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JAL-3621 corrected sequence feature sort and test
[jalview.git]
/
src
/
jalview
/
datamodel
/
features
/
SequenceFeatures.java
diff --git
a/src/jalview/datamodel/features/SequenceFeatures.java
b/src/jalview/datamodel/features/SequenceFeatures.java
index
db2f0e1
..
8ac4991
100644
(file)
--- a/
src/jalview/datamodel/features/SequenceFeatures.java
+++ b/
src/jalview/datamodel/features/SequenceFeatures.java
@@
-20,11
+20,8
@@
*/
package jalview.datamodel.features;
*/
package jalview.datamodel.features;
-import jalview.datamodel.SequenceFeature;
-import jalview.io.gff.SequenceOntologyFactory;
-import jalview.io.gff.SequenceOntologyI;
-
import java.util.ArrayList;
import java.util.ArrayList;
+import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
@@
-33,6
+30,9
@@
import java.util.Set;
import java.util.TreeMap;
import intervalstore.api.IntervalI;
import java.util.TreeMap;
import intervalstore.api.IntervalI;
+import jalview.datamodel.SequenceFeature;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyI;
/**
* A class that stores sequence features in a way that supports efficient
/**
* A class that stores sequence features in a way that supports efficient
@@
-44,7
+44,6
@@
import intervalstore.api.IntervalI;
*/
public class SequenceFeatures implements SequenceFeaturesI
{
*/
public class SequenceFeatures implements SequenceFeaturesI
{
-
/*
* map from feature type to structured store of features for that type
* null types are permitted (but not a good idea!)
/*
* map from feature type to structured store of features for that type
* null types are permitted (but not a good idea!)
@@
-414,7
+413,10
@@
public class SequenceFeatures implements SequenceFeaturesI
public static void sortFeatures(List<? extends IntervalI> features,
final boolean forwardStrand)
{
public static void sortFeatures(List<? extends IntervalI> features,
final boolean forwardStrand)
{
- IntervalI.sortIntervals(features, forwardStrand);
+ Collections.sort(features,
+ forwardStrand
+ ? IntervalI.COMPARE_BEGIN_ASC_END_DESC
+ : IntervalI.COMPARE_END_DESC);
}
/**
}
/**