X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=4b6dc4e4c3beedaf19b8eef0fb47e0f71ae11d1e;hb=c4160cf5c69643d0af950db63214b2067a04b061;hp=7a0023195a41b77917571cc891696fcf029a9591;hpb=e20cd4d53a73081a49b378f276aa17cd5d7948fb;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 7a00231..4b6dc4e 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -33,8 +33,10 @@ import jalview.datamodel.SequenceGroup;
 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;
@@ -46,9 +48,13 @@ import java.util.Map;
 public interface AlignViewportI extends ViewStyleI
 {
 
-  int getEndRes();
-
-  int getStartRes();
+  /**
+   * Get the ranges object containing details of the start and end sequences and
+   * residues
+   * 
+   * @return
+   */
+  public ViewportRanges getRanges();
 
   /**
    * calculate the height for visible annotation, revalidating bounds where
@@ -80,6 +86,12 @@ public interface AlignViewportI extends ViewStyleI
 
   boolean isNormaliseSequenceLogo();
 
+  boolean isShowInformationHistogram();
+
+  boolean isShowHMMSequenceLogo();
+
+  boolean isNormaliseHMMSequenceLogo();
+
   ColourSchemeI getGlobalColourScheme();
 
   /**
@@ -96,6 +108,8 @@ public interface AlignViewportI extends ViewStyleI
 
   ProfilesI getSequenceConsensusHash();
 
+  ProfilesI getSequenceInformationHash();
+
   /**
    * Get consensus data table for the cDNA complement of this alignment (if any)
    * 
@@ -107,6 +121,8 @@ public interface AlignViewportI extends ViewStyleI
 
   boolean isIgnoreGapsConsensus();
 
+  boolean isIgnoreBelowBackground();
+
   boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
 
   AlignmentAnnotation getAlignmentQualityAnnot();
@@ -121,6 +137,20 @@ 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
+   */
+  AlignmentAnnotation getAlignmentGapAnnotation();
+
+  /**
    * get the container for cDNA complement consensus annotation
    * 
    * @return
@@ -160,6 +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
@@ -459,7 +496,30 @@ public interface AlignViewportI extends ViewStyleI
    */
   SearchResultsI getSearchResults();
 
-  int getStartSeq();
+  /**
+   * 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);
 
-  int getEndSeq();
+  ProfilesI setSequenceInformationHash();
 }