X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=5715a957edd91f56706fa7d1f34f5e40279d80a4;hb=31714b90648bba773f68736b8c1700ae53805eee;hp=9e6d1c05b955f2d895be047a313e755168f23121;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 9e6d1c0..5715a95 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -20,11 +20,19 @@
  */
 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;
+import jalview.datamodel.AlignmentExportData;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
-import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SearchResultsI;
@@ -34,12 +42,7 @@ import jalview.datamodel.SequenceI;
 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;
+import jalview.viewmodel.seqfeatures.IdColumns;
 
 /**
  * @author jimp
@@ -107,9 +110,9 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
-  Hashtable[] getComplementConsensusHash();
+  Hashtable<String, Object>[] getComplementConsensusHash();
 
-  Hashtable[] getRnaStructureConsensusHash();
+  Hashtable<String, Object>[] getRnaStructureConsensusHash();
 
   boolean isIgnoreGapsConsensus();
 
@@ -177,7 +180,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @param hconsensus
    */
-  void setComplementConsensusHash(Hashtable[] hconsensus);
+  void setComplementConsensusHash(Hashtable<String, Object>[] hconsensus);
 
   /**
    * 
@@ -191,7 +194,8 @@ 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
@@ -243,16 +247,6 @@ 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
    * 
@@ -441,9 +435,19 @@ 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.
    * 
@@ -486,6 +490,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
+  @Override
   boolean isProteinFontAsCdna();
 
   /**
@@ -493,5 +498,61 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
+  @Override
   void setProteinFontAsCdna(boolean b);
+
+  TreeModel getCurrentTree();
+
+  void setCurrentTree(TreeModel tree);
+
+  /**
+   * Answers a data bean containing data for export as configured by the
+   * supplied options
+   * 
+   * @param options
+   * @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);
+
+  IdColumns getIdColumns();
 }