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JAL-2381 copy and paste sequence also copies contact matrix annotation
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceI.java
diff --git
a/src/jalview/datamodel/SequenceI.java
b/src/jalview/datamodel/SequenceI.java
index
2f365e6
..
2e1daa3
100755
(executable)
--- a/
src/jalview/datamodel/SequenceI.java
+++ b/
src/jalview/datamodel/SequenceI.java
@@
-20,17
+20,16
@@
*/
package jalview.datamodel;
*/
package jalview.datamodel;
-import jalview.datamodel.Sequence.DBModList;
-import jalview.datamodel.features.SequenceFeaturesI;
-import jalview.util.MapList;
-import jalview.ws.params.InvalidArgumentException;
-
import java.util.BitSet;
import java.util.Iterator;
import java.util.List;
import java.util.Vector;
import fr.orsay.lri.varna.models.rna.RNA;
import java.util.BitSet;
import java.util.Iterator;
import java.util.List;
import java.util.Vector;
import fr.orsay.lri.varna.models.rna.RNA;
+import jalview.datamodel.Sequence.DBModList;
+import jalview.datamodel.features.SequenceFeaturesI;
+import jalview.util.MapList;
+import jalview.ws.params.InvalidArgumentException;
/**
* Methods for manipulating a sequence, its metadata and related annotation in
/**
* Methods for manipulating a sequence, its metadata and related annotation in
@@
-39,7
+38,7
@@
import fr.orsay.lri.varna.models.rna.RNA;
* @author $author$
* @version $Revision$
*/
* @author $author$
* @version $Revision$
*/
-public interface SequenceI extends ASequenceI
+public interface SequenceI extends ASequenceI, ContactMapHolderI
{
/**
* Set the display name for the sequence
{
/**
* Set the display name for the sequence
@@
-416,7
+415,7
@@
public interface SequenceI extends ASequenceI
/**
* Derive a sequence (using this one's dataset or as the dataset)
*
/**
* Derive a sequence (using this one's dataset or as the dataset)
*
- * @return duplicate sequence with valid dataset sequence
+ * @return duplicate sequence and any annotation present with valid dataset sequence
*/
public SequenceI deriveSequence();
*/
public SequenceI deriveSequence();
@@
-597,4
+596,7
@@
public interface SequenceI extends ASequenceI
*/
public int firstResidueOutsideIterator(Iterator<int[]> it);
*/
public int firstResidueOutsideIterator(Iterator<int[]> it);
+ public void addContactListFor(AlignmentAnnotation annotation,
+ ContactMatrixI cm);
+
}
}