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Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID
[jalview.git]
/
src
/
jalview
/
api
/
AlignViewportI.java
diff --git
a/src/jalview/api/AlignViewportI.java
b/src/jalview/api/AlignViewportI.java
index
b09538e
..
ba3ed75
100644
(file)
--- a/
src/jalview/api/AlignViewportI.java
+++ b/
src/jalview/api/AlignViewportI.java
@@
-20,6
+20,13
@@
*/
package jalview.api;
*/
package jalview.api;
+import java.awt.Color;
+import java.awt.Font;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
import jalview.analysis.Conservation;
import jalview.analysis.TreeModel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.analysis.Conservation;
import jalview.analysis.TreeModel;
import jalview.datamodel.AlignmentAnnotation;
@@
-28,6
+35,7
@@
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;
@@
-36,13
+44,7
@@
import jalview.datamodel.SequenceI;
import jalview.renderer.ResidueShaderI;
import jalview.schemes.ColourSchemeI;
import jalview.viewmodel.ViewportRanges;
import jalview.renderer.ResidueShaderI;
import jalview.schemes.ColourSchemeI;
import jalview.viewmodel.ViewportRanges;
-
-import java.awt.Color;
-import java.awt.Font;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
+import jalview.viewmodel.seqfeatures.IdColumns;
/**
* @author jimp
/**
* @author jimp
@@
-476,6
+478,15
@@
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
+566,8
@@
public interface AlignViewportI extends ViewStyleI
* @return
*/
Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
* @return
*/
Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
+
+ IdColumns getIdColumns();
+
+ ContactMatrixI getContactMatrix(AlignmentAnnotation alignmentAnnotation);
}
}