JAL-1114 - refactor methods handling Vectors and Hashtables to Lists and Maps, and...

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

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 11fa615..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
@@ -48,4 +53,60 @@ public interface AlignViewportI
   boolean getCentreColumnLabels();
 
   boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
+
+  AlignmentAnnotation getAlignmentQualityAnnot();
+
+  AlignmentAnnotation getAlignmentConservationAnnotation();
+  /**
+   * get the container for alignment consensus annotation
+   * @return
+   */
+  AlignmentAnnotation getAlignmentConsensusAnnotation();
+
+  /**
+   * Test to see if viewport is still open and active
+   * @return true indicates that all references to viewport should be dropped 
+   */
+  boolean isClosed();
+  /**
+   * get the associated calculation thread manager for the view
+   * @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);
+
 }