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JAL-3490 unit test for ignore hidden regions with selection group
[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
5390975
..
db2f0e1
100644
(file)
--- a/
src/jalview/datamodel/features/SequenceFeatures.java
+++ b/
src/jalview/datamodel/features/SequenceFeatures.java
@@
-25,7
+25,6
@@
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
import java.util.ArrayList;
import jalview.io.gff.SequenceOntologyI;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
@@
-204,7
+203,9
@@
public class SequenceFeatures implements SequenceFeaturesI
/**
* A convenience method that converts a vararg for feature types to an
/**
* A convenience method that converts a vararg for feature types to an
- * Iterable over matched feature sets in key order
+ * Iterable over matched feature sets. If no types are specified, all feature
+ * sets are returned. If one or more types are specified, feature sets for
+ * those types are returned, preserving the order of the types.
*
* @param type
* @return
*
* @param type
* @return
@@
-220,12
+221,11
@@
public class SequenceFeatures implements SequenceFeaturesI
}
List<FeatureStore> types = new ArrayList<>();
}
List<FeatureStore> types = new ArrayList<>();
- List<String> args = Arrays.asList(type);
- for (Entry<String, FeatureStore> featureType : featureStore.entrySet())
+ for (String theType : type)
{
{
- if (args.contains(featureType.getKey()))
+ if (theType != null && featureStore.containsKey(theType))
{
{
- types.add(featureType.getValue());
+ types.add(featureStore.get(theType));
}
}
return types;
}
}
return types;
@@
-447,13
+447,22
@@
public class SequenceFeatures implements SequenceFeaturesI
* {@inheritDoc}
*/
@Override
* {@inheritDoc}
*/
@Override
- public boolean shiftFeatures(int shift)
+ public boolean shiftFeatures(int fromPosition, int shiftBy)
{
boolean modified = false;
for (FeatureStore fs : featureStore.values())
{
{
boolean modified = false;
for (FeatureStore fs : featureStore.values())
{
- modified |= fs.shiftFeatures(shift);
+ modified |= fs.shiftFeatures(fromPosition, shiftBy);
}
return modified;
}
}
return modified;
}
-}
\ No newline at end of file
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public void deleteAll()
+ {
+ featureStore.clear();
+ }
+}