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JAL-1933 consensus calculation doesn’t depend on occupancy row being materialised
[jalview.git]
/
src
/
jalview
/
api
/
AlignViewportI.java
diff --git
a/src/jalview/api/AlignViewportI.java
b/src/jalview/api/AlignViewportI.java
index
7a00231
..
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;
@@
-46,9
+47,13
@@
import java.util.Map;
public interface AlignViewportI extends ViewStyleI
{
public interface AlignViewportI extends ViewStyleI
{
- int getEndRes();
-
- int getStartRes();
+ /**
+ * 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
@@
-121,6
+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
@@
-458,8
+470,4
@@
public interface AlignViewportI extends ViewStyleI
* @return search results or null
*/
SearchResultsI getSearchResults();
* @return search results or null
*/
SearchResultsI getSearchResults();
-
- int getStartSeq();
-
- int getEndSeq();
}
}