X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=6ebde3cac9a89a7fa24a7da962d46751597b5f05;hb=refs%2Fheads%2Ffeatures%2Fhmmer_statistics;hp=9e6d1c05b955f2d895be047a313e755168f23121;hpb=96356075a122b745936738f478a8ee33ac7e0f0a;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 9e6d1c0..6ebde3c 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -86,6 +86,12 @@ public interface AlignViewportI extends ViewStyleI
 
   boolean isNormaliseSequenceLogo();
 
+  boolean isShowInformationHistogram();
+
+  boolean isShowHMMSequenceLogo();
+
+  boolean isNormaliseHMMSequenceLogo();
+
   ColourSchemeI getGlobalColourScheme();
 
   /**
@@ -113,6 +119,8 @@ public interface AlignViewportI extends ViewStyleI
 
   boolean isIgnoreGapsConsensus();
 
+  boolean isIgnoreBelowBackground();
+
   boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
 
   AlignmentAnnotation getAlignmentQualityAnnot();
@@ -127,6 +135,13 @@ 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
@@ -486,6 +501,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
+  @Override
   boolean isProteinFontAsCdna();
 
   /**
@@ -493,5 +509,6 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
+  @Override
   void setProteinFontAsCdna(boolean b);
 }