JAL-961 store result of conservation analysis worker on the alignment viewport

[jalview.git] / src / jalview / api / AlignViewportI.java

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index f42293d..44fef0e 100644 (file)
--- 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 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,16 +14,22 @@
  * 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;
 
+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;
+import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 
@@ -155,4 +161,33 @@ 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);
+
+  AlignmentView getAlignmentView(boolean selectedOnly);
+
+  AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups);
+
+  String[] getViewAsString(boolean selectedRegionOnly);
+
+  void setSelectionGroup(SequenceGroup sg);
+
+  char getGapCharacter();
+
+  void setColumnSelection(ColumnSelection cs);
+
+  void setConservation(Conservation cons);
+
+
 }