X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=b976a3d94d1f51c9f9488d171821ebe217913ff4;hb=2d8dfad8a0aa6a6febfc0c3bc0379de0b46e0cfc;hp=9fcf89aa5fece5050b94b3741e7755b623353564;hpb=b2b7e99113e1f0962140fc72d989cc826799a2d4;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 9fcf89a..b976a3d 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -21,10 +21,11 @@
 package jalview.api;
 
 import jalview.analysis.Conservation;
+import jalview.analysis.TreeModel;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentExportData;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
-import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SearchResultsI;
@@ -33,8 +34,10 @@ 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;
@@ -46,7 +49,13 @@ import java.util.Map;
 public interface AlignViewportI extends ViewStyleI
 {
 
-  int getEndRes();
+  /**
+   * 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
@@ -80,7 +89,13 @@ public interface AlignViewportI extends ViewStyleI
 
   ColourSchemeI getGlobalColourScheme();
 
-  ResidueShaderI getViewportColourScheme();
+  /**
+   * Returns an object that describes colouring (including any thresholding or
+   * fading) of the alignment
+   * 
+   * @return
+   */
+  ResidueShaderI getResidueShading();
 
   AlignmentI getAlignment();
 
@@ -113,6 +128,13 @@ 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
@@ -160,7 +182,7 @@ public interface AlignViewportI extends ViewStyleI
 
   /**
    * 
-   * @return the alignment annotatino row for the structure consensus
+   * @return the alignment annotation row for the structure consensus
    *         calculation
    */
   AlignmentAnnotation getAlignmentStrucConsensusAnnotation();
@@ -173,11 +195,13 @@ public interface AlignViewportI extends ViewStyleI
   void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
 
   /**
-   * set global colourscheme
+   * Sets the colour scheme for the background alignment (as distinct from
+   * sub-groups, which may have their own colour schemes). A null value is used
+   * for no residue colour (white).
    * 
-   * @param rhc
+   * @param cs
    */
-  void setGlobalColourScheme(ColourSchemeI rhc);
+  void setGlobalColourScheme(ColourSchemeI cs);
 
   Map<SequenceI, SequenceCollectionI> getHiddenRepSequences();
 
@@ -220,16 +244,6 @@ public interface AlignViewportI extends ViewStyleI
   void clearSequenceColours();
 
   /**
-   * This method returns the visible alignment as text, as seen on the GUI, ie
-   * if columns are hidden they will not be returned in the result. Use this for
-   * calculating trees, PCA, redundancy etc on views which contain hidden
-   * columns.
-   * 
-   * @return String[]
-   */
-  CigarArray getViewAsCigars(boolean selectedRegionOnly);
-
-  /**
    * return a compact representation of the current alignment selection to pass
    * to an analysis function
    * 
@@ -448,4 +462,42 @@ 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);
+
+  TreeModel getCurrentTree();
+
+  void setCurrentTree(TreeModel tree);
+
+  /**
+   * Answers a data bean containing data for export as configured by the
+   * supplied options
+   * 
+   * @param options
+   * @return
+   */
+  AlignmentExportData getAlignExportData(AlignExportSettingsI options);
 }