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JAL-244 Fix mismatched vertical positioning of sequences and their labels in wrap...
[jalview.git]
/
src
/
jalview
/
api
/
AlignViewportI.java
diff --git
a/src/jalview/api/AlignViewportI.java
b/src/jalview/api/AlignViewportI.java
index
b09538e
..
0cfd03d
100644
(file)
--- a/
src/jalview/api/AlignViewportI.java
+++ b/
src/jalview/api/AlignViewportI.java
@@
-28,6
+28,7
@@
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.ContactListI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.ProfilesI;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.ProfilesI;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceCollectionI;
@@
-476,6
+477,15
@@
public interface AlignViewportI extends ViewStyleI
*/
SearchResultsI getSearchResults();
*/
SearchResultsI getSearchResults();
+ /**
+ * Retrieve a ContactListI corresponding to column in an annotation row in an
+ * alignment.
+ *
+ * @param _aa
+ * - annotation with associated matrix data
+ * @param column
+ * - column in alignment where _aa is associated
+ */
ContactListI getContactList(AlignmentAnnotation _aa, int column);
/**
ContactListI getContactList(AlignmentAnnotation _aa, int column);
/**
@@
-555,4
+565,6
@@
public interface AlignViewportI extends ViewStyleI
* @return
*/
Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
* @return
*/
Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
+
+ ContactMatrixI getContactMatrix(AlignmentAnnotation alignmentAnnotation);
}
}