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 java.awt.Container;
24 import java.awt.Dimension;
26 import java.awt.FontMetrics;
27 import java.awt.Rectangle;
29 import java.util.ArrayList;
30 import java.util.Hashtable;
31 import java.util.List;
33 import javax.swing.JInternalFrame;
35 import jalview.analysis.AlignmentUtils;
36 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
37 import jalview.api.AlignViewportI;
38 import jalview.api.AlignmentViewPanel;
39 import jalview.api.FeatureColourI;
40 import jalview.api.FeatureSettingsModelI;
41 import jalview.api.FeaturesDisplayedI;
42 import jalview.api.ViewStyleI;
43 import jalview.bin.Cache;
44 import jalview.bin.Console;
45 import jalview.commands.CommandI;
46 import jalview.datamodel.AlignedCodonFrame;
47 import jalview.datamodel.Alignment;
48 import jalview.datamodel.AlignmentI;
49 import jalview.datamodel.ColumnSelection;
50 import jalview.datamodel.ContactMatrixI;
51 import jalview.datamodel.HiddenColumns;
52 import jalview.datamodel.SearchResults;
53 import jalview.datamodel.SearchResultsI;
54 import jalview.datamodel.SequenceGroup;
55 import jalview.datamodel.SequenceI;
56 import jalview.io.AppletFormatAdapter;
57 import jalview.io.DataSourceType;
58 import jalview.io.FileFormatException;
59 import jalview.io.FileFormatI;
60 import jalview.io.FileFormats;
61 import jalview.io.FileLoader;
62 import jalview.io.IdentifyFile;
63 import jalview.renderer.ResidueShader;
64 import jalview.schemes.ColourSchemeI;
65 import jalview.schemes.ColourSchemeProperty;
66 import jalview.schemes.ResidueColourScheme;
67 import jalview.schemes.UserColourScheme;
68 import jalview.structure.SelectionSource;
69 import jalview.structure.StructureSelectionManager;
70 import jalview.structure.VamsasSource;
71 import jalview.util.ColorUtils;
72 import jalview.util.MessageManager;
73 import jalview.viewmodel.AlignmentViewport;
74 import jalview.ws.params.AutoCalcSetting;
80 * @version $Revision: 1.141 $
82 public class AlignViewport extends AlignmentViewport
83 implements SelectionSource
87 boolean cursorMode = false;
89 boolean antiAlias = false;
91 private Rectangle explodedGeometry = null;
93 private String viewName = null;
96 * Flag set true on the view that should 'gather' multiple views of the same
97 * sequence set id when a project is reloaded. Set false on all views when
98 * they are 'exploded' into separate windows. Set true on the current view
99 * when 'Gather' is performed, and also on the first tab when the first new
102 private boolean gatherViewsHere = false;
104 private AnnotationColumnChooser annotationColumnSelectionState;
107 * Creates a new AlignViewport object.
112 public AlignViewport(AlignmentI al)
119 * Create a new AlignViewport object with a specific sequence set ID
123 * (may be null - but potential for ambiguous constructor exception)
125 public AlignViewport(AlignmentI al, String seqsetid)
127 this(al, seqsetid, null);
130 public AlignViewport(AlignmentI al, String seqsetid, String viewid)
133 sequenceSetID = seqsetid;
135 // TODO remove these once 2.4.VAMSAS release finished
136 if (seqsetid != null)
139 "Setting viewport's sequence set id : " + sequenceSetID);
143 Console.debug("Setting viewport's view id : " + viewId);
150 * Create a new AlignViewport with hidden regions
154 * @param hiddenColumns
157 public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns)
160 if (hiddenColumns != null)
162 al.setHiddenColumns(hiddenColumns);
168 * New viewport with hidden columns and an existing sequence set id
171 * @param hiddenColumns
175 public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
178 this(al, hiddenColumns, seqsetid, null);
182 * New viewport with hidden columns and an existing sequence set id and viewid
185 * @param hiddenColumns
191 public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
192 String seqsetid, String viewid)
195 sequenceSetID = seqsetid;
197 // TODO remove these once 2.4.VAMSAS release finished
198 if (seqsetid != null)
201 "Setting viewport's sequence set id : " + sequenceSetID);
205 Console.debug("Setting viewport's view id : " + viewId);
208 if (hiddenColumns != null)
210 al.setHiddenColumns(hiddenColumns);
216 * Apply any settings saved in user preferences
218 private void applyViewProperties()
220 antiAlias = Cache.getDefault("ANTI_ALIAS", true);
222 viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
223 setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
225 setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
226 setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false));
227 autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
229 setPadGaps(Cache.getDefault("PAD_GAPS", true));
230 setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
231 setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
232 viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true));
233 viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false));
234 viewStyle.setShowUnconserved(
235 Cache.getDefault("SHOW_UNCONSERVED", false));
236 sortByTree = Cache.getDefault("SORT_BY_TREE", false);
237 followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
238 sortAnnotationsBy = SequenceAnnotationOrder
239 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
240 SequenceAnnotationOrder.NONE.name()));
241 showAutocalculatedAbove = Cache
242 .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
243 viewStyle.setScaleProteinAsCdna(
244 Cache.getDefault(Preferences.SCALE_PROTEIN_TO_CDNA, true));
249 applyViewProperties();
251 String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
252 String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
253 String fontSize = Cache.getDefault("FONT_SIZE", "10");
257 if (fontStyle.equals("bold"))
261 else if (fontStyle.equals("italic"))
266 setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
269 .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
271 // We must set conservation and consensus before setting colour,
272 // as Blosum and Clustal require this to be done
273 if (hconsensus == null && !isDataset)
275 if (!alignment.isNucleotide())
277 showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
278 showQuality = Cache.getDefault("SHOW_QUALITY", true);
279 showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
282 showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
284 showSSConsensusHistogram = Cache.getDefault("SHOW_SSCONSENSUS_HISTOGRAM",
286 showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", true);
287 normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
289 showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
290 showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
292 showSSConsensus = Cache.getDefault("SHOW_SS_CONSENSUS", false);
294 showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
296 initAutoAnnotation();
297 String colourProperty = alignment.isNucleotide()
298 ? Preferences.DEFAULT_COLOUR_NUC
299 : Preferences.DEFAULT_COLOUR_PROT;
300 String schemeName = Cache.getProperty(colourProperty);
301 if (schemeName == null)
303 // only DEFAULT_COLOUR available in Jalview before 2.9
304 schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
305 ResidueColourScheme.NONE);
307 ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(this,
308 alignment, schemeName);
309 residueShading = new ResidueShader(colourScheme);
311 if (colourScheme instanceof UserColourScheme)
313 residueShading = new ResidueShader(
314 UserDefinedColours.loadDefaultColours());
315 residueShading.setThreshold(0, isIgnoreGapsConsensus());
318 if (residueShading != null)
320 residueShading.setConsensus(hconsensus);
321 residueShading.setSsConsensus(hSSConsensus);
323 setColourAppliesToAllGroups(true);
326 boolean validCharWidth;
332 public void setFont(Font f, boolean setGrid)
336 Container c = new Container();
340 FontMetrics fm = c.getFontMetrics(font);
341 int ww = fm.charWidth('M');
342 setCharHeight(fm.getHeight());
345 viewStyle.setFontName(font.getName());
346 viewStyle.setFontStyle(font.getStyle());
347 viewStyle.setFontSize(font.getSize());
349 validCharWidth = true;
353 public void setViewStyle(ViewStyleI settingsForView)
355 super.setViewStyle(settingsForView);
356 setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
357 viewStyle.getFontSize()), false);
363 * @return DOCUMENT ME!
365 public Font getFont()
377 public void setAlignment(AlignmentI align)
379 replaceMappings(align);
380 super.setAlignment(align);
384 * Replace any codon mappings for this viewport with those for the given
389 public void replaceMappings(AlignmentI align)
393 * Deregister current mappings (if any)
395 deregisterMappings();
398 * Register new mappings (if any)
402 StructureSelectionManager ssm = StructureSelectionManager
403 .getStructureSelectionManager(Desktop.instance);
404 ssm.registerMappings(align.getCodonFrames());
408 * replace mappings on our alignment
410 if (alignment != null && align != null)
412 alignment.setCodonFrames(align.getCodonFrames());
416 protected void deregisterMappings()
418 AlignmentI al = getAlignment();
421 List<AlignedCodonFrame> mappings = al.getCodonFrames();
422 if (mappings != null)
424 StructureSelectionManager ssm = StructureSelectionManager
425 .getStructureSelectionManager(Desktop.instance);
426 for (AlignedCodonFrame acf : mappings)
428 if (noReferencesTo(acf))
430 ssm.deregisterMapping(acf);
440 * @return DOCUMENT ME!
443 public char getGapCharacter()
445 return getAlignment().getGapCharacter();
454 public void setGapCharacter(char gap)
456 if (getAlignment() != null)
458 getAlignment().setGapCharacter(gap);
463 * get hash of undo and redo list for the alignment
465 * @return long[] { historyList.hashCode, redoList.hashCode };
467 public long[] getUndoRedoHash()
470 if (historyList == null || redoList == null)
472 return new long[] { -1, -1 };
474 return new long[] { historyList.hashCode(), this.redoList.hashCode() };
478 * test if a particular set of hashcodes are different to the hashcodes for
479 * the undo and redo list.
482 * the stored set of hashcodes as returned by getUndoRedoHash
483 * @return true if the hashcodes differ (ie the alignment has been edited) or
484 * the stored hashcode array differs in size
486 public boolean isUndoRedoHashModified(long[] undoredo)
488 if (undoredo == null)
492 long[] cstate = getUndoRedoHash();
493 if (cstate.length != undoredo.length)
498 for (int i = 0; i < cstate.length; i++)
500 if (cstate[i] != undoredo[i])
508 public boolean followSelection = true;
511 * @return true if view selection should always follow the selections
512 * broadcast by other selection sources
514 public boolean getFollowSelection()
516 return followSelection;
520 * Send the current selection to be broadcast to any selection listeners.
523 public void sendSelection()
525 jalview.structure.StructureSelectionManager
526 .getStructureSelectionManager(Desktop.instance)
527 .sendSelection(new SequenceGroup(getSelectionGroup()),
528 new ColumnSelection(getColumnSelection()),
529 new HiddenColumns(getAlignment().getHiddenColumns()),
534 * return the alignPanel containing the given viewport. Use this to get the
535 * components currently handling the given viewport.
538 * @return null or an alignPanel guaranteed to have non-null alignFrame
541 public AlignmentPanel getAlignPanel()
543 AlignmentPanel[] aps = PaintRefresher
544 .getAssociatedPanels(this.getSequenceSetId());
545 for (int p = 0; aps != null && p < aps.length; p++)
547 if (aps[p].av == this)
555 public boolean getSortByTree()
560 public void setSortByTree(boolean sort)
566 * Returns the (Desktop) instance of the StructureSelectionManager
569 public StructureSelectionManager getStructureSelectionManager()
571 return StructureSelectionManager
572 .getStructureSelectionManager(Desktop.instance);
576 public boolean isNormaliseSequenceLogo()
578 return normaliseSequenceLogo;
581 public void setNormaliseSequenceLogo(boolean state)
583 normaliseSequenceLogo = state;
588 * @return true if alignment characters should be displayed
591 public boolean isValidCharWidth()
593 return validCharWidth;
596 private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
598 public AutoCalcSetting getCalcIdSettingsFor(String calcId)
600 return calcIdParams.get(calcId);
603 public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings,
606 calcIdParams.put(calcId, settings);
607 // TODO: create a restart list to trigger any calculations that need to be
608 // restarted after load
609 // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
612 Console.debug("trigger update for " + calcId);
617 * Method called when another alignment's edit (or possibly other) command is
620 * To allow for sequence mappings (e.g. protein to cDNA), we have to first
621 * 'unwind' the command on the source sequences (in simulation, not in fact),
622 * and then for each edit in turn:
624 * <li>compute the equivalent edit on the mapped sequences</li>
625 * <li>apply the mapped edit</li>
626 * <li>'apply' the source edit to the working copy of the source
635 public void mirrorCommand(CommandI command, boolean undo,
636 StructureSelectionManager ssm, VamsasSource source)
639 * Do nothing unless we are a 'complement' of the source. May replace this
640 * with direct calls not via SSM.
642 if (source instanceof AlignViewportI
643 && ((AlignViewportI) source).getCodingComplement() == this)
652 CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
654 if (mappedCommand != null)
656 AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments();
657 mappedCommand.doCommand(views);
658 getAlignPanel().alignmentChanged();
663 * Add the sequences from the given alignment to this viewport. Optionally,
664 * may give the user the option to open a new frame, or split panel, with cDNA
665 * and protein linked.
670 public void addAlignment(AlignmentI toAdd, String title)
672 // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different
674 // JBPComment: title is a largely redundant parameter at the moment
675 // JBPComment: this really should be an 'insert/pre/append' controller
676 // JBPComment: but the DNA/Protein check makes it a bit more complex
678 // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with
680 // TODO: create undo object for this JAL-1101
683 * Ensure datasets are created for the new alignment as
684 * mappings operate on dataset sequences
686 toAdd.setDataset(null);
689 * Check if any added sequence could be the object of a mapping or
690 * cross-reference; if so, make the mapping explicit
692 getAlignment().realiseMappings(toAdd.getSequences());
695 * If any cDNA/protein mappings exist or can be made between the alignments,
696 * offer to open a split frame with linked alignments
698 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
700 if (AlignmentUtils.isMappable(toAdd, getAlignment()))
702 openLinkedAlignment(toAdd, title);
706 addDataToAlignment(toAdd);
710 * adds sequences to this alignment
714 void addDataToAlignment(AlignmentI toAdd)
716 // TODO: JAL-407 regardless of above - identical sequences (based on ID and
717 // provenance) should share the same dataset sequence
719 AlignmentI al = getAlignment();
720 String gap = String.valueOf(al.getGapCharacter());
721 for (int i = 0; i < toAdd.getHeight(); i++)
723 SequenceI seq = toAdd.getSequenceAt(i);
726 * - 'align' any mapped sequences as per existing
727 * e.g. cdna to genome, domain hit to protein sequence
728 * very experimental! (need a separate menu option for this)
729 * - only add mapped sequences ('select targets from a dataset')
731 if (true /*AlignmentUtils.alignSequenceAs(seq, al, gap, true, true)*/)
736 for (ContactMatrixI cm : toAdd.getContactMaps())
738 al.addContactList(cm);
740 ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18
741 firePropertyChange("alignment", null, getAlignment().getSequences());
745 * Load a File into this AlignViewport attempting to detect format if not
746 * given or given as null.
751 public void addFile(File file, FileFormatI format)
753 addFile(file, format, true);
756 public void addFile(File file, FileFormatI format, boolean async)
758 DataSourceType protocol = AppletFormatAdapter.checkProtocol(file);
764 format = new IdentifyFile().identify(file, protocol);
765 } catch (FileFormatException e1)
767 jalview.bin.Console.error("Unknown file format for '" + file + "'");
770 else if (FileFormats.getInstance().isIdentifiable(format))
774 format = new IdentifyFile().identify(file, protocol);
775 } catch (FileFormatException e)
777 jalview.bin.Console.error("Unknown file format for '" + file + "'",
782 new FileLoader().LoadFile(this, file, DataSourceType.FILE, format,
786 public void addFile(File file)
792 * Show a dialog with the option to open and link (cDNA <-> protein) as a new
793 * alignment, either as a standalone alignment or in a split frame. Returns
794 * true if the new alignment was opened, false if not, because the user
795 * declined the offer.
800 protected void openLinkedAlignment(AlignmentI al, String title)
802 String[] options = new String[] { MessageManager.getString("action.no"),
803 MessageManager.getString("label.split_window"),
804 MessageManager.getString("label.new_window"), };
805 final String question = JvSwingUtils.wrapTooltip(true,
806 MessageManager.getString("label.open_split_window?"));
807 final AlignViewport us = this;
810 * options No, Split Window, New Window correspond to
811 * dialog responses 0, 1, 2 (even though JOptionPane shows them
814 JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
815 .setResponseHandler(0, () -> {
816 addDataToAlignment(al);
817 }).setResponseHandler(1, () -> {
818 us.openLinkedAlignmentAs(al, title, true);
819 }).setResponseHandler(2, () -> {
820 us.openLinkedAlignmentAs(al, title, false);
822 dialog.showDialog(question,
823 MessageManager.getString("label.open_split_window"),
824 JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
825 options, options[0]);
828 protected void openLinkedAlignmentAs(AlignmentI al, String title,
829 boolean newWindowOrSplitPane)
832 * Identify protein and dna alignments. Make a copy of this one if opening
833 * in a new split pane.
835 AlignmentI thisAlignment = newWindowOrSplitPane
836 ? new Alignment(getAlignment())
838 AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
839 final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
842 * Map sequences. At least one should get mapped as we have already passed
843 * the test for 'mappability'. Any mappings made will be added to the
844 * protein alignment. Note creating dataset sequences on the new alignment
845 * is a pre-requisite for building mappings.
848 AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna);
851 * Create the AlignFrame for the added alignment. If it is protein, mappings
852 * are registered with StructureSelectionManager as a side-effect.
854 AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
855 AlignFrame.DEFAULT_HEIGHT);
856 newAlignFrame.setTitle(title);
857 newAlignFrame.setStatus(MessageManager
858 .formatMessage("label.successfully_loaded_file", new Object[]
861 // TODO if we want this (e.g. to enable reload of the alignment from file),
862 // we will need to add parameters to the stack.
863 // if (!protocol.equals(DataSourceType.PASTE))
865 // alignFrame.setFileName(file, format);
868 if (!newWindowOrSplitPane)
870 Desktop.addInternalFrame(newAlignFrame, title,
871 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
876 newAlignFrame.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false));
877 } catch (java.beans.PropertyVetoException ex)
881 if (newWindowOrSplitPane)
883 al.alignAs(thisAlignment);
884 protein = openSplitFrame(newAlignFrame, thisAlignment);
889 * Helper method to open a new SplitFrame holding linked dna and protein
892 * @param newAlignFrame
893 * containing a new alignment to be shown
895 * cdna/protein complement alignment to show in the other split half
896 * @return the protein alignment in the split frame
898 protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
899 AlignmentI complement)
902 * Make a new frame with a copy of the alignment we are adding to. If this
903 * is protein, the mappings to cDNA will be registered with
904 * StructureSelectionManager as a side-effect.
906 AlignFrame copyMe = new AlignFrame(complement, AlignFrame.DEFAULT_WIDTH,
907 AlignFrame.DEFAULT_HEIGHT);
908 copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
910 AlignmentI al = newAlignFrame.viewport.getAlignment();
911 final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
913 final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe;
914 cdnaFrame.setVisible(true);
915 proteinFrame.setVisible(true);
916 String linkedTitle = MessageManager
917 .getString("label.linked_view_title");
920 * Open in split pane. DNA sequence above, protein below.
922 JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
923 Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
925 return proteinFrame.viewport.getAlignment();
928 public AnnotationColumnChooser getAnnotationColumnSelectionState()
930 return annotationColumnSelectionState;
933 public void setAnnotationColumnSelectionState(
934 AnnotationColumnChooser currentAnnotationColumnSelectionState)
936 this.annotationColumnSelectionState = currentAnnotationColumnSelectionState;
940 public void setIdWidth(int i)
943 AlignmentPanel ap = getAlignPanel();
946 // modify GUI elements to reflect geometry change
947 Dimension idw = ap.getIdPanel().getIdCanvas().getPreferredSize();
949 ap.getIdPanel().getIdCanvas().setPreferredSize(idw);
953 public Rectangle getExplodedGeometry()
955 return explodedGeometry;
958 public void setExplodedGeometry(Rectangle explodedPosition)
960 this.explodedGeometry = explodedPosition;
963 public boolean isGatherViewsHere()
965 return gatherViewsHere;
968 public void setGatherViewsHere(boolean gatherViewsHere)
970 this.gatherViewsHere = gatherViewsHere;
974 * If this viewport has a (Protein/cDNA) complement, then scroll the
975 * complementary alignment to match this one.
977 public void scrollComplementaryAlignment()
980 * Populate a SearchResults object with the mapped location to scroll to. If
981 * there is no complement, or it is not following highlights, or no mapping
982 * is found, the result will be empty.
984 SearchResultsI sr = new SearchResults();
985 int verticalOffset = findComplementScrollTarget(sr);
988 // TODO would like next line without cast but needs more refactoring...
989 final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
991 complementPanel.setToScrollComplementPanel(false);
992 complementPanel.scrollToCentre(sr, verticalOffset);
993 complementPanel.setToScrollComplementPanel(true);
998 * Answers true if no alignment holds a reference to the given mapping
1003 protected boolean noReferencesTo(AlignedCodonFrame acf)
1005 AlignFrame[] frames = Desktop.getDesktopAlignFrames();
1010 for (AlignFrame af : frames)
1014 for (AlignmentViewPanel ap : af.getAlignPanels())
1016 AlignmentI al = ap.getAlignment();
1017 if (al != null && al.getCodonFrames().contains(acf))
1028 * Applies the supplied feature settings descriptor to currently known
1029 * features. This supports an 'initial configuration' of feature colouring
1030 * based on a preset or user favourite. This may then be modified in the usual
1031 * way using the Feature Settings dialogue.
1033 * @param featureSettings
1036 public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
1038 transferFeaturesStyles(featureSettings, false);
1042 * Applies the supplied feature settings descriptor to currently known
1043 * features. This supports an 'initial configuration' of feature colouring
1044 * based on a preset or user favourite. This may then be modified in the usual
1045 * way using the Feature Settings dialogue.
1047 * @param featureSettings
1050 public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings)
1052 transferFeaturesStyles(featureSettings, true);
1056 * when mergeOnly is set, then group and feature visibility or feature colours
1057 * are not modified for features and groups already known to the feature
1058 * renderer. Feature ordering is always adjusted, and transparency is always
1061 * @param featureSettings
1064 private void transferFeaturesStyles(FeatureSettingsModelI featureSettings,
1067 if (featureSettings == null)
1072 FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
1073 .getFeatureRenderer();
1074 List<String> origRenderOrder = new ArrayList<>();
1075 List<String> origGroups = new ArrayList<>();
1076 // preserve original render order - allows differentiation between user
1077 // configured colours and autogenerated ones
1078 origRenderOrder.addAll(fr.getRenderOrder());
1079 origGroups.addAll(fr.getFeatureGroups());
1081 fr.findAllFeatures(true);
1082 List<String> renderOrder = fr.getRenderOrder();
1083 FeaturesDisplayedI displayed = fr.getFeaturesDisplayed();
1086 // only clear displayed features if we are mergeing
1087 // displayed.clear();
1089 // TODO this clears displayed.featuresRegistered - do we care?
1091 // JAL-3330 - JBP - yes we do - calling applyFeatureStyle to a view where
1092 // feature visibility has already been configured is not very friendly
1094 * set feature colour if specified by feature settings
1095 * set visibility of all features
1097 for (String type : renderOrder)
1099 FeatureColourI preferredColour = featureSettings
1100 .getFeatureColour(type);
1101 FeatureColourI origColour = fr.getFeatureStyle(type);
1102 if (!mergeOnly || (!origRenderOrder.contains(type)
1103 || origColour == null
1104 || (!origColour.isGraduatedColour()
1105 && origColour.getColour() != null
1106 && origColour.getColour().equals(
1107 ColorUtils.createColourFromName(type)))))
1109 // if we are merging, only update if there wasn't already a colour
1112 if (preferredColour != null)
1114 fr.setColour(type, preferredColour);
1116 if (featureSettings.isFeatureDisplayed(type))
1118 displayed.setVisible(type);
1120 else if (featureSettings.isFeatureHidden(type))
1122 displayed.setHidden(type);
1128 * set visibility of feature groups
1130 for (String group : fr.getFeatureGroups())
1132 if (!mergeOnly || !origGroups.contains(group))
1134 // when merging, display groups only if the aren't already marked as not
1136 fr.setGroupVisibility(group,
1137 featureSettings.isGroupDisplayed(group));
1142 * order the features
1144 if (featureSettings.optimiseOrder())
1146 // TODO not supported (yet?)
1150 fr.orderFeatures(featureSettings);
1152 fr.setTransparency(featureSettings.getTransparency());
1154 fr.notifyFeaturesChanged();
1157 public String getViewName()
1162 public void setViewName(String viewName)
1164 this.viewName = viewName;