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Merge branch 'features/JAL-2388OverviewWindow' into develop
[jalview.git]
/
src
/
jalview
/
api
/
AlignViewportI.java
diff --git
a/src/jalview/api/AlignViewportI.java
b/src/jalview/api/AlignViewportI.java
index
9fcf89a
..
8b07340
100644
(file)
--- a/
src/jalview/api/AlignViewportI.java
+++ b/
src/jalview/api/AlignViewportI.java
@@
-33,6
+33,7
@@
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.renderer.ResidueShaderI;
import jalview.schemes.ColourSchemeI;
import jalview.datamodel.SequenceI;
import jalview.renderer.ResidueShaderI;
import jalview.schemes.ColourSchemeI;
+import jalview.viewmodel.ViewportRanges;
import java.awt.Color;
import java.util.Hashtable;
import java.awt.Color;
import java.util.Hashtable;
@@
-46,7
+47,13
@@
import java.util.Map;
public interface AlignViewportI extends ViewStyleI
{
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
/**
* calculate the height for visible annotation, revalidating bounds where
@@
-80,7
+87,13
@@
public interface AlignViewportI extends ViewStyleI
ColourSchemeI getGlobalColourScheme();
ColourSchemeI getGlobalColourScheme();
- ResidueShaderI getViewportColourScheme();
+ /**
+ * Returns an object that describes colouring (including any thresholding or
+ * fading) of the alignment
+ *
+ * @return
+ */
+ ResidueShaderI getResidueShading();
AlignmentI getAlignment();
AlignmentI getAlignment();
@@
-113,6
+126,13
@@
public interface AlignViewportI extends ViewStyleI
AlignmentAnnotation getAlignmentConsensusAnnotation();
/**
AlignmentAnnotation getAlignmentConsensusAnnotation();
/**
+ * get the container for alignment gap annotation
+ *
+ * @return
+ */
+ AlignmentAnnotation getAlignmentGapAnnotation();
+
+ /**
* get the container for cDNA complement consensus annotation
*
* @return
* get the container for cDNA complement consensus annotation
*
* @return
@@
-160,7
+180,7
@@
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
+193,13
@@
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();