import jalview.analysis.Conservation;
import jalview.analysis.TreeModel;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentExportData;
import jalview.datamodel.AlignmentI;
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 java.awt.Color;
import java.awt.Font;
import java.util.Hashtable;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
*
* @return
*/
- Hashtable[] getComplementConsensusHash();
+ Hashtable<String, Object>[] getComplementConsensusHash();
- Hashtable[] getRnaStructureConsensusHash();
+ Hashtable<String, Object>[] getRnaStructureConsensusHash();
boolean isIgnoreGapsConsensus();
*
* @param hconsensus
*/
- void setComplementConsensusHash(Hashtable[] hconsensus);
+ void setComplementConsensusHash(Hashtable<String, Object>[] hconsensus);
/**
*
*
* @param hStrucConsensus
*/
- void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus);
+ void setRnaStructureConsensusHash(
+ Hashtable<String, Object>[] hStrucConsensus);
/**
* Sets the colour scheme for the background alignment (as distinct from
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);
+
+ /**
* Updates view settings with the given font. You may need to call
* AlignmentPanel.fontChanged to update the layout geometry.
*
@Override
void setProteinFontAsCdna(boolean b);
- public abstract TreeModel getCurrentTree();
+ TreeModel getCurrentTree();
- public abstract void setCurrentTree(TreeModel tree);
+ void setCurrentTree(TreeModel tree);
+
+ /**
+ * Answers a data bean containing data for export as configured by the
+ * supplied options
+ *
+ * @param options
+ * @return
+ */
+ AlignmentExportData getAlignExportData(AlignExportSettingsI options);
/**
* @param update
* - a group defined on sequences in the alignment held by the view
*/
void addSequenceGroup(SequenceGroup sequenceGroup);
+
+ /**
+ * Returns an interator over the [start, end] column positions of the visible
+ * regions of the alignment
+ *
+ * @param selectedRegionOnly
+ * if true, and the view has a selection region, then only the
+ * intersection of visible columns with the selection region is
+ * returned
+ * @return
+ */
+ Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
+
+ ContactMatrixI getContactMatrix(AlignmentAnnotation alignmentAnnotation);
}