X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdatamodel%2FMappableContactMatrixI.java;h=9ca88cc14278f84fc8c276309691ae6b3aaa207c;hb=bc1a3842b31a35a7794f4afec4911ad421c7c3e4;hp=4abaa5deb5b99123ad0da1333347aad6f13ea08a;hpb=9e40070f757fc662aba39ba6314be4937276ead4;p=jalview.git

diff --git a/src/jalview/ws/datamodel/MappableContactMatrixI.java b/src/jalview/ws/datamodel/MappableContactMatrixI.java
index 4abaa5d..9ca88cc 100644
--- a/src/jalview/ws/datamodel/MappableContactMatrixI.java
+++ b/src/jalview/ws/datamodel/MappableContactMatrixI.java
@@ -1,9 +1,30 @@
+/*
+ * 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;
 import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.SequenceI;
+import jalview.util.MapList;
 
 public interface MappableContactMatrixI extends ContactMatrixI
 {
@@ -11,21 +32,68 @@ public interface MappableContactMatrixI extends ContactMatrixI
   boolean hasReferenceSeq();
 
   SequenceI getReferenceSeq();
+
   /**
    * remaps the matrix to a new reference sequence
-   * @param dsq 
-   * @param sqmpping - mapping from current reference to new reference - 1:1 only
+   * 
+   * @param dsq
+   * @param sqmpping
+   *          - mapping from current reference to new reference - 1:1 only
    * @return new ContactMatrixI instance with updated mapping
    */
   MappableContactMatrixI liftOver(SequenceI dsq, Mapping sqmpping);
-  
+
   /**
    * like ContactMatrixI.getContactList(int column) but
-   * @param localFrame - sequence or other object that this contact matrix is associated with
-   * @param column - position in localFrame
+   * 
+   * @param localFrame
+   *          - sequence or other object that this contact matrix is associated
+   *          with
+   * @param column
+   *          - position in localFrame
    * @return ContactListI that returns contacts w.r.t. localFrame
    */
-  
+
   ContactListI getMappableContactList(SequenceI localFrame, int column);
 
+  /**
+   * 
+   * Similar to AlignedCodonFrame.getMappingBetween
+   * 
+   * @param sequenceRef
+   *          - a reference sequence mappable to this contactMatrix - may be
+   *          null
+   * @return null or the MapList mapping to the coordinates of the reference
+   *         sequence (or if hasReferenceSeq() is false, and sequenceRef is
+   *         null, any mapping present)
+   * 
+   */
+  MapList getMapFor(SequenceI sequenceRef);
+
+  /**
+   * Locate a position in the mapped sequence for a single column in the matrix.
+   * 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);
+
+  /**
+   * 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();
 }