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JAL-2385 more tests/bug fixes mostly for gui.SliderPanel and some
[jalview.git]
/
src
/
jalview
/
api
/
AlignViewportI.java
diff --git
a/src/jalview/api/AlignViewportI.java
b/src/jalview/api/AlignViewportI.java
index
ee03852
..
33a0061
100644
(file)
--- a/
src/jalview/api/AlignViewportI.java
+++ b/
src/jalview/api/AlignViewportI.java
@@
-31,7
+31,7
@@
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.schemes.CollectionColourSchemeI;
+import jalview.renderer.ResidueShaderI;
import jalview.schemes.ColourSchemeI;
import java.awt.Color;
import jalview.schemes.ColourSchemeI;
import java.awt.Color;
@@
-80,7
+80,13
@@
public interface AlignViewportI extends ViewStyleI
ColourSchemeI getGlobalColourScheme();
ColourSchemeI getGlobalColourScheme();
- CollectionColourSchemeI getViewportColourScheme();
+ /**
+ * Returns an object that describes colouring (including any thresholding or
+ * fading) of the alignment
+ *
+ * @return
+ */
+ ResidueShaderI getViewportColourScheme();
AlignmentI getAlignment();
AlignmentI getAlignment();
@@
-160,7
+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();
* calculation
*/
AlignmentAnnotation getAlignmentStrucConsensusAnnotation();
@@
-173,11
+179,13
@@
public interface AlignViewportI extends ViewStyleI
void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
/**
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();
Map<SequenceI, SequenceCollectionI> getHiddenRepSequences();