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JAL-2822 verify start/end is correctly updated and restored after edit, undo, and...
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceI.java
diff --git
a/src/jalview/datamodel/SequenceI.java
b/src/jalview/datamodel/SequenceI.java
index
6e6d1aa
..
f1a4140
100755
(executable)
--- a/
src/jalview/datamodel/SequenceI.java
+++ b/
src/jalview/datamodel/SequenceI.java
@@
-192,22
+192,26
@@
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
+ * Returns the sequence positions for first and last residues lying within the
+ * given column positions [fromColum,toColumn] (where columns are numbered
+ * from 1), or null if no residues are included in the range
*
* @param fromColum
*
* @param fromColum
+ * - first column base 1
* @param toColumn
* @param toColumn
+ * - last column, base 1
* @return
*/
public Range findPositions(int fromColum, int toColumn);
* @return
*/
public Range findPositions(int fromColum, int toColumn);
@@
-533,5
+537,5
@@
public interface SequenceI extends ASequenceI
* @param c1
* @param c2
*/
* @param c1
* @param c2
*/
- public int replace(char c1, char c2);
+ int replace(char c1, char c2);
}
}