JAL-1136 JAL-811 JAL-812 store/recover autocalc alignment annotation based on calcId...

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

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 914f010..ab9efb1 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -4,11 +4,16 @@
 package jalview.api;
 
 import java.util.Hashtable;
+import java.util.Map;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
+import jalview.schemes.RNAHelicesColour;
 
 /**
  * @author jimp
@@ -93,4 +98,15 @@ public interface AlignViewportI
    */
   void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
 
+  /**
+   * set global colourscheme
+   * @param rhc
+   */
+  void setGlobalColourScheme(ColourSchemeI rhc);
+
+  Map<SequenceI, SequenceCollectionI> getHiddenRepSequences();
+
+  void setHiddenRepSequences(
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
+
 }