X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=20a9d026139b45b48258a58ce3f96fa5ad488c72;hb=65074fc4efb2d445593e16c157e25fafb4191fde;hp=dcd325850bf2b212561e6f056239bd84b36ecc40;hpb=042832306c7e7aa0484079f3bab1e141b2944de5;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index dcd3258..20a9d02 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -39,6 +39,7 @@ 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;
 
@@ -55,7 +56,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
-  public ViewportRanges getRanges();
+  ViewportRanges getRanges();
 
   /**
    * calculate the height for visible annotation, revalidating bounds where
@@ -63,7 +64,7 @@ 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
@@ -87,6 +88,12 @@ public interface AlignViewportI extends ViewStyleI
 
   boolean isNormaliseSequenceLogo();
 
+  boolean isShowInformationHistogram();
+
+  boolean isShowHMMSequenceLogo();
+
+  boolean isNormaliseHMMSequenceLogo();
+
   ColourSchemeI getGlobalColourScheme();
 
   /**
@@ -114,6 +121,8 @@ public interface AlignViewportI extends ViewStyleI
 
   boolean isIgnoreGapsConsensus();
 
+  boolean isIgnoreBelowBackground();
+
   boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
 
   AlignmentAnnotation getAlignmentQualityAnnot();
@@ -158,7 +167,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
-  AlignCalcManagerI getCalcManager();
+  AlignCalcManagerI2 getCalcManager();
 
   /**
    * get the percentage gaps allowed in a conservation calculation
@@ -433,9 +442,19 @@ 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.
    * 
@@ -489,9 +508,21 @@ public interface AlignViewportI extends ViewStyleI
   @Override
   void setProteinFontAsCdna(boolean b);
 
-  TreeModel getCurrentTree();
+  void setHmmProfiles(ProfilesI info);
 
-  void setCurrentTree(TreeModel tree);
+  ProfilesI getHmmProfiles();
+
+  /**
+   * 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();
+
+  public abstract TreeModel getCurrentTree();
 
   /**
    * Answers a data bean containing data for export as configured by the
@@ -502,6 +533,8 @@ public interface AlignViewportI extends ViewStyleI
    */
   AlignmentExportData getAlignExportData(AlignExportSettingsI options);
 
+  public abstract void setCurrentTree(TreeModel tree);
+
   /**
    * @param update
    *          - set the flag for updating structures on next repaint
@@ -529,4 +562,16 @@ public interface AlignViewportI extends ViewStyleI
    *          - 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);
 }