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.datamodel.features.FeatureMatcherSetI;
43 import jalview.renderer.ResidueShader;
44 import jalview.schemes.ColourSchemeI;
45 import jalview.schemes.ColourSchemeProperty;
46 import jalview.schemes.ResidueColourScheme;
47 import jalview.schemes.UserColourScheme;
48 import jalview.structure.SelectionSource;
49 import jalview.structure.StructureSelectionManager;
50 import jalview.structure.VamsasSource;
51 import jalview.util.ColorUtils;
52 import jalview.util.MessageManager;
53 import jalview.viewmodel.AlignmentViewport;
54 import jalview.ws.params.AutoCalcSetting;
56 import java.awt.Container;
57 import java.awt.Dimension;
59 import java.awt.FontMetrics;
60 import java.awt.Rectangle;
61 import java.util.ArrayList;
62 import java.util.Hashtable;
63 import java.util.Iterator;
64 import java.util.List;
66 import javax.swing.JInternalFrame;
72 * @version $Revision: 1.141 $
74 public class AlignViewport extends AlignmentViewport
75 implements SelectionSource
78 public final static int NO_SPLIT = 0;
80 public final static int SPLIT_FRAME = 1;
82 public final static int NEW_WINDOW = 2;
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 (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
139 "Setting viewport's sequence set id : " + sequenceSetID);
141 if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
143 Cache.log.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 (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
201 "Setting viewport's sequence set id : " + sequenceSetID);
203 if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
205 Cache.log.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 autoCalculateConsensusAndConservation = 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);
268 alignment.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
270 // We must set conservation and consensus before setting colour,
271 // as Blosum and Clustal require this to be done
272 if (hconsensus == null && !isDataset)
274 if (!alignment.isNucleotide())
276 showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
277 showQuality = Cache.getDefault("SHOW_QUALITY", true);
278 showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
281 showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
283 showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
284 normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
286 // for now, use consensus options for Information till it gets its own
287 setShowHMMSequenceLogo(showSequenceLogo);
288 setNormaliseHMMSequenceLogo(normaliseSequenceLogo);
289 setShowInformationHistogram(showConsensusHistogram);
290 showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
291 showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
293 showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
295 initAutoAnnotation();
296 // initInformation();
298 String colourProperty = alignment.isNucleotide()
299 ? Preferences.DEFAULT_COLOUR_NUC
300 : Preferences.DEFAULT_COLOUR_PROT;
301 String schemeName = Cache.getProperty(colourProperty);
302 if (schemeName == null)
304 // only DEFAULT_COLOUR available in Jalview before 2.9
305 schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
306 ResidueColourScheme.NONE);
308 ColourSchemeI colourScheme = ColourSchemeProperty
309 .getColourScheme(this, alignment, schemeName);
310 residueShading = new ResidueShader(colourScheme);
312 if (colourScheme instanceof UserColourScheme)
314 residueShading = new ResidueShader(
315 UserDefinedColours.loadDefaultColours());
316 residueShading.setThreshold(0, isIgnoreGapsConsensus());
319 if (residueShading != null)
321 residueShading.setConsensus(hconsensus);
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.getInstance());
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.getInstance());
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 * Returns an iterator over the visible column regions of the alignment
465 * @param selectedRegionOnly
466 * true to just return the contigs intersecting with the selected
470 public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
474 if (selectedRegionOnly && selectionGroup != null)
476 start = selectionGroup.getStartRes();
477 end = selectionGroup.getEndRes() + 1;
481 end = alignment.getWidth();
484 return (alignment.getHiddenColumns().getVisContigsIterator(start,
489 * get hash of undo and redo list for the alignment
491 * @return long[] { historyList.hashCode, redoList.hashCode };
493 public long[] getUndoRedoHash()
496 if (historyList == null || redoList == null)
498 return new long[] { -1, -1 };
500 return new long[] { historyList.hashCode(), this.redoList.hashCode() };
504 * test if a particular set of hashcodes are different to the hashcodes for
505 * the undo and redo list.
508 * the stored set of hashcodes as returned by getUndoRedoHash
509 * @return true if the hashcodes differ (ie the alignment has been edited) or
510 * the stored hashcode array differs in size
512 public boolean isUndoRedoHashModified(long[] undoredo)
514 if (undoredo == null)
518 long[] cstate = getUndoRedoHash();
519 if (cstate.length != undoredo.length)
524 for (int i = 0; i < cstate.length; i++)
526 if (cstate[i] != undoredo[i])
534 public boolean followSelection = true;
537 * @return true if view selection should always follow the selections
538 * broadcast by other selection sources
540 public boolean getFollowSelection()
542 return followSelection;
546 * Send the current selection to be broadcast to any selection listeners.
549 public void sendSelection()
551 jalview.structure.StructureSelectionManager
552 .getStructureSelectionManager(Desktop.getInstance())
553 .sendSelection(new SequenceGroup(getSelectionGroup()),
554 new ColumnSelection(getColumnSelection()),
555 new HiddenColumns(getAlignment().getHiddenColumns()),
560 * return the alignPanel containing the given viewport. Use this to get the
561 * components currently handling the given viewport.
564 * @return null or an alignPanel guaranteed to have non-null alignFrame
567 public AlignmentPanel getAlignPanel()
569 AlignmentPanel[] aps = PaintRefresher
570 .getAssociatedPanels(this.getSequenceSetId());
571 for (int p = 0; aps != null && p < aps.length; p++)
573 if (aps[p].av == this)
581 public boolean getSortByTree()
586 public void setSortByTree(boolean sort)
592 * Returns the (Desktop) instance of the StructureSelectionManager
595 public StructureSelectionManager getStructureSelectionManager()
597 return StructureSelectionManager
598 .getStructureSelectionManager(Desktop.getInstance());
602 public boolean isNormaliseSequenceLogo()
604 return normaliseSequenceLogo;
608 public void setNormaliseSequenceLogo(boolean state)
610 normaliseSequenceLogo = state;
616 * @return true if alignment characters should be displayed
619 public boolean isValidCharWidth()
621 return validCharWidth;
624 private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
626 public AutoCalcSetting getCalcIdSettingsFor(String calcId)
628 return calcIdParams.get(calcId);
631 public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings,
634 calcIdParams.put(calcId, settings);
635 // TODO: create a restart list to trigger any calculations that need to be
636 // restarted after load
637 // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
640 Cache.log.debug("trigger update for " + calcId);
645 * Method called when another alignment's edit (or possibly other) command is
648 * To allow for sequence mappings (e.g. protein to cDNA), we have to first
649 * 'unwind' the command on the source sequences (in simulation, not in fact),
650 * and then for each edit in turn:
652 * <li>compute the equivalent edit on the mapped sequences</li>
653 * <li>apply the mapped edit</li>
654 * <li>'apply' the source edit to the working copy of the source
663 public void mirrorCommand(CommandI command, boolean undo,
664 StructureSelectionManager ssm, VamsasSource source)
667 * Do nothing unless we are a 'complement' of the source. May replace this
668 * with direct calls not via SSM.
670 if (source instanceof AlignViewportI
671 && ((AlignViewportI) source).getCodingComplement() == this)
680 CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
682 if (mappedCommand != null)
684 AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments();
685 mappedCommand.doCommand(views);
686 getAlignPanel().alignmentChanged();
691 * Add the sequences from the given alignment to this viewport. Optionally,
692 * may give the user the option to open a new frame, or split panel, with cDNA
693 * and protein linked.
698 public void addAlignment(AlignmentI toAdd, String title)
700 // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different
702 // JBPComment: title is a largely redundant parameter at the moment
703 // JBPComment: this really should be an 'insert/pre/append' controller
704 // JBPComment: but the DNA/Protein check makes it a bit more complex
706 // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with
708 // TODO: create undo object for this JAL-1101
711 * Ensure datasets are created for the new alignment as
712 * mappings operate on dataset sequences
714 toAdd.setDataset(null);
717 * Check if any added sequence could be the object of a mapping or
718 * cross-reference; if so, make the mapping explicit
720 getAlignment().realiseMappings(toAdd.getSequences());
723 * If any cDNA/protein mappings exist or can be made between the alignments,
724 * offer to open a split frame with linked alignments
726 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
728 if (AlignmentUtils.isMappable(toAdd, getAlignment()))
730 openLinkedAlignment(toAdd, title);
734 addDataToAlignment(toAdd);
738 * adds sequences to this alignment
742 void addDataToAlignment(AlignmentI toAdd)
744 // TODO: JAL-407 regardless of above - identical sequences (based on ID and
745 // provenance) should share the same dataset sequence
747 AlignmentI al = getAlignment();
748 String gap = String.valueOf(al.getGapCharacter());
749 for (int i = 0; i < toAdd.getHeight(); i++)
751 SequenceI seq = toAdd.getSequenceAt(i);
754 * - 'align' any mapped sequences as per existing
755 * e.g. cdna to genome, domain hit to protein sequence
756 * very experimental! (need a separate menu option for this)
757 * - only add mapped sequences ('select targets from a dataset')
759 if (true /*AlignmentUtils.alignSequenceAs(seq, al, gap, true, true)*/)
765 ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18
771 * Show a dialog with the option to open and link (cDNA <-> protein) as a new
772 * alignment, either as a standalone alignment or in a split frame. Returns
773 * true if the new alignment was opened, false if not, because the user
774 * declined the offer.
779 protected void openLinkedAlignment(AlignmentI al, String title)
781 String[] options = new String[] { MessageManager.getString("action.no"),
782 MessageManager.getString("label.split_window"),
783 MessageManager.getString("label.new_window"), };
784 final String question = JvSwingUtils.wrapTooltip(true,
785 MessageManager.getString("label.open_split_window?"));
786 final AlignViewport us = this;
789 * options No, Split Window, New Window correspond to
790 * dialog responses 0, 1, 2 (even though JOptionPane shows them
793 JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane())
794 .setResponseHandler(NO_SPLIT, new Runnable()
799 addDataToAlignment(al);
801 }).setResponseHandler(SPLIT_FRAME, new Runnable()
806 openLinkedAlignmentAs(getAlignPanel().alignFrame,
807 new Alignment(getAlignment()), al, title,
809 // us.openLinkedAlignmentAs(al, title, true);
811 }).setResponseHandler(NEW_WINDOW, new Runnable()
816 openLinkedAlignmentAs(null, getAlignment(), al, title,
820 dialog.showDialog(question,
821 MessageManager.getString("label.open_split_window"),
822 JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
823 options, options[0]);
826 * Open a split frame or a new window
831 * SPLIT_FRAME or NEW_WINDOW
833 public static void openLinkedAlignmentAs(AlignFrame thisFrame,
834 AlignmentI thisAlignment, AlignmentI al, String title, int mode)
837 * Identify protein and dna alignments. Make a copy of this one if opening
838 * in a new split pane.
840 AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
841 AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
843 * Map sequences. At least one should get mapped as we have already passed
844 * the test for 'mappability'. Any mappings made will be added to the
845 * protein alignment. Note creating dataset sequences on the new alignment
846 * is a pre-requisite for building mappings.
849 AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna);
852 * Create the AlignFrame for the added alignment. If it is protein, mappings
853 * are registered with StructureSelectionManager as a side-effect.
855 AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
856 AlignFrame.DEFAULT_HEIGHT);
857 newAlignFrame.setTitle(title);
858 newAlignFrame.setStatus(MessageManager
859 .formatMessage("label.successfully_loaded_file", new Object[]
862 // TODO if we want this (e.g. to enable reload of the alignment from file),
863 // we will need to add parameters to the stack.
864 // if (!protocol.equals(DataSourceType.PASTE))
866 // alignFrame.setFileName(file, format);
869 if (mode == NEW_WINDOW)
871 Desktop.addInternalFrame(newAlignFrame, title,
872 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
877 newAlignFrame.setMaximum(
878 jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
879 } catch (java.beans.PropertyVetoException ex)
883 if (mode == SPLIT_FRAME)
885 al.alignAs(thisAlignment);
886 openSplitFrame(thisFrame, newAlignFrame, thisAlignment);
891 * Helper method to open a new SplitFrame holding linked dna and protein
894 * @param newAlignFrame
895 * containing a new alignment to be shown
897 * cdna/protein complement alignment to show in the other split half
898 * @return the protein alignment in the split frame
900 static protected AlignmentI openSplitFrame(AlignFrame thisFrame,
901 AlignFrame newAlignFrame, AlignmentI complement)
904 * Make a new frame with a copy of the alignment we are adding to. If this
905 * is protein, the mappings to cDNA will be registered with
906 * StructureSelectionManager as a side-effect.
908 AlignFrame copyMe = new AlignFrame(complement, AlignFrame.DEFAULT_WIDTH,
909 AlignFrame.DEFAULT_HEIGHT);
910 copyMe.setTitle(thisFrame.getTitle());
913 AlignmentI al = newAlignFrame.viewport.getAlignment();
914 final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
916 final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe;
917 cdnaFrame.setVisible(true);
918 proteinFrame.setVisible(true);
919 String linkedTitle = MessageManager
920 .getString("label.linked_view_title");
923 * Open in split pane. DNA sequence above, protein below.
925 JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
926 Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
928 return proteinFrame.viewport.getAlignment();
931 public AnnotationColumnChooser getAnnotationColumnSelectionState()
933 return annotationColumnSelectionState;
936 public void setAnnotationColumnSelectionState(
937 AnnotationColumnChooser currentAnnotationColumnSelectionState)
939 this.annotationColumnSelectionState = currentAnnotationColumnSelectionState;
943 public void setIdWidth(int i)
946 AlignmentPanel ap = getAlignPanel();
949 // modify GUI elements to reflect geometry change
950 Dimension idw = ap.getIdPanel().getIdCanvas().getPreferredSize();
952 ap.getIdPanel().getIdCanvas().setPreferredSize(idw);
956 public Rectangle getExplodedGeometry()
958 return explodedGeometry;
961 public void setExplodedGeometry(Rectangle explodedPosition)
963 this.explodedGeometry = explodedPosition;
966 public boolean isGatherViewsHere()
968 return gatherViewsHere;
971 public void setGatherViewsHere(boolean gatherViewsHere)
973 this.gatherViewsHere = gatherViewsHere;
977 * If this viewport has a (Protein/cDNA) complement, then scroll the
978 * complementary alignment to match this one.
980 public void scrollComplementaryAlignment()
983 * Populate a SearchResults object with the mapped location to scroll to. If
984 * there is no complement, or it is not following highlights, or no mapping
985 * is found, the result will be empty.
987 SearchResultsI sr = new SearchResults();
988 int verticalOffset = findComplementScrollTarget(sr);
991 // TODO would like next line without cast but needs more refactoring...
992 final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
994 complementPanel.setToScrollComplementPanel(false);
995 complementPanel.scrollToCentre(sr, verticalOffset);
996 complementPanel.setToScrollComplementPanel(true);
1001 * Answers true if no alignment holds a reference to the given mapping
1006 protected boolean noReferencesTo(AlignedCodonFrame acf)
1008 AlignFrame[] frames = Desktop.getAlignFrames();
1013 for (AlignFrame af : frames)
1017 for (AlignmentViewPanel ap : af.getAlignPanels())
1019 AlignmentI al = ap.getAlignment();
1020 if (al != null && al.getCodonFrames().contains(acf))
1031 * Applies the supplied feature settings descriptor to currently known
1032 * features. This supports an 'initial configuration' of feature colouring
1033 * based on a preset or user favourite. This may then be modified in the usual
1034 * way using the Feature Settings dialogue.
1036 * @param featureSettings
1039 public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
1041 transferFeaturesStyles(featureSettings, false);
1045 * Applies the supplied feature settings descriptor to currently known features.
1046 * This supports an 'initial configuration' of feature colouring based on a
1047 * preset or user favourite. This may then be modified in the usual way using
1048 * the Feature Settings dialogue.
1050 * @param featureSettings
1053 public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings)
1055 transferFeaturesStyles(featureSettings, true);
1059 * when mergeOnly is set, then group and feature visibility or feature colours
1060 * are not modified for features and groups already known to the feature
1061 * renderer. Feature ordering is always adjusted, and transparency is always set
1064 * @param featureSettings
1067 private void transferFeaturesStyles(FeatureSettingsModelI featureSettings,
1070 if (featureSettings == null)
1075 FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
1076 .getFeatureRenderer();
1077 List<String> origRenderOrder = new ArrayList(),
1078 origGroups = new ArrayList();
1079 // preserve original render order - allows differentiation between user configured colours and autogenerated ones
1080 origRenderOrder.addAll(fr.getRenderOrder());
1081 origGroups.addAll(fr.getFeatureGroups());
1083 fr.findAllFeatures(true);
1084 List<String> renderOrder = fr.getRenderOrder();
1085 FeaturesDisplayedI displayed = fr.getFeaturesDisplayed();
1088 // only clear displayed features if we are mergeing
1091 // TODO this clears displayed.featuresRegistered - do we care?
1093 // JAL-3330 - JBP - yes we do - calling applyFeatureStyle to a view where
1094 // feature visibility has already been configured is not very friendly
1096 * set feature colour if specified by feature settings
1097 * set visibility of all features
1099 for (String type : renderOrder)
1101 FeatureColourI preferredColour = featureSettings
1102 .getFeatureColour(type);
1103 FeatureMatcherSetI preferredFilters = featureSettings
1104 .getFeatureFilters(type);
1106 FeatureColourI origColour = fr.getFeatureStyle(type);
1107 if (!mergeOnly || (!origRenderOrder.contains(type)
1108 || origColour == null
1109 || (!origColour.isGraduatedColour()
1110 && origColour.getColour() != null
1111 && origColour.getColour().equals(
1112 ColorUtils.createColourFromName(type)))))
1114 // if we are merging, only update if there wasn't already a colour defined for
1116 if (preferredColour != null)
1118 fr.setColour(type, preferredColour);
1120 if (preferredFilters != null
1121 && (!mergeOnly || fr.getFeatureFilter(type) != null))
1123 fr.setFeatureFilter(type, preferredFilters);
1125 if (featureSettings.isFeatureDisplayed(type))
1127 displayed.setVisible(type);
1133 * set visibility of feature groups
1135 for (String group : fr.getFeatureGroups())
1137 if (!mergeOnly || !origGroups.contains(group))
1139 // when merging, display groups only if the aren't already marked as not visible
1140 fr.setGroupVisibility(group,
1141 featureSettings.isGroupDisplayed(group));
1146 * order the features
1148 if (featureSettings.optimiseOrder())
1150 // TODO not supported (yet?)
1154 fr.orderFeatures(featureSettings);
1156 fr.setTransparency(featureSettings.getTransparency());
1159 public String getViewName()
1164 public void setViewName(String viewName)
1166 this.viewName = viewName;