X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=a35c2a4996e865119171eb77eae765952677f36a;hb=87b304d55f0dd005dd1d04cf162103bff4435a83;hp=fa73194239fbbf77709f2dd234288a43bb9cdc27;hpb=2e2e6d269fbaa505151fe777374f41111f2910d5;p=jalview.git diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java index fa73194..a35c2a4 100644 --- a/src/jalview/api/AlignViewportI.java +++ b/src/jalview/api/AlignViewportI.java @@ -20,21 +20,26 @@ */ package jalview.api; -import java.awt.Color; -import java.util.Hashtable; -import java.util.List; -import java.util.Map; - import jalview.analysis.Conservation; 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; /** * @author jimp @@ -43,7 +48,13 @@ import jalview.schemes.ColourSchemeI; public interface AlignViewportI extends ViewStyleI { - int getEndRes(); + /** + * Get the ranges object containing details of the start and end sequences and + * residues + * + * @return + */ + public ViewportRanges getRanges(); /** * calculate the height for visible annotation, revalidating bounds where @@ -53,6 +64,18 @@ public interface AlignViewportI extends ViewStyleI */ public int calcPanelHeight(); + /** + * Answers true if the viewport has at least one column selected + * + * @return + */ + boolean hasSelectedColumns(); + + /** + * Answers true if the viewport has at least one hidden column + * + * @return + */ boolean hasHiddenColumns(); boolean isValidCharWidth(); @@ -63,13 +86,27 @@ 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(); - Hashtable[] getSequenceConsensusHash(); + ProfilesI getSequenceConsensusHash(); /** * Get consensus data table for the cDNA complement of this alignment (if any) @@ -82,6 +119,8 @@ public interface AlignViewportI extends ViewStyleI boolean isIgnoreGapsConsensus(); + boolean isIgnoreBelowBackground(); + boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation); AlignmentAnnotation getAlignmentQualityAnnot(); @@ -96,6 +135,13 @@ 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 @@ -110,6 +156,11 @@ public interface AlignViewportI extends ViewStyleI boolean isClosed(); /** + * Dispose of all references or resources held by the viewport + */ + void dispose(); + + /** * get the associated calculation thread manager for the view * * @return @@ -127,7 +178,7 @@ public interface AlignViewportI extends ViewStyleI * * @param hconsensus */ - void setSequenceConsensusHash(Hashtable[] hconsensus); + void setSequenceConsensusHash(ProfilesI hconsensus); /** * Set the cDNA complement consensus for the viewport @@ -138,7 +189,7 @@ public interface AlignViewportI extends ViewStyleI /** * - * @return the alignment annotatino row for the structure consensus + * @return the alignment annotation row for the structure consensus * calculation */ AlignmentAnnotation getAlignmentStrucConsensusAnnotation(); @@ -151,11 +202,13 @@ public interface AlignViewportI extends ViewStyleI 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(); @@ -178,7 +231,7 @@ public interface AlignViewportI extends ViewStyleI */ void updateGroupAnnotationSettings(boolean applyGlobalSettings, boolean preserveNewGroupSettings); - + void setSequenceColour(SequenceI seq, Color col); Color getSequenceColour(SequenceI seq); @@ -235,11 +288,31 @@ public interface AlignViewportI extends ViewStyleI * 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. This method doesn't exclude hidden sequences from the output. + * + * @param selectedRegionOnly + * - determines if only the selected region or entire alignment is + * exported + * @return String[] + */ + String[] getViewAsString(boolean selectedRegionOnly); + + /** + * 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. * + * @param selectedRegionOnly + * - determines if only the selected region or entire alignment is + * exported + * @param isExportHiddenSeqs + * - determines if hidden sequences would be exported or not. + * * @return String[] */ - String[] getViewAsString(boolean selectedRegionOnly); + String[] getViewAsString(boolean selectedRegionOnly, + boolean isExportHiddenSeqs); void setSelectionGroup(SequenceGroup sg); @@ -251,8 +324,11 @@ public interface AlignViewportI extends ViewStyleI /** * get a copy of the currently visible alignment annotation - * @param selectedOnly if true - trim to selected regions on the alignment - * @return an empty list or new alignment annotation objects shown only visible columns trimmed to selected region only + * + * @param selectedOnly + * if true - trim to selected regions on the alignment + * @return an empty list or new alignment annotation objects shown only + * visible columns trimmed to selected region only */ List getVisibleAlignmentAnnotation( boolean selectedOnly); @@ -373,25 +449,84 @@ public interface AlignViewportI extends ViewStyleI */ void setFollowHighlight(boolean b); + public void applyFeaturesStyle(FeatureSettingsModelI featureSettings); + /** - * Returns a FeatureRenderer instance + * check if current selection group is defined on the view, or is simply a + * temporary group. * - * @return + * @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 */ - public FeatureRenderer getFeatureRenderer(); + SearchResultsI getSearchResults(); /** - * Sets a FeatureRenderer for a viewport + * Updates view settings with the given font. You may need to call + * AlignmentPanel.fontChanged to update the layout geometry. * - * @param featureRenderer + * @param setGrid + * when true, charWidth/height is set according to font metrics */ - public void setFeatureRenderer(FeatureRenderer featureRenderer); + void setFont(Font newFont, boolean b); /** - * Returns Settings for exporting an Alignment + * Answers true if split screen protein and cDNA use the same font * * @return */ - public AlignExportSettingI getExportSettings(); + @Override + boolean isProteinFontAsCdna(); + + /** + * Set the flag for whether split screen protein and cDNA use the same font + * + * @return + */ + @Override + void setProteinFontAsCdna(boolean b); + + void setSequenceInformationHashes(List info); + + List getSequenceInformationHashes(); + + ProfilesI getSequenceInformationHash(int index); + + List getInformationAnnotations(); + + AlignmentAnnotation getInformationAnnotation(int index); + + void setSequenceInformationHash(ProfilesI info, int index); + + /** + * Initiates the information annotation for all uninitiated sequences. + */ + void initInformation(); + + /** + * Updates all information annotations. + * + * @param ap + */ + void updateInformation(AlignmentViewPanel ap); }