JAL-4134 support recovery of mapped positions for raw matrix column index in Mappable...

[jalview.git] / src / jalview / ws / datamodel / MappableContactMatrixI.java

diff --git a/src/jalview/ws/datamodel/MappableContactMatrixI.java b/src/jalview/ws/datamodel/MappableContactMatrixI.java
index 052bc2f..d1a5ff7 100644 (file)
--- a/src/jalview/ws/datamodel/MappableContactMatrixI.java
+++ b/src/jalview/ws/datamodel/MappableContactMatrixI.java
@@ -38,5 +38,16 @@ public interface MappableContactMatrixI extends ContactMatrixI
    * 
    */
   MapList getMapFor(SequenceI sequenceRef);
-
+  
+  /**
+   * Locate a position in the mapped sequence for a column in the matrix - use
+   * this to resolve positions corresponding to column clusters
+   * 
+   * @param localFrame
+   *          - sequence derivced from reference sequence
+   * @param column
+   *          - matrix row/column
+   * @return sequence position(s) corresponding to column in contact matrix
+   */
+  int[] getMappedPositionsFor(SequenceI localFrame, int column);
 }