X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=a35c2a4996e865119171eb77eae765952677f36a;hb=87b304d55f0dd005dd1d04cf162103bff4435a83;hp=6cdc998cb380dc4b51d75fa6675f1d9f08fa5516;hpb=2baf7a0fe3faf4133a387359b8ce2ba475176eec;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 6cdc998..a35c2a4 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -33,9 +33,10 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.ResidueShaderI;
 import jalview.schemes.ColourSchemeI;
-import jalview.viewmodel.ViewportPositionProps;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.Color;
+import java.awt.Font;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
@@ -47,11 +48,13 @@ import java.util.Map;
 public interface AlignViewportI extends ViewStyleI
 {
 
-  ViewportPositionProps getPosProps();
-  
-  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
@@ -83,6 +86,12 @@ public interface AlignViewportI extends ViewStyleI
 
   boolean isNormaliseSequenceLogo();
 
+  boolean isShowInformationHistogram();
+
+  boolean isShowHMMSequenceLogo();
+
+  boolean isNormaliseHMMSequenceLogo();
+
   ColourSchemeI getGlobalColourScheme();
 
   /**
@@ -110,6 +119,8 @@ public interface AlignViewportI extends ViewStyleI
 
   boolean isIgnoreGapsConsensus();
 
+  boolean isIgnoreBelowBackground();
+
   boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
 
   AlignmentAnnotation getAlignmentQualityAnnot();
@@ -124,6 +135,13 @@ public interface AlignViewportI extends ViewStyleI
   AlignmentAnnotation getAlignmentConsensusAnnotation();
 
   /**
+   * get the container for alignment gap annotation
+   * 
+   * @return
+   */
+  AlignmentAnnotation getAlignmentGapAnnotation();
+
+  /**
    * get the container for cDNA complement consensus annotation
    * 
    * @return
@@ -462,7 +480,53 @@ 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);
+
+  void setSequenceInformationHashes(List<ProfilesI> info);
+
+  List<ProfilesI> getSequenceInformationHashes();
+
+  ProfilesI getSequenceInformationHash(int index);
+
+  List<AlignmentAnnotation> getInformationAnnotations();
+
+  AlignmentAnnotation getInformationAnnotation(int index);
+
+  void setSequenceInformationHash(ProfilesI info, int index);
+
+  /**
+   * Initiates the information annotation for all uninitiated sequences.
+   */
+  void initInformation();
+
+  /**
+   * Updates all information annotations.
+   * 
+   * @param ap
+   */
+  void updateInformation(AlignmentViewPanel ap);
 
-  int getEndSeq();
 }