JAL-2349 store/restore mappable contact matrix in project and fix up interactive...

[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 4abaa5d..052bc2f 100644 (file)
--- a/src/jalview/ws/datamodel/MappableContactMatrixI.java
+++ b/src/jalview/ws/datamodel/MappableContactMatrixI.java
@@ -4,6 +4,7 @@ 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
 {
@@ -28,4 +29,14 @@ public interface MappableContactMatrixI extends ContactMatrixI
   
   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);
+
 }