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.datamodel.SequenceI;
import jalview.renderer.ResidueShaderI;
import jalview.schemes.ColourSchemeI;
-import jalview.viewmodel.ViewportPositionProps;
+import jalview.viewmodel.ViewportRanges;
import java.awt.Color;
+import java.awt.Font;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
public interface AlignViewportI extends ViewStyleI
{
- ViewportPositionProps getPosProps();
-
- int getEndRes();
-
- int getStartRes();
+ /**
+ * Get the ranges object containing details of the start and end sequences and
+ * residues
+ *
+ * @return
+ */
+ ViewportRanges getRanges();
/**
* calculate the height for visible annotation, revalidating bounds where
*
* @return total height of annotation
*/
- public int calcPanelHeight();
+ int calcPanelHeight();
/**
* Answers true if the viewport has at least one column selected
boolean isNormaliseSequenceLogo();
+ boolean isShowInformationHistogram();
+
+ boolean isShowHMMSequenceLogo();
+
+ boolean isNormaliseHMMSequenceLogo();
+
ColourSchemeI getGlobalColourScheme();
/**
ColumnSelection getColumnSelection();
- ProfilesI getSequenceConsensusHash();
+ ProfilesI getConsensusProfiles();
/**
* Get consensus data table for the cDNA complement of this alignment (if any)
boolean isIgnoreGapsConsensus();
+ boolean isIgnoreBelowBackground();
+
boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
AlignmentAnnotation getAlignmentQualityAnnot();
AlignmentAnnotation getAlignmentConsensusAnnotation();
/**
+ * get the container for alignment gap annotation
+ *
+ * @return
+ */
+ AlignmentAnnotation getOccupancyAnnotation();
+
+ /**
* get the container for cDNA complement consensus annotation
*
* @return
*
* @param hconsensus
*/
- void setSequenceConsensusHash(ProfilesI hconsensus);
+ void setConsensusProfiles(ProfilesI hconsensus);
/**
* Set the cDNA complement consensus for the viewport
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
*
*
* @return a copy of this view's current display settings
*/
- public ViewStyleI getViewStyle();
+ ViewStyleI getViewStyle();
/**
* update the view's display settings with the given style set
*
* @param settingsForView
*/
- public void setViewStyle(ViewStyleI settingsForView);
+ void setViewStyle(ViewStyleI settingsForView);
/**
* Returns a viewport which holds the cDna for this (protein), or vice versa,
*/
void setFollowHighlight(boolean b);
- public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
+ void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
/**
* check if current selection group is defined on the view, or is simply a
*/
SearchResultsI getSearchResults();
- int getStartSeq();
+ /**
+ * 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);
- int getEndSeq();
+ /**
+ * 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);
+
+ void setHmmProfiles(ProfilesI info);
+
+ ProfilesI getHmmProfiles();
+
+ /**
+ * Registers and starts a worker thread to calculate Information Content
+ * annotation, if it is not already registered
+ *
+ * @param ap
+ */
+ void initInformationWorker(AlignmentViewPanel ap);
+
+ boolean isInfoLetterHeight();
+
+ abstract TreeModel getCurrentTree();
+
+ 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);
}