X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=e7afee0b9bd8ea2f9323171549e0d296d9c96f46;hb=c8d80485038ab96fb06bd0885c323803646d8e57;hp=2bed6053e6c2090dfbfdb17e2d7c628545dcf8bf;hpb=d7361eaa08dc9af7d996851f39b7a2007d1b8832;p=jalview.git diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java index 2bed605..e7afee0 100644 --- a/src/jalview/api/AlignViewportI.java +++ b/src/jalview/api/AlignViewportI.java @@ -20,22 +20,30 @@ */ package jalview.api; +import java.awt.Color; +import java.awt.Font; +import java.util.Hashtable; +import java.util.Iterator; +import java.util.List; +import java.util.Map; + import jalview.analysis.Conservation; +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.ContactListI; +import jalview.datamodel.ContactMatrixI; +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 java.awt.Color; -import java.util.Hashtable; -import java.util.List; -import java.util.Map; +import jalview.viewmodel.ViewportRanges; /** * @author jimp @@ -44,7 +52,13 @@ 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 + */ + public ViewportRanges getRanges(); /** * calculate the height for visible annotation, revalidating bounds where @@ -78,20 +92,28 @@ public interface AlignViewportI extends ViewStyleI 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) * * @return */ - Hashtable[] getComplementConsensusHash(); + Hashtable[] getComplementConsensusHash(); - Hashtable[] getRnaStructureConsensusHash(); + Hashtable[] getRnaStructureConsensusHash(); boolean isIgnoreGapsConsensus(); @@ -109,6 +131,13 @@ 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 @@ -145,18 +174,18 @@ public interface AlignViewportI extends ViewStyleI * * @param hconsensus */ - void setSequenceConsensusHash(Hashtable[] 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 +195,17 @@ 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 +248,6 @@ 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 * @@ -414,9 +436,19 @@ 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. * @@ -444,4 +476,105 @@ public interface AlignViewportI extends ViewStyleI * @return search results or null */ SearchResultsI getSearchResults(); + + /** + * Retrieve a ContactListI corresponding to column in an annotation row in an + * alignment. + * + * @param _aa + * - annotation with associated matrix data + * @param column + * - column in alignment where _aa is associated + */ + ContactListI getContactList(AlignmentAnnotation _aa, int column); + + /** + * 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); + + TreeModel getCurrentTree(); + + void setCurrentTree(TreeModel tree); + + /** + * Answers a data bean containing data for export as configured by the + * supplied options + * + * @param options + * @return + */ + AlignmentExportData getAlignExportData(AlignExportSettingsI options); + + /** + * @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 getViewAsVisibleContigs(boolean selectedRegionOnly); + /** + * notify all concerned that the alignment data has changed and derived data + * needs to be recalculated + */ + public void notifyAlignmentChanged(); + + /** + * retrieve a matrix associated with the view's alignment's annotation + * @param alignmentAnnotation + * @return contact matrix or NULL + */ + ContactMatrixI getContactMatrix(AlignmentAnnotation alignmentAnnotation); }