X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;fp=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=2802684c1140bc0a26f6775e9cfd23218d65ea9a;hb=e6e92a1314a7b7557401b829846ac55dcffbfbe2;hp=72542b3ab1dec36afd2abecefea03c43863e37f8;hpb=e77ec70cef4efba54974739e86673925396f0e92;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 72542b3..2802684 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -31,6 +31,7 @@ import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.renderer.ResidueShaderI;
 import jalview.schemes.ColourSchemeI;
 
 import java.awt.Color;
@@ -79,6 +80,14 @@ public interface AlignViewportI extends ViewStyleI
 
   ColourSchemeI getGlobalColourScheme();
 
+  /**
+   * Returns an object that describes colouring (including any thresholding or
+   * fading) of the alignment
+   * 
+   * @return
+   */
+  ResidueShaderI getResidueShading();
+
   AlignmentI getAlignment();
 
   ColumnSelection getColumnSelection();
@@ -157,7 +166,7 @@ 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();
@@ -170,11 +179,13 @@ 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();