X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=2f992a6f499fac16a4edc0d3f55fa943f967085f;hb=6a6fb5010c2cd06b14a1e055eabaeb4848e65d2d;hp=70463e7e8a5b3338bd1676f471189b541266b700;hpb=b7c6fbe6d47b510f7ac845eb5c29e971ffb41cfb;p=jalview.git diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java index 70463e7..2f992a6 100644 --- a/src/jalview/api/AlignViewportI.java +++ b/src/jalview/api/AlignViewportI.java @@ -21,18 +21,23 @@ package jalview.api; import jalview.analysis.Conservation; -import jalview.analysis.Profile; +import jalview.analysis.TreeModel; import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentExportData; 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; @@ -44,7 +49,13 @@ import java.util.Map; public interface AlignViewportI extends ViewStyleI { - int getEndRes(); + /** + * 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 @@ -52,7 +63,7 @@ public interface AlignViewportI extends ViewStyleI * * @return total height of annotation */ - public int calcPanelHeight(); + int calcPanelHeight(); /** * Answers true if the viewport has at least one column selected @@ -76,25 +87,41 @@ public interface AlignViewportI extends ViewStyleI 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(); - Profile[] getSequenceConsensusHash(); + ProfilesI getSequenceConsensusHash(); /** * Get consensus data table for the cDNA complement of this alignment (if any) * * @return */ - Hashtable[] getComplementConsensusHash(); + Hashtable[] getComplementConsensusHash(); - Hashtable[] getRnaStructureConsensusHash(); + Hashtable[] getRnaStructureConsensusHash(); boolean isIgnoreGapsConsensus(); + boolean isIgnoreBelowBackground(); + boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation); AlignmentAnnotation getAlignmentQualityAnnot(); @@ -109,6 +136,13 @@ public interface AlignViewportI extends ViewStyleI AlignmentAnnotation getAlignmentConsensusAnnotation(); /** + * get the container for alignment gap annotation + * + * @return + */ + AlignmentAnnotation getAlignmentGapAnnotation(); + + /** * get the container for cDNA complement consensus annotation * * @return @@ -132,7 +166,7 @@ public interface AlignViewportI extends ViewStyleI * * @return */ - AlignCalcManagerI getCalcManager(); + AlignCalcManagerI2 getCalcManager(); /** * get the percentage gaps allowed in a conservation calculation @@ -145,18 +179,18 @@ public interface AlignViewportI extends ViewStyleI * * @param hconsensus */ - void setSequenceConsensusHash(Profile[] hconsensus); + void setSequenceConsensusHash(ProfilesI hconsensus); /** * Set the cDNA complement consensus for the viewport * * @param hconsensus */ - void setComplementConsensusHash(Hashtable[] hconsensus); + void setComplementConsensusHash(Hashtable[] hconsensus); /** * - * @return the alignment annotatino row for the structure consensus + * @return the alignment annotation row for the structure consensus * calculation */ AlignmentAnnotation getAlignmentStrucConsensusAnnotation(); @@ -166,14 +200,17 @@ public interface AlignViewportI extends ViewStyleI * * @param hStrucConsensus */ - void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus); + 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 getHiddenRepSequences(); @@ -216,16 +253,6 @@ public interface AlignViewportI extends ViewStyleI 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 * @@ -414,13 +441,124 @@ public interface AlignViewportI extends ViewStyleI */ 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 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(); + + /** + * 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(); + + public abstract TreeModel getCurrentTree(); + + /** + * Answers a data bean containing data for export as configured by the + * supplied options + * + * @param options + * @return + */ + AlignmentExportData getAlignExportData(AlignExportSettingsI options); + + 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); }