X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=224ba0f5e6fca44608bbdcdd70279274ec50091f;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=15e5f1d868b7c3074ca7fe09e5e99673ec35ce97;hpb=a6ca346b004955c9db88f437ecafa24919119443;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 15e5f1d..224ba0f 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,6 +14,7 @@
  * 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.api;
 
@@ -21,6 +22,7 @@ import java.awt.Color;
 import java.util.Hashtable;
 import java.util.Map;
 
+import jalview.analysis.Conservation;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
@@ -159,11 +161,17 @@ public interface AlignViewportI
   void updateGroupAnnotationSettings(boolean applyGlobalSettings,
           boolean preserveNewGroupSettings);
 
+  void setSequenceColour(SequenceI seq, Color col);
+
+  Color getSequenceColour(SequenceI seq);
+
+  void updateSequenceIdColours();
 
   SequenceGroup getSelectionGroup();
 
   SequenceI[] getSequenceSelection();
 
+  void clearSequenceColours();
 
   CigarArray getViewAsCigars(boolean selectedRegionOnly);
 
@@ -177,5 +185,9 @@ public interface AlignViewportI
 
   char getGapCharacter();
 
+  void setColumnSelection(ColumnSelection cs);
+
+  void setConservation(Conservation cons);
+
 
 }