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JAL-2541 save/Undo only 'diffs' for features with Cut command
[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
f263938
..
d1bae50
100644
(file)
--- a/
src/jalview/datamodel/features/SequenceFeatures.java
+++ b/
src/jalview/datamodel/features/SequenceFeatures.java
@@
-1,5
+1,6
@@
package jalview.datamodel.features;
package jalview.datamodel.features;
+import jalview.datamodel.ContiguousI;
import jalview.datamodel.SequenceFeature;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
import jalview.datamodel.SequenceFeature;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
@@
-62,7
+63,7
@@
public class SequenceFeatures implements SequenceFeaturesI
{
/*
* use a TreeMap so that features are returned in alphabetical order of type
{
/*
* use a TreeMap so that features are returned in alphabetical order of type
- * wrap as a synchronized map for add and delete operations
+ * ? wrap as a synchronized map for add and delete operations
*/
// featureStore = Collections
// .synchronizedSortedMap(new TreeMap<String, FeatureStore>());
*/
// featureStore = Collections
// .synchronizedSortedMap(new TreeMap<String, FeatureStore>());
@@
-70,6
+71,21
@@
public class SequenceFeatures implements SequenceFeaturesI
}
/**
}
/**
+ * Constructor given a list of features
+ */
+ public SequenceFeatures(List<SequenceFeature> features)
+ {
+ this();
+ if (features != null)
+ {
+ for (SequenceFeature feature : features)
+ {
+ add(feature);
+ }
+ }
+ }
+
+ /**
* {@inheritDoc}
*/
@Override
* {@inheritDoc}
*/
@Override
@@
-466,13
+482,22
@@
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;
}
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public void deleteAll()
+ {
+ featureStore.clear();
+ }
}
\ No newline at end of file
}
\ No newline at end of file