package jalview.api;
import jalview.analysis.Conservation;
+import jalview.analysis.TreeModel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
-import jalview.datamodel.CigarArray;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.ProfilesI;
import jalview.datamodel.SearchResultsI;
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;
AlignmentAnnotation getAlignmentConsensusAnnotation();
/**
+ * get the container for alignment gap annotation
+ *
+ * @return
+ */
+ AlignmentAnnotation getAlignmentGapAnnotation();
+
+ /**
* get the container for cDNA complement consensus annotation
*
* @return
void clearSequenceColours();
/**
- * This method returns the visible alignment as text, as seen on the GUI, ie
- * if columns are hidden they will not be returned in the result. Use this for
- * calculating trees, PCA, redundancy etc on views which contain hidden
- * columns.
- *
- * @return String[]
- */
- CigarArray getViewAsCigars(boolean selectedRegionOnly);
-
- /**
* return a compact representation of the current alignment selection to pass
* to an analysis function
*
AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups);
/**
+ * @return an alignment view, optionally without a complement view
+ * @param selectedOnly
+ * @param markGroups
+ * @param withComplement - false if no complement view required
+ */
+ AlignmentView getAlignmentViewWithComplement(boolean selectedOnly,
+ boolean markGroups, boolean withComplement);
+
+ /**
* This method returns the visible alignment as text, as seen on the GUI, ie
* if columns are hidden they will not be returned in the result. Use this for
* calculating trees, PCA, redundancy etc on views which contain hidden
*/
void setFollowHighlight(boolean b);
+ /**
+ * configure the feature renderer with predefined feature settings
+ *
+ * @param featureSettings
+ */
public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
/**
+ * Apply the given feature settings on top of existing feature settings.
+ */
+ public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings);
+
+ /**
* check if current selection group is defined on the view, or is simply a
* temporary group.
*
* @return search results or null
*/
SearchResultsI getSearchResults();
+
+ /**
+ * Updates view settings with the given font. You may need to call
+ * AlignmentPanel.fontChanged to update the layout geometry.
+ *
+ * @param setGrid
+ * when true, charWidth/height is set according to font metrics
+ */
+ void setFont(Font newFont, boolean b);
+
+ /**
+ * Answers true if split screen protein and cDNA use the same font
+ *
+ * @return
+ */
+ @Override
+ boolean isProteinFontAsCdna();
+
+ /**
+ * Set the flag for whether split screen protein and cDNA use the same font
+ *
+ * @return
+ */
+ @Override
+ void setProteinFontAsCdna(boolean b);
+
+ public abstract TreeModel getCurrentTree();
+
+ public abstract void setCurrentTree(TreeModel tree);
+
+ /**
+ * @param update
+ * - set the flag for updating structures on next repaint
+ */
+ void setUpdateStructures(boolean update);
+
+ /**
+ *
+ * @return true if structure views will be updated on next refresh
+ */
+ boolean isUpdateStructures();
+
+ /**
+ * check if structure views need to be updated, and clear the flag afterwards.
+ *
+ * @return if an update is needed
+ */
+ boolean needToUpdateStructureViews();
+
+ /**
+ * Adds sequencegroup to the alignment in the view. Also adds a group to the
+ * complement view if one is defined.
+ *
+ * @param sequenceGroup
+ * - 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);
}