2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentUtils;
24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
25 import jalview.api.AlignViewportI;
26 import jalview.api.AlignmentViewPanel;
27 import jalview.api.FeatureColourI;
28 import jalview.api.FeatureSettingsModelI;
29 import jalview.api.FeaturesDisplayedI;
30 import jalview.api.ViewStyleI;
31 import jalview.bin.Cache;
32 import jalview.commands.CommandI;
33 import jalview.datamodel.AlignedCodonFrame;
34 import jalview.datamodel.Alignment;
35 import jalview.datamodel.AlignmentI;
36 import jalview.datamodel.ColumnSelection;
37 import jalview.datamodel.HiddenColumns;
38 import jalview.datamodel.SearchResults;
39 import jalview.datamodel.SearchResultsI;
40 import jalview.datamodel.SequenceGroup;
41 import jalview.datamodel.SequenceI;
42 import jalview.renderer.ResidueShader;
43 import jalview.schemes.ColourSchemeI;
44 import jalview.schemes.ColourSchemeProperty;
45 import jalview.schemes.ResidueColourScheme;
46 import jalview.schemes.UserColourScheme;
47 import jalview.structure.SelectionSource;
48 import jalview.structure.StructureSelectionManager;
49 import jalview.structure.VamsasSource;
50 import jalview.util.ColorUtils;
51 import jalview.util.MessageManager;
52 import jalview.viewmodel.AlignmentViewport;
53 import jalview.ws.params.AutoCalcSetting;
55 import java.awt.Container;
56 import java.awt.Dimension;
58 import java.awt.FontMetrics;
59 import java.awt.Rectangle;
60 import java.util.ArrayList;
61 import java.util.Hashtable;
62 import java.util.Iterator;
63 import java.util.List;
65 import javax.swing.JInternalFrame;
71 * @version $Revision: 1.141 $
73 public class AlignViewport extends AlignmentViewport
74 implements SelectionSource
78 boolean cursorMode = false;
80 boolean antiAlias = false;
82 private Rectangle explodedGeometry;
84 private String viewName;
87 * Flag set true on the view that should 'gather' multiple views of the same
88 * sequence set id when a project is reloaded. Set false on all views when
89 * they are 'exploded' into separate windows. Set true on the current view
90 * when 'Gather' is performed, and also on the first tab when the first new
93 private boolean gatherViewsHere = false;
95 private AnnotationColumnChooser annotationColumnSelectionState;
98 * Creates a new AlignViewport object.
103 public AlignViewport(AlignmentI al)
110 * Create a new AlignViewport object with a specific sequence set ID
114 * (may be null - but potential for ambiguous constructor exception)
116 public AlignViewport(AlignmentI al, String seqsetid)
118 this(al, seqsetid, null);
121 public AlignViewport(AlignmentI al, String seqsetid, String viewid)
124 sequenceSetID = seqsetid;
126 // TODO remove these once 2.4.VAMSAS release finished
127 if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
130 "Setting viewport's sequence set id : " + sequenceSetID);
132 if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
134 Cache.log.debug("Setting viewport's view id : " + viewId);
141 * Create a new AlignViewport with hidden regions
145 * @param hiddenColumns
148 public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns)
151 if (hiddenColumns != null)
153 al.setHiddenColumns(hiddenColumns);
159 * New viewport with hidden columns and an existing sequence set id
162 * @param hiddenColumns
166 public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
169 this(al, hiddenColumns, seqsetid, null);
173 * New viewport with hidden columns and an existing sequence set id and viewid
176 * @param hiddenColumns
182 public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
183 String seqsetid, String viewid)
186 sequenceSetID = seqsetid;
188 // TODO remove these once 2.4.VAMSAS release finished
189 if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
192 "Setting viewport's sequence set id : " + sequenceSetID);
194 if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
196 Cache.log.debug("Setting viewport's view id : " + viewId);
199 if (hiddenColumns != null)
201 al.setHiddenColumns(hiddenColumns);
207 * Apply any settings saved in user preferences
209 private void applyViewProperties()
211 antiAlias = Cache.getDefault("ANTI_ALIAS", false);
213 viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
214 setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
216 setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
217 setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false));
218 autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
220 setPadGaps(Cache.getDefault("PAD_GAPS", true));
221 setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
222 setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
223 viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true));
224 viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false));
225 viewStyle.setShowUnconserved(
226 Cache.getDefault("SHOW_UNCONSERVED", false));
227 sortByTree = Cache.getDefault("SORT_BY_TREE", false);
228 followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
229 sortAnnotationsBy = SequenceAnnotationOrder
230 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
231 SequenceAnnotationOrder.NONE.name()));
232 showAutocalculatedAbove = Cache
233 .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
234 viewStyle.setScaleProteinAsCdna(
235 Cache.getDefault(Preferences.SCALE_PROTEIN_TO_CDNA, true));
240 applyViewProperties();
242 String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
243 String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
244 String fontSize = Cache.getDefault("FONT_SIZE", "10");
248 if (fontStyle.equals("bold"))
252 else if (fontStyle.equals("italic"))
257 setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
260 .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
262 // We must set conservation and consensus before setting colour,
263 // as Blosum and Clustal require this to be done
264 if (hconsensus == null && !isDataset)
266 if (!alignment.isNucleotide())
268 showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
269 showQuality = Cache.getDefault("SHOW_QUALITY", true);
270 showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
273 showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
275 showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
276 normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
278 showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
279 showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
281 showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
283 initAutoAnnotation();
284 String colourProperty = alignment.isNucleotide()
285 ? Preferences.DEFAULT_COLOUR_NUC
286 : Preferences.DEFAULT_COLOUR_PROT;
287 String schemeName = Cache.getProperty(colourProperty);
288 if (schemeName == null)
290 // only DEFAULT_COLOUR available in Jalview before 2.9
291 schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
292 ResidueColourScheme.NONE);
294 ColourSchemeI colourScheme = ColourSchemeProperty
295 .getColourScheme(this, alignment, schemeName);
296 residueShading = new ResidueShader(colourScheme);
298 if (colourScheme instanceof UserColourScheme)
300 residueShading = new ResidueShader(
301 UserDefinedColours.loadDefaultColours());
302 residueShading.setThreshold(0, isIgnoreGapsConsensus());
305 if (residueShading != null)
307 residueShading.setConsensus(hconsensus);
309 setColourAppliesToAllGroups(true);
312 boolean validCharWidth;
318 public void setFont(Font f, boolean setGrid)
322 Container c = new Container();
326 FontMetrics fm = c.getFontMetrics(font);
327 int ww = fm.charWidth('M');
328 setCharHeight(fm.getHeight());
331 viewStyle.setFontName(font.getName());
332 viewStyle.setFontStyle(font.getStyle());
333 viewStyle.setFontSize(font.getSize());
335 validCharWidth = true;
339 public void setViewStyle(ViewStyleI settingsForView)
341 super.setViewStyle(settingsForView);
342 setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
343 viewStyle.getFontSize()), false);
349 * @return DOCUMENT ME!
351 public Font getFont()
363 public void setAlignment(AlignmentI align)
365 replaceMappings(align);
366 super.setAlignment(align);
370 * Replace any codon mappings for this viewport with those for the given
375 public void replaceMappings(AlignmentI align)
379 * Deregister current mappings (if any)
381 deregisterMappings();
384 * Register new mappings (if any)
388 StructureSelectionManager ssm = StructureSelectionManager
389 .getStructureSelectionManager(Desktop.instance);
390 ssm.registerMappings(align.getCodonFrames());
394 * replace mappings on our alignment
396 if (alignment != null && align != null)
398 alignment.setCodonFrames(align.getCodonFrames());
402 protected void deregisterMappings()
404 AlignmentI al = getAlignment();
407 List<AlignedCodonFrame> mappings = al.getCodonFrames();
408 if (mappings != null)
410 StructureSelectionManager ssm = StructureSelectionManager
411 .getStructureSelectionManager(Desktop.instance);
412 for (AlignedCodonFrame acf : mappings)
414 if (noReferencesTo(acf))
416 ssm.deregisterMapping(acf);
426 * @return DOCUMENT ME!
429 public char getGapCharacter()
431 return getAlignment().getGapCharacter();
440 public void setGapCharacter(char gap)
442 if (getAlignment() != null)
444 getAlignment().setGapCharacter(gap);
449 * returns the visible column regions of the alignment
451 * @param selectedRegionOnly
452 * true to just return the contigs intersecting with the selected
456 public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
460 if (selectedRegionOnly && selectionGroup != null)
462 start = selectionGroup.getStartRes();
463 end = selectionGroup.getEndRes() + 1;
467 end = alignment.getWidth();
469 return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
474 * get hash of undo and redo list for the alignment
476 * @return long[] { historyList.hashCode, redoList.hashCode };
478 public long[] getUndoRedoHash()
481 if (historyList == null || redoList == null)
483 return new long[] { -1, -1 };
485 return new long[] { historyList.hashCode(), this.redoList.hashCode() };
489 * test if a particular set of hashcodes are different to the hashcodes for
490 * the undo and redo list.
493 * the stored set of hashcodes as returned by getUndoRedoHash
494 * @return true if the hashcodes differ (ie the alignment has been edited) or
495 * the stored hashcode array differs in size
497 public boolean isUndoRedoHashModified(long[] undoredo)
499 if (undoredo == null)
503 long[] cstate = getUndoRedoHash();
504 if (cstate.length != undoredo.length)
509 for (int i = 0; i < cstate.length; i++)
511 if (cstate[i] != undoredo[i])
519 public boolean followSelection = true;
522 * @return true if view selection should always follow the selections
523 * broadcast by other selection sources
525 public boolean getFollowSelection()
527 return followSelection;
531 * Send the current selection to be broadcast to any selection listeners.
534 public void sendSelection()
536 jalview.structure.StructureSelectionManager
537 .getStructureSelectionManager(Desktop.instance)
538 .sendSelection(new SequenceGroup(getSelectionGroup()),
539 new ColumnSelection(getColumnSelection()),
540 new HiddenColumns(getAlignment().getHiddenColumns()),
545 * return the alignPanel containing the given viewport. Use this to get the
546 * components currently handling the given viewport.
549 * @return null or an alignPanel guaranteed to have non-null alignFrame
552 public AlignmentPanel getAlignPanel()
554 AlignmentPanel[] aps = PaintRefresher
555 .getAssociatedPanels(this.getSequenceSetId());
556 for (int p = 0; aps != null && p < aps.length; p++)
558 if (aps[p].av == this)
566 public boolean getSortByTree()
571 public void setSortByTree(boolean sort)
577 * Returns the (Desktop) instance of the StructureSelectionManager
580 public StructureSelectionManager getStructureSelectionManager()
582 return StructureSelectionManager
583 .getStructureSelectionManager(Desktop.instance);
587 public boolean isNormaliseSequenceLogo()
589 return normaliseSequenceLogo;
592 public void setNormaliseSequenceLogo(boolean state)
594 normaliseSequenceLogo = state;
599 * @return true if alignment characters should be displayed
602 public boolean isValidCharWidth()
604 return validCharWidth;
607 private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
609 public AutoCalcSetting getCalcIdSettingsFor(String calcId)
611 return calcIdParams.get(calcId);
614 public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings,
617 calcIdParams.put(calcId, settings);
618 // TODO: create a restart list to trigger any calculations that need to be
619 // restarted after load
620 // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
623 Cache.log.debug("trigger update for " + calcId);
628 * Method called when another alignment's edit (or possibly other) command is
631 * To allow for sequence mappings (e.g. protein to cDNA), we have to first
632 * 'unwind' the command on the source sequences (in simulation, not in fact),
633 * and then for each edit in turn:
635 * <li>compute the equivalent edit on the mapped sequences</li>
636 * <li>apply the mapped edit</li>
637 * <li>'apply' the source edit to the working copy of the source
646 public void mirrorCommand(CommandI command, boolean undo,
647 StructureSelectionManager ssm, VamsasSource source)
650 * Do nothing unless we are a 'complement' of the source. May replace this
651 * with direct calls not via SSM.
653 if (source instanceof AlignViewportI
654 && ((AlignViewportI) source).getCodingComplement() == this)
663 CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
665 if (mappedCommand != null)
667 AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments();
668 mappedCommand.doCommand(views);
669 getAlignPanel().alignmentChanged();
674 * Add the sequences from the given alignment to this viewport. Optionally,
675 * may give the user the option to open a new frame, or split panel, with cDNA
676 * and protein linked.
681 public void addAlignment(AlignmentI toAdd, String title)
683 // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different
685 // JBPComment: title is a largely redundant parameter at the moment
686 // JBPComment: this really should be an 'insert/pre/append' controller
687 // JBPComment: but the DNA/Protein check makes it a bit more complex
689 // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with
691 // TODO: create undo object for this JAL-1101
694 * Ensure datasets are created for the new alignment as
695 * mappings operate on dataset sequences
697 toAdd.setDataset(null);
700 * Check if any added sequence could be the object of a mapping or
701 * cross-reference; if so, make the mapping explicit
703 getAlignment().realiseMappings(toAdd.getSequences());
706 * If any cDNA/protein mappings exist or can be made between the alignments,
707 * offer to open a split frame with linked alignments
709 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
711 if (AlignmentUtils.isMappable(toAdd, getAlignment()))
713 if (openLinkedAlignment(toAdd, title))
721 * No mappings, or offer declined - add sequences to this alignment
723 // TODO: JAL-407 regardless of above - identical sequences (based on ID and
724 // provenance) should share the same dataset sequence
726 AlignmentI al = getAlignment();
727 String gap = String.valueOf(al.getGapCharacter());
728 for (int i = 0; i < toAdd.getHeight(); i++)
730 SequenceI seq = toAdd.getSequenceAt(i);
733 * - 'align' any mapped sequences as per existing
734 * e.g. cdna to genome, domain hit to protein sequence
735 * very experimental! (need a separate menu option for this)
736 * - only add mapped sequences ('select targets from a dataset')
738 if (true /*AlignmentUtils.alignSequenceAs(seq, al, gap, true, true)*/)
744 ranges.setEndSeq(getAlignment().getHeight());
745 firePropertyChange("alignment", null, getAlignment().getSequences());
749 * Show a dialog with the option to open and link (cDNA <-> protein) as a new
750 * alignment, either as a standalone alignment or in a split frame. Returns
751 * true if the new alignment was opened, false if not, because the user
752 * declined the offer.
757 protected boolean openLinkedAlignment(AlignmentI al, String title)
759 String[] options = new String[] { MessageManager.getString("action.no"),
760 MessageManager.getString("label.split_window"),
761 MessageManager.getString("label.new_window"), };
762 final String question = JvSwingUtils.wrapTooltip(true,
763 MessageManager.getString("label.open_split_window?"));
764 int response = JvOptionPane.showOptionDialog(Desktop.desktop, question,
765 MessageManager.getString("label.open_split_window"),
766 JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
767 options, options[0]);
769 if (response != 1 && response != 2)
773 final boolean openSplitPane = (response == 1);
774 final boolean openInNewWindow = (response == 2);
777 * Identify protein and dna alignments. Make a copy of this one if opening
778 * in a new split pane.
780 AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment())
782 AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
783 final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
786 * Map sequences. At least one should get mapped as we have already passed
787 * the test for 'mappability'. Any mappings made will be added to the
788 * protein alignment. Note creating dataset sequences on the new alignment
789 * is a pre-requisite for building mappings.
792 AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna);
795 * Create the AlignFrame for the added alignment. If it is protein, mappings
796 * are registered with StructureSelectionManager as a side-effect.
798 AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
799 AlignFrame.DEFAULT_HEIGHT);
800 newAlignFrame.setTitle(title);
801 newAlignFrame.setStatus(MessageManager
802 .formatMessage("label.successfully_loaded_file", new Object[]
805 // TODO if we want this (e.g. to enable reload of the alignment from file),
806 // we will need to add parameters to the stack.
807 // if (!protocol.equals(DataSourceType.PASTE))
809 // alignFrame.setFileName(file, format);
814 Desktop.addInternalFrame(newAlignFrame, title,
815 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
820 newAlignFrame.setMaximum(
821 jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
822 } catch (java.beans.PropertyVetoException ex)
828 al.alignAs(thisAlignment);
829 protein = openSplitFrame(newAlignFrame, thisAlignment);
836 * Helper method to open a new SplitFrame holding linked dna and protein
839 * @param newAlignFrame
840 * containing a new alignment to be shown
842 * cdna/protein complement alignment to show in the other split half
843 * @return the protein alignment in the split frame
845 protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
846 AlignmentI complement)
849 * Make a new frame with a copy of the alignment we are adding to. If this
850 * is protein, the mappings to cDNA will be registered with
851 * StructureSelectionManager as a side-effect.
853 AlignFrame copyMe = new AlignFrame(complement, AlignFrame.DEFAULT_WIDTH,
854 AlignFrame.DEFAULT_HEIGHT);
855 copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
857 AlignmentI al = newAlignFrame.viewport.getAlignment();
858 final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
860 final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe;
861 cdnaFrame.setVisible(true);
862 proteinFrame.setVisible(true);
863 String linkedTitle = MessageManager
864 .getString("label.linked_view_title");
867 * Open in split pane. DNA sequence above, protein below.
869 JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
870 Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
872 return proteinFrame.viewport.getAlignment();
875 public AnnotationColumnChooser getAnnotationColumnSelectionState()
877 return annotationColumnSelectionState;
880 public void setAnnotationColumnSelectionState(
881 AnnotationColumnChooser currentAnnotationColumnSelectionState)
883 this.annotationColumnSelectionState = currentAnnotationColumnSelectionState;
887 public void setIdWidth(int i)
890 AlignmentPanel ap = getAlignPanel();
893 // modify GUI elements to reflect geometry change
894 Dimension idw = getAlignPanel().getIdPanel().getIdCanvas()
897 getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw);
901 public Rectangle getExplodedGeometry()
903 return explodedGeometry;
906 public void setExplodedGeometry(Rectangle explodedPosition)
908 this.explodedGeometry = explodedPosition;
911 public boolean isGatherViewsHere()
913 return gatherViewsHere;
916 public void setGatherViewsHere(boolean gatherViewsHere)
918 this.gatherViewsHere = gatherViewsHere;
922 * If this viewport has a (Protein/cDNA) complement, then scroll the
923 * complementary alignment to match this one.
925 public void scrollComplementaryAlignment()
928 * Populate a SearchResults object with the mapped location to scroll to. If
929 * there is no complement, or it is not following highlights, or no mapping
930 * is found, the result will be empty.
932 SearchResultsI sr = new SearchResults();
933 int verticalOffset = findComplementScrollTarget(sr);
936 // TODO would like next line without cast but needs more refactoring...
937 final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
939 complementPanel.setToScrollComplementPanel(false);
940 complementPanel.scrollToCentre(sr, verticalOffset);
941 complementPanel.setToScrollComplementPanel(true);
946 * Answers true if no alignment holds a reference to the given mapping
951 protected boolean noReferencesTo(AlignedCodonFrame acf)
953 AlignFrame[] frames = Desktop.getAlignFrames();
958 for (AlignFrame af : frames)
962 for (AlignmentViewPanel ap : af.getAlignPanels())
964 AlignmentI al = ap.getAlignment();
965 if (al != null && al.getCodonFrames().contains(acf))
976 * Applies the supplied feature settings descriptor to currently known
977 * features. This supports an 'initial configuration' of feature colouring
978 * based on a preset or user favourite. This may then be modified in the usual
979 * way using the Feature Settings dialogue.
981 * @param featureSettings
984 public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
986 transferFeaturesStyles(featureSettings, false);
990 * Applies the supplied feature settings descriptor to currently known features.
991 * This supports an 'initial configuration' of feature colouring based on a
992 * preset or user favourite. This may then be modified in the usual way using
993 * the Feature Settings dialogue.
995 * @param featureSettings
998 public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings)
1000 transferFeaturesStyles(featureSettings, true);
1004 * when mergeOnly is set, then group and feature visibility or feature colours
1005 * are not modified for features and groups already known to the feature
1006 * renderer. Feature ordering is always adjusted, and transparency is always set
1009 * @param featureSettings
1012 private void transferFeaturesStyles(FeatureSettingsModelI featureSettings,
1015 if (featureSettings == null)
1020 FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
1021 .getFeatureRenderer();
1022 List<String> origRenderOrder = new ArrayList(),
1023 origGroups = new ArrayList();
1024 // preserve original render order - allows differentiation between user configured colours and autogenerated ones
1025 origRenderOrder.addAll(fr.getRenderOrder());
1026 origGroups.addAll(fr.getFeatureGroups());
1028 fr.findAllFeatures(true);
1029 List<String> renderOrder = fr.getRenderOrder();
1030 FeaturesDisplayedI displayed = fr.getFeaturesDisplayed();
1033 // only clear displayed features if we are mergeing
1036 // TODO this clears displayed.featuresRegistered - do we care?
1038 // JAL-3330 - JBP - yes we do - calling applyFeatureStyle to a view where
1039 // feature visibility has already been configured is not very friendly
1041 * set feature colour if specified by feature settings
1042 * set visibility of all features
1044 for (String type : renderOrder)
1046 FeatureColourI preferredColour = featureSettings
1047 .getFeatureColour(type);
1048 FeatureColourI origColour = fr.getFeatureStyle(type);
1049 if (!mergeOnly || (!origRenderOrder.contains(type)
1050 || origColour == null
1051 || (!origColour.isGraduatedColour()
1052 && origColour.getColour() != null
1053 && origColour.getColour().equals(
1054 ColorUtils.createColourFromName(type)))))
1056 // if we are merging, only update if there wasn't already a colour defined for
1058 if (preferredColour != null)
1060 fr.setColour(type, preferredColour);
1062 if (featureSettings.isFeatureDisplayed(type))
1064 displayed.setVisible(type);
1070 * set visibility of feature groups
1072 for (String group : fr.getFeatureGroups())
1074 if (!mergeOnly || !origGroups.contains(group))
1076 // when merging, display groups only if the aren't already marked as not visible
1077 fr.setGroupVisibility(group,
1078 featureSettings.isGroupDisplayed(group));
1083 * order the features
1085 if (featureSettings.optimiseOrder())
1087 // TODO not supported (yet?)
1091 fr.orderFeatures(featureSettings);
1093 fr.setTransparency(featureSettings.getTransparency());
1096 public String getViewName()
1101 public void setViewName(String viewName)
1103 this.viewName = viewName;