JAL-4386 Fixed some identified bugs in recent changes

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

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index b7747f5..126c8c1 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -20,6 +20,13 @@
  */
 package jalview.api;
 
+import java.awt.Color;
+import java.awt.Font;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
 import jalview.analysis.Conservation;
 import jalview.analysis.TreeModel;
 import jalview.datamodel.AlignmentAnnotation;
@@ -38,13 +45,6 @@ import jalview.renderer.ResidueShaderI;
 import jalview.schemes.ColourSchemeI;
 import jalview.viewmodel.ViewportRanges;
 
-import java.awt.Color;
-import java.awt.Font;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
 /**
  * @author jimp
  * 
@@ -134,7 +134,7 @@ public interface AlignViewportI extends ViewStyleI
    */
   AlignmentAnnotation getAlignmentConsensusAnnotation();
   
-  AlignmentAnnotation getAlignmentSecondaryStructureConsensusAnnotation();
+  List<AlignmentAnnotation> getAlignmentSecondaryStructureConsensusAnnotation();
 
 
   /**
@@ -183,7 +183,7 @@ public interface AlignViewportI extends ViewStyleI
    */
   void setSequenceConsensusHash(ProfilesI hconsensus);
   
-  void setSequenceSSConsensusHash(ProfilesI hSSConsensus);
+  void setSequenceSSConsensusHash(Map<String, ProfilesI> hSSConsesnusProfileMap);
   
 
   /**
@@ -575,9 +575,23 @@ public interface AlignViewportI extends ViewStyleI
    * @return
    */
   Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
+  /**
+   * notify all concerned that the alignment data has changed and derived data
+   * needs to be recalculated
+   */
+  public void notifyAlignmentChanged();
 
+  /**
+   * retrieve a matrix associated with the view's alignment's annotation 
+   * @param alignmentAnnotation
+   * @return contact matrix or NULL
+   */
   ContactMatrixI getContactMatrix(AlignmentAnnotation alignmentAnnotation);
 
-  ProfilesI getSequenceSSConsensusHash();
+  Map<String, ProfilesI> getSequenceSSConsensusHash();
+
+  List<String> getSecondaryStructureSources();
+
+  void setSecondaryStructureSources(List<String> secondaryStructureSources);
 
 }