return null;
+ } catch (ReflectiveOperationException roe)
+ {
+ return null;
}
}
}
}
@@
-124,8
+127,8
@@
public class FeatureDistanceModel extends DistanceScoreModel
/*
* first record feature types in this column for each sequence
*/
/*
* first record feature types in this column for each sequence
*/
- Map<SeqCigar, Set<String>> sfap = findFeatureTypesAtColumn(
- seqs, cpos);
+ Map<SeqCigar, Set<String>> sfap = findFeatureTypesAtColumn(seqs,
+ cpos);
/*
* count feature types on either i'th or j'th sequence but not both
/*
* count feature types on either i'th or j'th sequence but not both
@@
-188,7
+191,7
@@
public class FeatureDistanceModel extends DistanceScoreModel
protected Map<SeqCigar, Set<String>> findFeatureTypesAtColumn(
SeqCigar[] seqs, int columnPosition)
{
protected Map<SeqCigar, Set<String>> findFeatureTypesAtColumn(
SeqCigar[] seqs, int columnPosition)
{
- Map<SeqCigar, Set<String>> sfap = new HashMap<SeqCigar, Set<String>>();
+ Map<SeqCigar, Set<String>> sfap = new HashMap<>();
for (SeqCigar seq : seqs)
{
int spos = seq.findPosition(columnPosition);
for (SeqCigar seq : seqs)
{
int spos = seq.findPosition(columnPosition);
@@
-197,9
+200,9
@@
public class FeatureDistanceModel extends DistanceScoreModel
/*
* position is not a gap
*/
/*
* position is not a gap
*/
- Set<String> types = new HashSet<String>();
+ Set<String> types = new HashSet<>();
List<SequenceFeature> sfs = fr.findFeaturesAtResidue(
List<SequenceFeature> sfs = fr.findFeaturesAtResidue(
- seq.getRefSeq(), spos);
+ seq.getRefSeq(), spos, spos);
for (SequenceFeature sf : sfs)
{
types.add(sf.getType());
for (SequenceFeature sf : sfs)
{
types.add(sf.getType());