X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=e7afee0b9bd8ea2f9323171549e0d296d9c96f46;hb=c8d80485038ab96fb06bd0885c323803646d8e57;hp=b976a3d94d1f51c9f9488d171821ebe217913ff4;hpb=dd8112aefe2c3a08c51f1684d5cda16be938c74f;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index b976a3d..e7afee0 100644
--- 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;
@@ -27,6 +34,8 @@ import jalview.datamodel.AlignmentExportData;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceCollectionI;
@@ -36,12 +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.List;
-import java.util.Map;
-
 /**
  * @author jimp
  * 
@@ -108,9 +111,9 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
-  Hashtable[] getComplementConsensusHash();
+  Hashtable<String, Object>[] getComplementConsensusHash();
 
-  Hashtable[] getRnaStructureConsensusHash();
+  Hashtable<String, Object>[] getRnaStructureConsensusHash();
 
   boolean isIgnoreGapsConsensus();
 
@@ -178,7 +181,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @param hconsensus
    */
-  void setComplementConsensusHash(Hashtable[] hconsensus);
+  void setComplementConsensusHash(Hashtable<String, Object>[] hconsensus);
 
   /**
    * 
@@ -192,7 +195,8 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @param hStrucConsensus
    */
-  void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
+  void setRnaStructureConsensusHash(
+          Hashtable<String, Object>[] hStrucConsensus);
 
   /**
    * Sets the colour scheme for the background alignment (as distinct from
@@ -432,9 +436,19 @@ public interface AlignViewportI extends ViewStyleI
    */
   void setFollowHighlight(boolean b);
 
+  /**
+   * configure the feature renderer with predefined feature settings
+   * 
+   * @param featureSettings
+   */
   public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
 
   /**
+   * Apply the given feature settings on top of existing feature settings.
+   */
+  public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings);
+
+  /**
    * check if current selection group is defined on the view, or is simply a
    * temporary group.
    * 
@@ -464,6 +478,17 @@ public interface AlignViewportI extends ViewStyleI
   SearchResultsI getSearchResults();
 
   /**
+   * Retrieve a ContactListI corresponding to column in an annotation row in an
+   * alignment.
+   * 
+   * @param _aa
+   *          - annotation with associated matrix data
+   * @param column
+   *          - column in alignment where _aa is associated
+   */
+  ContactListI getContactList(AlignmentAnnotation _aa, int column);
+
+  /**
    * Updates view settings with the given font. You may need to call
    * AlignmentPanel.fontChanged to update the layout geometry.
    * 
@@ -500,4 +525,56 @@ public interface AlignViewportI extends ViewStyleI
    * @return
    */
   AlignmentExportData getAlignExportData(AlignExportSettingsI options);
+
+  /**
+   * @param update
+   *          - set the flag for updating structures on next repaint
+   */
+  void setUpdateStructures(boolean update);
+
+  /**
+   *
+   * @return true if structure views will be updated on next refresh
+   */
+  boolean isUpdateStructures();
+
+  /**
+   * check if structure views need to be updated, and clear the flag afterwards.
+   * 
+   * @return if an update is needed
+   */
+  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);
+
+  /**
+   * Returns an interator over the [start, end] column positions of the visible
+   * regions of the alignment
+   * 
+   * @param selectedRegionOnly
+   *          if true, and the view has a selection region, then only the
+   *          intersection of visible columns with the selection region is
+   *          returned
+   * @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);
 }