X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=cb11886f5bd5cad34e663a09f2ff0d33b0bb0751;hb=6fc163433164d93374330fa0a603eea1e1fd42b3;hp=df57cc0b06554ec4f7d2de6b70a17b7060699821;hpb=fc2dbe249bddd693c94bfa88b3468abc41c6d80b;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index df57cc0..cb11886 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -26,6 +26,9 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ContactListI;
+import jalview.datamodel.ProfilesI;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -53,6 +56,18 @@ public interface AlignViewportI extends ViewStyleI
    */
   public int calcPanelHeight();
 
+  /**
+   * Answers true if the viewport has at least one column selected
+   * 
+   * @return
+   */
+  boolean hasSelectedColumns();
+
+  /**
+   * Answers true if the viewport has at least one hidden column
+   * 
+   * @return
+   */
   boolean hasHiddenColumns();
 
   boolean isValidCharWidth();
@@ -69,7 +84,7 @@ public interface AlignViewportI extends ViewStyleI
 
   ColumnSelection getColumnSelection();
 
-  Hashtable[] getSequenceConsensusHash();
+  ProfilesI getSequenceConsensusHash();
 
   /**
    * Get consensus data table for the cDNA complement of this alignment (if any)
@@ -110,6 +125,11 @@ public interface AlignViewportI extends ViewStyleI
   boolean isClosed();
 
   /**
+   * Dispose of all references or resources held by the viewport
+   */
+  void dispose();
+
+  /**
    * get the associated calculation thread manager for the view
    * 
    * @return
@@ -127,7 +147,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @param hconsensus
    */
-  void setSequenceConsensusHash(Hashtable[] hconsensus);
+  void setSequenceConsensusHash(ProfilesI hconsensus);
 
   /**
    * Set the cDNA complement consensus for the viewport
@@ -243,7 +263,7 @@ public interface AlignViewportI extends ViewStyleI
    * @return String[]
    */
   String[] getViewAsString(boolean selectedRegionOnly);
-  
+
   /**
    * 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
@@ -258,7 +278,8 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return String[]
    */
-  String[] getViewAsString(boolean selectedRegionOnly, boolean isExportHiddenSeqs);
+  String[] getViewAsString(boolean selectedRegionOnly,
+          boolean isExportHiddenSeqs);
 
   void setSelectionGroup(SequenceGroup sg);
 
@@ -395,7 +416,6 @@ public interface AlignViewportI extends ViewStyleI
    */
   void setFollowHighlight(boolean b);
 
-
   public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
 
   /**
@@ -405,4 +425,27 @@ public interface AlignViewportI extends ViewStyleI
    * @return true if group is defined on the alignment
    */
   boolean isSelectionDefinedGroup();
+
+  /**
+   * 
+   * @return true if there are search results on the view
+   */
+  boolean hasSearchResults();
+
+  /**
+   * set the search results for the view
+   * 
+   * @param results
+   *          - or null to clear current results
+   */
+  void setSearchResults(SearchResultsI results);
+
+  /**
+   * get search results for this view (if any)
+   * 
+   * @return search results or null
+   */
+  SearchResultsI getSearchResults();
+
+  ContactListI getContactList(AlignmentAnnotation _aa, int column);
 }