X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=ab9efb164a835304991570aeb22ba87ded8b8121;hb=aeb173dd7daa4559e760548d955ee83aac6828d8;hp=dd442f6da769cae65f090d15fd8ed60e68f947a0;hpb=d47a462ddd7bd3dd2a0529b6da03b220370c8ae5;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index dd442f6..ab9efb1 100644
--- 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
@@ -52,6 +57,11 @@ public interface AlignViewportI
   AlignmentAnnotation getAlignmentQualityAnnot();
 
   AlignmentAnnotation getAlignmentConservationAnnotation();
+  /**
+   * get the container for alignment consensus annotation
+   * @return
+   */
+  AlignmentAnnotation getAlignmentConsensusAnnotation();
 
   /**
    * Test to see if viewport is still open and active
@@ -63,4 +73,40 @@ public interface AlignViewportI
    * @return
    */
   AlignCalcManagerI getCalcManager();
+  
+  /**
+   * get the percentage gaps allowed in a conservation calculation
+   * 
+   */
+  public int getConsPercGaps();
+
+  /**
+   * set the consensus result object for the viewport
+   * @param hconsensus
+   */
+  void setSequenceConsensusHash(Hashtable[] hconsensus);
+
+  /**
+   * 
+   * @return the alignment annotatino row for the structure consensus calculation
+   */
+  AlignmentAnnotation getAlignmentStrucConsensusAnnotation();
+
+  /**
+   * set the Rna structure consensus result object for the viewport
+   * @param hStrucConsensus 
+   */
+  void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
+
+  /**
+   * set global colourscheme
+   * @param rhc
+   */
+  void setGlobalColourScheme(ColourSchemeI rhc);
+
+  Map<SequenceI, SequenceCollectionI> getHiddenRepSequences();
+
+  void setHiddenRepSequences(
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
+
 }