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JAL-2632 Added paintAlignment(true) to show cols code
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceI.java
diff --git
a/src/jalview/datamodel/SequenceI.java
b/src/jalview/datamodel/SequenceI.java
index
aec68ab
..
12ddf60
100755
(executable)
--- a/
src/jalview/datamodel/SequenceI.java
+++ b/
src/jalview/datamodel/SequenceI.java
@@
-20,6
+20,7
@@
*/
package jalview.datamodel;
*/
package jalview.datamodel;
+import java.util.BitSet;
import java.util.List;
import java.util.Vector;
import java.util.List;
import java.util.Vector;
@@
-189,12
+190,13
@@
public interface SequenceI extends ASequenceI
public int findIndex(int pos);
/**
public int findIndex(int pos);
/**
- * Returns the sequence position for an alignment position
+ * Returns the sequence position for an alignment position.
*
* @param i
* column index in alignment (from 0..<length)
*
*
* @param i
* column index in alignment (from 0..<length)
*
- * @return residue number for residue (left of and) nearest ith column
+ * @return TODO: JAL-2562 - residue number for residue (left of and) nearest
+ * ith column
*/
public int findPosition(int i);
*/
public int findPosition(int i);
@@
-337,7
+339,14
@@
public interface SequenceI extends ASequenceI
*/
public void addDBRef(DBRefEntry entry);
*/
public void addDBRef(DBRefEntry entry);
- public void addSequenceFeature(SequenceFeature sf);
+ /**
+ * Adds the given sequence feature and returns true, or returns false if it is
+ * already present on the sequence
+ *
+ * @param sf
+ * @return
+ */
+ public boolean addSequenceFeature(SequenceFeature sf);
public void deleteFeature(SequenceFeature sf);
public void deleteFeature(SequenceFeature sf);
@@
-468,4
+477,11
@@
public interface SequenceI extends ASequenceI
* list
*/
public List<DBRefEntry> getPrimaryDBRefs();
* list
*/
public List<DBRefEntry> getPrimaryDBRefs();
+
+ /**
+ *
+ * @return BitSet corresponding to index [0,length) where Comparison.isGap()
+ * returns true.
+ */
+ BitSet getInsertionsAsBits();
}
}