X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=de98c642b87aa98df2f0b88b1bf8b7b99b9ec0b7;hb=3176c105e6751e32129840f5bfa410921a9c25e6;hp=b5987f4a237c54a59bdcf85a23d0397ce6adf115;hpb=4b7d3640209c4434d569c746672cf9eed4250ace;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index b5987f4..de98c64 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -308,6 +308,11 @@ public class AlignmentAnnotation
 
   public static final int CONTACT_MAP = 4;
 
+  /**
+   * property that when set to non-empty string disables display of column groups defined on the contact matrix
+   */
+  public static final String CONTACT_MAP_NOGROUPS = "CMNOGRPS";
+
   public boolean belowAlignment = true;
 
   public SequenceGroup groupRef = null;
@@ -1745,5 +1750,23 @@ public class AlignmentAnnotation
     }
     return aa;
   }
+  
+  /**
+   * convenience method to check for the 'CONTACT_MAP_NOGROUPS' property for this alignment annotation row
+   * @return true if no CONTACT_MAP_NOGROUPS property is found, or it is set to ""
+   */
+  public boolean isShowGroupsForContactMatrix()
+  {
+    return getProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS)==null || "".equals(getProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS));
+  }
+  /**
+   * set the 'CONTACT_MAP_NOGROUPS' property for this alignment annotation row
+   * @see isShowGroupsForContactMatrix
+   */
+  public void setShowGroupsForContactMatrix(boolean showGroups)
+  {
+    setProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS, showGroups ? "" : "nogroups");
+  }
+
 
 }