JAL-2599 fix for information annotation buttons

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

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 8b07340..4b6dc4e 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -36,6 +36,7 @@ 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;
@@ -85,6 +86,12 @@ public interface AlignViewportI extends ViewStyleI
 
   boolean isNormaliseSequenceLogo();
 
+  boolean isShowInformationHistogram();
+
+  boolean isShowHMMSequenceLogo();
+
+  boolean isNormaliseHMMSequenceLogo();
+
   ColourSchemeI getGlobalColourScheme();
 
   /**
@@ -101,6 +108,8 @@ public interface AlignViewportI extends ViewStyleI
 
   ProfilesI getSequenceConsensusHash();
 
+  ProfilesI getSequenceInformationHash();
+
   /**
    * Get consensus data table for the cDNA complement of this alignment (if any)
    * 
@@ -112,6 +121,8 @@ public interface AlignViewportI extends ViewStyleI
 
   boolean isIgnoreGapsConsensus();
 
+  boolean isIgnoreBelowBackground();
+
   boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
 
   AlignmentAnnotation getAlignmentQualityAnnot();
@@ -126,6 +137,13 @@ public interface AlignViewportI extends ViewStyleI
   AlignmentAnnotation getAlignmentConsensusAnnotation();
 
   /**
+   * get the container for alignment information content annotation
+   * 
+   * @return
+   */
+  AlignmentAnnotation getAlignmentInformationAnnotation();
+
+  /**
    * get the container for alignment gap annotation
    * 
    * @return
@@ -172,6 +190,13 @@ public interface AlignViewportI extends ViewStyleI
   void setSequenceConsensusHash(ProfilesI hconsensus);
 
   /**
+   * set the information result object for the viewport
+   * 
+   * @param hconsensus
+   */
+  void setSequenceInformationHash(ProfilesI hinformation);
+
+  /**
    * Set the cDNA complement consensus for the viewport
    * 
    * @param hconsensus
@@ -470,4 +495,31 @@ public interface AlignViewportI extends ViewStyleI
    * @return search results or null
    */
   SearchResultsI getSearchResults();
+
+  /**
+   * Updates view settings with the given font. You may need to call
+   * AlignmentPanel.fontChanged to update the layout geometry.
+   * 
+   * @param setGrid
+   *          when true, charWidth/height is set according to font metrics
+   */
+  void setFont(Font newFont, boolean b);
+
+  /**
+   * Answers true if split screen protein and cDNA use the same font
+   * 
+   * @return
+   */
+  @Override
+  boolean isProteinFontAsCdna();
+
+  /**
+   * Set the flag for whether split screen protein and cDNA use the same font
+   * 
+   * @return
+   */
+  @Override
+  void setProteinFontAsCdna(boolean b);
+
+  ProfilesI setSequenceInformationHash();
 }