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.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.awt.Font;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
public interface AlignViewportI extends ViewStyleI
{
- 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();
+ /**
+ * Returns an object that describes colouring (including any thresholding or
+ * fading) of the alignment
+ *
+ * @return
+ */
+ ResidueShaderI getResidueShading();
+
AlignmentI getAlignment();
ColumnSelection getColumnSelection();
boolean isIgnoreGapsConsensus();
+ boolean isIgnoreBelowBackground();
+
boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
AlignmentAnnotation getAlignmentQualityAnnot();
AlignmentAnnotation getAlignmentConsensusAnnotation();
/**
+ * get the container for alignment gap annotation
+ *
+ * @return
+ */
+ AlignmentAnnotation getAlignmentGapAnnotation();
+
+ /**
* get the container for cDNA complement consensus annotation
*
* @return
/**
*
- * @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();
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
*
*/
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);
+
+ /**
+ * 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();
- int getEndSeq();
+ 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);
}