JAL-4134 properly resolve positions in associated aligned sequence for matrix group...

[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 b8a9779..9762428 100644 (file)
--- a/src/jalview/ws/datamodel/MappableContactMatrixI.java
+++ b/src/jalview/ws/datamodel/MappableContactMatrixI.java
@@ -51,7 +51,7 @@ public interface MappableContactMatrixI extends ContactMatrixI
   MapList getMapFor(SequenceI sequenceRef);
 
   /**
-   * Locate a position in the mapped sequence for a column in the matrix - use
+   * Locate a position in the mapped sequence for a single column in the matrix. 
    * this to resolve positions corresponding to column clusters
    * 
    * @param localFrame
@@ -61,4 +61,16 @@ public interface MappableContactMatrixI extends ContactMatrixI
    * @return sequence position(s) corresponding to column in contact matrix
    */
   int[] getMappedPositionsFor(SequenceI localFrame, int column);
+
+  /**
+   * Locate a position in the mapped sequence for a contiguous range of columns 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 from, int to);
 }