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Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges
[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
..
15c2c07
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!)
@@
-152,8
+151,8
@@
public class SequenceFeatures implements SequenceFeaturesI
return new ArrayList<>();
}
return new ArrayList<>();
}
- return getAllFeatures(featureTypes.toArray(new String[featureTypes
- .size()]));
+ return getAllFeatures(
+ featureTypes.toArray(new String[featureTypes.size()]));
}
/**
}
/**
@@
-321,8
+320,8
@@
public class SequenceFeatures implements SequenceFeaturesI
for (Entry<String, FeatureStore> featureType : featureStore.entrySet())
{
for (Entry<String, FeatureStore> featureType : featureStore.entrySet())
{
- Set<String> featureGroups = featureType.getValue().getFeatureGroups(
- positionalFeatures);
+ Set<String> featureGroups = featureType.getValue()
+ .getFeatureGroups(positionalFeatures);
for (String group : groups)
{
if (featureGroups.contains(group))
for (String group : groups)
{
if (featureGroups.contains(group))
@@
-373,7
+372,7
@@
public class SequenceFeatures implements SequenceFeaturesI
{
return true;
}
{
return true;
}
- SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
for (String term : soTerm)
{
if (type.equals(term) || so.isA(type, term))
for (String term : soTerm)
{
if (type.equals(term) || so.isA(type, term))
@@
-390,8
+389,9
@@
public class SequenceFeatures implements SequenceFeaturesI
@Override
public float getMinimumScore(String type, boolean positional)
{
@Override
public float getMinimumScore(String type, boolean positional)
{
- return featureStore.containsKey(type) ? featureStore.get(type)
- .getMinimumScore(positional) : Float.NaN;
+ return featureStore.containsKey(type)
+ ? featureStore.get(type).getMinimumScore(positional)
+ : Float.NaN;
}
/**
}
/**
@@
-400,8
+400,9
@@
public class SequenceFeatures implements SequenceFeaturesI
@Override
public float getMaximumScore(String type, boolean positional)
{
@Override
public float getMaximumScore(String type, boolean positional)
{
- return featureStore.containsKey(type) ? featureStore.get(type)
- .getMaximumScore(positional) : Float.NaN;
+ return featureStore.containsKey(type)
+ ? featureStore.get(type).getMaximumScore(positional)
+ : Float.NaN;
}
/**
}
/**
@@
-414,7
+415,9
@@
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);
}
/**
}
/**