Merge branch 'releases/Release_2_11_3_Branch'

[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..9ca88cc 100644 (file)
--- a/src/jalview/ws/datamodel/MappableContactMatrixI.java
+++ b/src/jalview/ws/datamodel/MappableContactMatrixI.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ws.datamodel;
 
 import jalview.datamodel.ContactListI;
@@ -51,7 +71,7 @@ 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 +81,19 @@ 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);
+
+  ContactMatrixI getMappedMatrix();
 }