X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=e2a13d451c8ea7e2108ab315164285686e13d995;hb=d71391d37943d1f6a5bf0af74996229f4d290cb0;hp=a35c2a4996e865119171eb77eae765952677f36a;hpb=0d8da9b627e1f4233963de2cd0a1d9c25b0871d2;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index a35c2a4..e2a13d4 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -21,10 +21,10 @@
 package jalview.api;
 
 import jalview.analysis.Conservation;
+import jalview.analysis.TreeModel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
-import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SearchResultsI;
@@ -54,7 +54,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
-  public ViewportRanges getRanges();
+  ViewportRanges getRanges();
 
   /**
    * calculate the height for visible annotation, revalidating bounds where
@@ -62,7 +62,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return total height of annotation
    */
-  public int calcPanelHeight();
+  int calcPanelHeight();
 
   /**
    * Answers true if the viewport has at least one column selected
@@ -251,16 +251,6 @@ public interface AlignViewportI extends ViewStyleI
   void clearSequenceColours();
 
   /**
-   * This method returns the visible alignment as text, as seen on the GUI, ie
-   * if columns are hidden they will not be returned in the result. Use this for
-   * calculating trees, PCA, redundancy etc on views which contain hidden
-   * columns.
-   * 
-   * @return String[]
-   */
-  CigarArray getViewAsCigars(boolean selectedRegionOnly);
-
-  /**
    * return a compact representation of the current alignment selection to pass
    * to an analysis function
    * 
@@ -505,28 +495,49 @@ public interface AlignViewportI extends ViewStyleI
   @Override
   void setProteinFontAsCdna(boolean b);
 
-  void setSequenceInformationHashes(List<ProfilesI> info);
+  void setHmmProfiles(ProfilesI info);
 
-  List<ProfilesI> getSequenceInformationHashes();
+  ProfilesI getHmmProfiles();
 
-  ProfilesI getSequenceInformationHash(int index);
+  /**
+   * Registers and starts a worker thread to calculate Information Content
+   * annotation, if it is not already registered
+   * 
+   * @param ap
+   */
+  void initInformationWorker(AlignmentViewPanel ap);
+
+  boolean isInfoLetterHeight();
 
-  List<AlignmentAnnotation> getInformationAnnotations();
+  abstract TreeModel getCurrentTree();
 
-  AlignmentAnnotation getInformationAnnotation(int index);
+  abstract void setCurrentTree(TreeModel tree);
 
-  void setSequenceInformationHash(ProfilesI info, int index);
+  /**
+   * @param update
+   *          - set the flag for updating structures on next repaint
+   */
+  void setUpdateStructures(boolean update);
 
   /**
-   * Initiates the information annotation for all uninitiated sequences.
+   *
+   * @return true if structure views will be updated on next refresh
    */
-  void initInformation();
+  boolean isUpdateStructures();
 
   /**
-   * Updates all information annotations.
+   * check if structure views need to be updated, and clear the flag afterwards.
    * 
-   * @param ap
+   * @return if an update is needed
    */
-  void updateInformation(AlignmentViewPanel ap);
+  boolean needToUpdateStructureViews();
 
+  /**
+   * Adds sequencegroup to the alignment in the view. Also adds a group to the
+   * complement view if one is defined.
+   * 
+   * @param sequenceGroup
+   *          - a group defined on sequences in the alignment held by the view
+   */
+  void addSequenceGroup(SequenceGroup sequenceGroup);
 }