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.analysis.TreeModel;
26 import jalview.api.AlignViewportI;
27 import jalview.api.AlignmentViewPanel;
28 import jalview.api.FeatureColourI;
29 import jalview.api.FeatureSettingsModelI;
30 import jalview.api.FeaturesDisplayedI;
31 import jalview.api.ViewStyleI;
32 import jalview.bin.Cache;
33 import jalview.commands.CommandI;
34 import jalview.datamodel.AlignedCodonFrame;
35 import jalview.datamodel.Alignment;
36 import jalview.datamodel.AlignmentI;
37 import jalview.datamodel.ColumnSelection;
38 import jalview.datamodel.HiddenColumns;
39 import jalview.datamodel.PDBEntry;
40 import jalview.datamodel.SearchResults;
41 import jalview.datamodel.SearchResultsI;
42 import jalview.datamodel.SequenceGroup;
43 import jalview.datamodel.SequenceI;
44 import jalview.renderer.ResidueShader;
45 import jalview.schemes.ColourSchemeI;
46 import jalview.schemes.ColourSchemeProperty;
47 import jalview.schemes.ResidueColourScheme;
48 import jalview.schemes.UserColourScheme;
49 import jalview.structure.SelectionSource;
50 import jalview.structure.StructureSelectionManager;
51 import jalview.structure.VamsasSource;
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.List;
64 import java.util.Vector;
66 import javax.swing.JInternalFrame;
72 * @version $Revision: 1.141 $
74 public class AlignViewport extends AlignmentViewport
75 implements SelectionSource
79 boolean cursorMode = false;
81 boolean antiAlias = false;
83 private Rectangle explodedGeometry;
88 * Flag set true on the view that should 'gather' multiple views of the same
89 * sequence set id when a project is reloaded. Set false on all views when
90 * they are 'exploded' into separate windows. Set true on the current view
91 * when 'Gather' is performed, and also on the first tab when the first new
94 private boolean gatherViewsHere = false;
96 private AnnotationColumnChooser annotationColumnSelectionState;
99 * Creates a new AlignViewport object.
104 public AlignViewport(AlignmentI al)
111 * Create a new AlignViewport object with a specific sequence set ID
115 * (may be null - but potential for ambiguous constructor exception)
117 public AlignViewport(AlignmentI al, String seqsetid)
119 this(al, seqsetid, null);
122 public AlignViewport(AlignmentI al, String seqsetid, String viewid)
125 sequenceSetID = seqsetid;
127 // TODO remove these once 2.4.VAMSAS release finished
128 if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
131 "Setting viewport's sequence set id : " + sequenceSetID);
133 if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
135 Cache.log.debug("Setting viewport's view id : " + viewId);
142 * Create a new AlignViewport with hidden regions
146 * @param hiddenColumns
149 public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns)
152 if (hiddenColumns != null)
154 al.setHiddenColumns(hiddenColumns);
160 * New viewport with hidden columns and an existing sequence set id
163 * @param hiddenColumns
167 public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
170 this(al, hiddenColumns, seqsetid, null);
174 * New viewport with hidden columns and an existing sequence set id and viewid
177 * @param hiddenColumns
183 public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
184 String seqsetid, String viewid)
187 sequenceSetID = seqsetid;
189 // TODO remove these once 2.4.VAMSAS release finished
190 if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
193 "Setting viewport's sequence set id : " + sequenceSetID);
195 if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
197 Cache.log.debug("Setting viewport's view id : " + viewId);
200 if (hiddenColumns != null)
202 al.setHiddenColumns(hiddenColumns);
208 * Apply any settings saved in user preferences
210 private void applyViewProperties()
212 antiAlias = Cache.getDefault("ANTI_ALIAS", false);
214 viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
215 setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
217 setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
218 setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false));
219 autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
221 setPadGaps(Cache.getDefault("PAD_GAPS", true));
222 setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
223 setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
224 viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true));
225 viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false));
226 viewStyle.setShowUnconserved(
227 Cache.getDefault("SHOW_UNCONSERVED", false));
228 sortByTree = Cache.getDefault("SORT_BY_TREE", false);
229 followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
230 sortAnnotationsBy = SequenceAnnotationOrder
231 .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
232 SequenceAnnotationOrder.NONE.name()));
233 showAutocalculatedAbove = Cache
234 .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
235 viewStyle.setScaleProteinAsCdna(
236 Cache.getDefault(Preferences.SCALE_PROTEIN_TO_CDNA, true));
241 applyViewProperties();
243 String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
244 String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
245 String fontSize = Cache.getDefault("FONT_SIZE", "10");
249 if (fontStyle.equals("bold"))
253 else if (fontStyle.equals("italic"))
258 setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
261 .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
263 // We must set conservation and consensus before setting colour,
264 // as Blosum and Clustal require this to be done
265 if (hconsensus == null && !isDataset)
267 if (!alignment.isNucleotide())
269 showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
270 showQuality = Cache.getDefault("SHOW_QUALITY", true);
271 showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
274 showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
276 showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
277 normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
279 showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
280 showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
282 showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
284 initAutoAnnotation();
285 String colourProperty = alignment.isNucleotide()
286 ? Preferences.DEFAULT_COLOUR_NUC
287 : Preferences.DEFAULT_COLOUR_PROT;
288 String schemeName = Cache.getProperty(colourProperty);
289 if (schemeName == null)
291 // only DEFAULT_COLOUR available in Jalview before 2.9
292 schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
293 ResidueColourScheme.NONE);
295 ColourSchemeI colourScheme = ColourSchemeProperty
296 .getColourScheme(alignment, schemeName);
297 residueShading = new ResidueShader(colourScheme);
299 if (colourScheme instanceof UserColourScheme)
301 residueShading = new ResidueShader(
302 UserDefinedColours.loadDefaultColours());
303 residueShading.setThreshold(0, isIgnoreGapsConsensus());
306 if (residueShading != null)
308 residueShading.setConsensus(hconsensus);
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 int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
458 int[] viscontigs = null;
459 int start = 0, end = 0;
460 if (selectedRegionOnly && selectionGroup != null)
462 start = selectionGroup.getStartRes();
463 end = selectionGroup.getEndRes() + 1;
467 end = alignment.getWidth();
469 viscontigs = alignment.getHiddenColumns().getVisibleContigs(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);
589 * @return an array of SequenceI arrays, one for each PDBEntry, listing which
590 * sequences in the alignment hold a reference to it
592 public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
594 List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
595 for (PDBEntry pdb : pdbEntries)
597 List<SequenceI> choosenSeqs = new ArrayList<SequenceI>();
598 for (SequenceI sq : alignment.getSequences())
600 Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence()
602 if (pdbRefEntries == null)
606 for (PDBEntry pdbRefEntry : pdbRefEntries)
608 if (pdbRefEntry.getId().equals(pdb.getId()))
610 if (pdbRefEntry.getChainCode() != null
611 && pdb.getChainCode() != null)
613 if (pdbRefEntry.getChainCode().equalsIgnoreCase(
614 pdb.getChainCode()) && !choosenSeqs.contains(sq))
622 if (!choosenSeqs.contains(sq))
633 .add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
635 return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
639 public boolean isNormaliseSequenceLogo()
641 return normaliseSequenceLogo;
644 public void setNormaliseSequenceLogo(boolean state)
646 normaliseSequenceLogo = state;
651 * @return true if alignment characters should be displayed
654 public boolean isValidCharWidth()
656 return validCharWidth;
659 private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
661 public AutoCalcSetting getCalcIdSettingsFor(String calcId)
663 return calcIdParams.get(calcId);
666 public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings,
669 calcIdParams.put(calcId, settings);
670 // TODO: create a restart list to trigger any calculations that need to be
671 // restarted after load
672 // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
675 Cache.log.debug("trigger update for " + calcId);
680 * Method called when another alignment's edit (or possibly other) command is
683 * To allow for sequence mappings (e.g. protein to cDNA), we have to first
684 * 'unwind' the command on the source sequences (in simulation, not in fact),
685 * and then for each edit in turn:
687 * <li>compute the equivalent edit on the mapped sequences</li>
688 * <li>apply the mapped edit</li>
689 * <li>'apply' the source edit to the working copy of the source
698 public void mirrorCommand(CommandI command, boolean undo,
699 StructureSelectionManager ssm, VamsasSource source)
702 * Do nothing unless we are a 'complement' of the source. May replace this
703 * with direct calls not via SSM.
705 if (source instanceof AlignViewportI
706 && ((AlignViewportI) source).getCodingComplement() == this)
715 CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
717 if (mappedCommand != null)
719 AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments();
720 mappedCommand.doCommand(views);
721 getAlignPanel().alignmentChanged();
726 * Add the sequences from the given alignment to this viewport. Optionally,
727 * may give the user the option to open a new frame, or split panel, with cDNA
728 * and protein linked.
733 public void addAlignment(AlignmentI toAdd, String title)
735 // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different
737 // JBPComment: title is a largely redundant parameter at the moment
738 // JBPComment: this really should be an 'insert/pre/append' controller
739 // JBPComment: but the DNA/Protein check makes it a bit more complex
741 // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with
743 // TODO: create undo object for this JAL-1101
746 * Ensure datasets are created for the new alignment as
747 * mappings operate on dataset sequences
749 toAdd.setDataset(null);
752 * Check if any added sequence could be the object of a mapping or
753 * cross-reference; if so, make the mapping explicit
755 getAlignment().realiseMappings(toAdd.getSequences());
758 * If any cDNA/protein mappings exist or can be made between the alignments,
759 * offer to open a split frame with linked alignments
761 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
763 if (AlignmentUtils.isMappable(toAdd, getAlignment()))
765 if (openLinkedAlignment(toAdd, title))
773 * No mappings, or offer declined - add sequences to this alignment
775 // TODO: JAL-407 regardless of above - identical sequences (based on ID and
776 // provenance) should share the same dataset sequence
778 AlignmentI al = getAlignment();
779 String gap = String.valueOf(al.getGapCharacter());
780 for (int i = 0; i < toAdd.getHeight(); i++)
782 SequenceI seq = toAdd.getSequenceAt(i);
785 * - 'align' any mapped sequences as per existing
786 * e.g. cdna to genome, domain hit to protein sequence
787 * very experimental! (need a separate menu option for this)
788 * - only add mapped sequences ('select targets from a dataset')
790 if (true /*AlignmentUtils.alignSequenceAs(seq, al, gap, true, true)*/)
796 ranges.setEndSeq(getAlignment().getHeight());
797 firePropertyChange("alignment", null, getAlignment().getSequences());
801 * Show a dialog with the option to open and link (cDNA <-> protein) as a new
802 * alignment, either as a standalone alignment or in a split frame. Returns
803 * true if the new alignment was opened, false if not, because the user
804 * declined the offer.
809 protected boolean openLinkedAlignment(AlignmentI al, String title)
811 String[] options = new String[] { MessageManager.getString("action.no"),
812 MessageManager.getString("label.split_window"),
813 MessageManager.getString("label.new_window"), };
814 final String question = JvSwingUtils.wrapTooltip(true,
815 MessageManager.getString("label.open_split_window?"));
816 int response = JvOptionPane.showOptionDialog(Desktop.desktop, question,
817 MessageManager.getString("label.open_split_window"),
818 JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
819 options, options[0]);
821 if (response != 1 && response != 2)
825 final boolean openSplitPane = (response == 1);
826 final boolean openInNewWindow = (response == 2);
829 * Identify protein and dna alignments. Make a copy of this one if opening
830 * in a new split pane.
832 AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment())
834 AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
835 final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
838 * Map sequences. At least one should get mapped as we have already passed
839 * the test for 'mappability'. Any mappings made will be added to the
840 * protein alignment. Note creating dataset sequences on the new alignment
841 * is a pre-requisite for building mappings.
844 AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna);
847 * Create the AlignFrame for the added alignment. If it is protein, mappings
848 * are registered with StructureSelectionManager as a side-effect.
850 AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
851 AlignFrame.DEFAULT_HEIGHT);
852 newAlignFrame.setTitle(title);
853 newAlignFrame.statusBar.setText(MessageManager
854 .formatMessage("label.successfully_loaded_file", new Object[]
857 // TODO if we want this (e.g. to enable reload of the alignment from file),
858 // we will need to add parameters to the stack.
859 // if (!protocol.equals(DataSourceType.PASTE))
861 // alignFrame.setFileName(file, format);
866 Desktop.addInternalFrame(newAlignFrame, title,
867 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
872 newAlignFrame.setMaximum(
873 jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
874 } catch (java.beans.PropertyVetoException ex)
880 al.alignAs(thisAlignment);
881 protein = openSplitFrame(newAlignFrame, thisAlignment);
888 * Helper method to open a new SplitFrame holding linked dna and protein
891 * @param newAlignFrame
892 * containing a new alignment to be shown
894 * cdna/protein complement alignment to show in the other split half
895 * @return the protein alignment in the split frame
897 protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
898 AlignmentI complement)
901 * Make a new frame with a copy of the alignment we are adding to. If this
902 * is protein, the mappings to cDNA will be registered with
903 * StructureSelectionManager as a side-effect.
905 AlignFrame copyMe = new AlignFrame(complement, AlignFrame.DEFAULT_WIDTH,
906 AlignFrame.DEFAULT_HEIGHT);
907 copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
909 AlignmentI al = newAlignFrame.viewport.getAlignment();
910 final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
912 final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe;
913 cdnaFrame.setVisible(true);
914 proteinFrame.setVisible(true);
915 String linkedTitle = MessageManager
916 .getString("label.linked_view_title");
919 * Open in split pane. DNA sequence above, protein below.
921 JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
922 Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
924 return proteinFrame.viewport.getAlignment();
927 public AnnotationColumnChooser getAnnotationColumnSelectionState()
929 return annotationColumnSelectionState;
932 public void setAnnotationColumnSelectionState(
933 AnnotationColumnChooser currentAnnotationColumnSelectionState)
935 this.annotationColumnSelectionState = currentAnnotationColumnSelectionState;
939 public void setIdWidth(int i)
942 AlignmentPanel ap = getAlignPanel();
945 // modify GUI elements to reflect geometry change
946 Dimension idw = getAlignPanel().getIdPanel().getIdCanvas()
949 getAlignPanel().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.getAlignFrames();
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 if (featureSettings == null)
1043 FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
1044 .getFeatureRenderer();
1045 fr.findAllFeatures(true);
1046 List<String> renderOrder = fr.getRenderOrder();
1047 FeaturesDisplayedI displayed = fr.getFeaturesDisplayed();
1049 // TODO this clears displayed.featuresRegistered - do we care?
1052 * set feature colour if specified by feature settings
1053 * set visibility of all features
1055 for (String type : renderOrder)
1057 FeatureColourI preferredColour = featureSettings
1058 .getFeatureColour(type);
1059 if (preferredColour != null)
1061 fr.setColour(type, preferredColour);
1063 if (featureSettings.isFeatureDisplayed(type))
1065 displayed.setVisible(type);
1070 * set visibility of feature groups
1072 for (String group : fr.getFeatureGroups())
1074 fr.setGroupVisibility(group, featureSettings.isGroupDisplayed(group));
1078 * order the features
1080 if (featureSettings.optimiseOrder())
1082 // TODO not supported (yet?)
1086 fr.orderFeatures(featureSettings);
1088 fr.setTransparency(featureSettings.getTransparency());