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JAL-2759 First pass instantiate hiddenColumns collection in constructor
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceI.java
diff --git
a/src/jalview/datamodel/SequenceI.java
b/src/jalview/datamodel/SequenceI.java
index
6840df8
..
6669d43
100755
(executable)
--- a/
src/jalview/datamodel/SequenceI.java
+++ b/
src/jalview/datamodel/SequenceI.java
@@
-192,17
+192,28
@@
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 (column) position. If at a
+ * gap, returns the position of the next residue to the right. If beyond the
+ * end of the sequence, returns 1 more than the last residue position.
*
* @param i
* column index in alignment (from 0..<length)
*
*
* @param i
* column index in alignment (from 0..<length)
*
- * @return TODO: JAL-2562 - residue number for residue (left of and) nearest
- * ith column
+ * @return
*/
public int findPosition(int i);
/**
*/
public int findPosition(int i);
/**
+ * Returns the from-to sequence positions (start..) for the given column
+ * positions (1..), or null if no residues are included in the range
+ *
+ * @param fromColum
+ * @param toColumn
+ * @return
+ */
+ public Range findPositions(int fromColum, int toColumn);
+
+ /**
* Returns an int array where indices correspond to each residue in the
* sequence and the element value gives its position in the alignment
*
* Returns an int array where indices correspond to each residue in the
* sequence and the element value gives its position in the alignment
*
@@
-212,6
+223,13
@@
public interface SequenceI extends ASequenceI
public int[] gapMap();
/**
public int[] gapMap();
/**
+ * Build a bitset corresponding to sequence gaps
+ *
+ * @return a BitSet where set values correspond to gaps in the sequence
+ */
+ public BitSet gapBitset();
+
+ /**
* Returns an int array where indices correspond to each position in sequence
* char array and the element value gives the result of findPosition for that
* index in the sequence.
* Returns an int array where indices correspond to each position in sequence
* char array and the element value gives the result of findPosition for that
* index in the sequence.
@@
-439,17
+457,6
@@
public interface SequenceI extends ASequenceI
public void transferAnnotation(SequenceI entry, Mapping mp);
/**
public void transferAnnotation(SequenceI entry, Mapping mp);
/**
- * @param index
- * The sequence index in the MSA
- */
- public void setIndex(int index);
-
- /**
- * @return The index of the sequence in the alignment
- */
- public int getIndex();
-
- /**
* @return The RNA of the sequence in the alignment
*/
* @return The RNA of the sequence in the alignment
*/