Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

[jalview.git] / src / jalview / api / AlignViewportI.java

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 93a5101..295a9c4 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -56,7 +56,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
-  public ViewportRanges getRanges();
+  ViewportRanges getRanges();
 
   /**
    * calculate the height for visible annotation, revalidating bounds where
@@ -64,7 +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
@@ -88,6 +88,12 @@ public interface AlignViewportI extends ViewStyleI
 
   boolean isNormaliseSequenceLogo();
 
+  boolean isShowInformationHistogram();
+
+  boolean isShowHMMSequenceLogo();
+
+  boolean isNormaliseHMMSequenceLogo();
+
   ColourSchemeI getGlobalColourScheme();
 
   /**
@@ -115,6 +121,8 @@ public interface AlignViewportI extends ViewStyleI
 
   boolean isIgnoreGapsConsensus();
 
+  boolean isIgnoreBelowBackground();
+
   boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
 
   AlignmentAnnotation getAlignmentQualityAnnot();
@@ -159,7 +167,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
-  AlignCalcManagerI getCalcManager();
+  AlignCalcManagerI2 getCalcManager();
 
   /**
    * get the percentage gaps allowed in a conservation calculation
@@ -500,9 +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
@@ -513,6 +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