import jalview.datamodel.AlignmentView;
import jalview.datamodel.CigarArray;
import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.ProfileI;
+import jalview.datamodel.ProfilesI;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.renderer.ResidueShaderI;
import jalview.schemes.ColourSchemeI;
+import jalview.viewmodel.ViewportRanges;
import java.awt.Color;
import java.util.Hashtable;
public interface AlignViewportI extends ViewStyleI
{
+ ViewportRanges getRanges();
+
int getEndRes();
+ int getStartRes();
+
/**
* calculate the height for visible annotation, revalidating bounds where
* necessary ABSTRACT GUI METHOD
ColourSchemeI getGlobalColourScheme();
+ /**
+ * Returns an object that describes colouring (including any thresholding or
+ * fading) of the alignment
+ *
+ * @return
+ */
+ ResidueShaderI getResidueShading();
+
AlignmentI getAlignment();
ColumnSelection getColumnSelection();
- ProfileI[] getSequenceConsensusHash();
+ ProfilesI getSequenceConsensusHash();
/**
* Get consensus data table for the cDNA complement of this alignment (if any)
*
* @param hconsensus
*/
- void setSequenceConsensusHash(ProfileI[] hconsensus);
+ void setSequenceConsensusHash(ProfilesI hconsensus);
/**
* Set the cDNA complement consensus for the viewport
/**
*
- * @return the alignment annotatino row for the structure consensus
+ * @return the alignment annotation row for the structure consensus
* calculation
*/
AlignmentAnnotation getAlignmentStrucConsensusAnnotation();
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();
* @return true if group is defined on the alignment
*/
boolean isSelectionDefinedGroup();
+
+ /**
+ *
+ * @return true if there are search results on the view
+ */
+ boolean hasSearchResults();
+
+ /**
+ * set the search results for the view
+ *
+ * @param results
+ * - or null to clear current results
+ */
+ void setSearchResults(SearchResultsI results);
+
+ /**
+ * get search results for this view (if any)
+ *
+ * @return search results or null
+ */
+ SearchResultsI getSearchResults();
+
+ int getStartSeq();
+
+ int getEndSeq();
}