import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.renderer.ResidueShaderI;
import jalview.schemes.ColourSchemeI;
import java.awt.Color;
ColourSchemeI getGlobalColourScheme();
+ /**
+ * Returns an object that describes colouring (including any thresholding or
+ * fading) of the alignment
+ *
+ * @return
+ */
+ ResidueShaderI getResidueShading();
+
AlignmentI getAlignment();
ColumnSelection getColumnSelection();
/**
*
- * @return the alignment annotatino row for the structure consensus
+ * @return the alignment annotation row for the structure consensus
* calculation
*/
AlignmentAnnotation getAlignmentStrucConsensusAnnotation();
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();