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.NJTree;
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.PDBEntry;
39 import jalview.datamodel.SearchResults;
40 import jalview.datamodel.SearchResultsI;
41 import jalview.datamodel.Sequence;
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.viewmodel.ViewportRanges;
55 import jalview.ws.params.AutoCalcSetting;
57 import java.awt.Container;
58 import java.awt.Dimension;
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 implements
79 NJTree currentTree = null;
81 boolean cursorMode = false;
83 boolean antiAlias = false;
85 private Rectangle explodedGeometry;
90 * Flag set true on the view that should 'gather' multiple views of the same
91 * sequence set id when a project is reloaded. Set false on all views when
92 * they are 'exploded' into separate windows. Set true on the current view
93 * when 'Gather' is performed, and also on the first tab when the first new
96 private boolean gatherViewsHere = false;
98 private AnnotationColumnChooser annotationColumnSelectionState;
101 * Creates a new AlignViewport object.
106 public AlignViewport(AlignmentI al)
113 * Create a new AlignViewport object with a specific sequence set ID
117 * (may be null - but potential for ambiguous constructor exception)
119 public AlignViewport(AlignmentI al, String seqsetid)
121 this(al, seqsetid, null);
124 public AlignViewport(AlignmentI al, String seqsetid, String viewid)
126 sequenceSetID = seqsetid;
128 // TODO remove these once 2.4.VAMSAS release finished
129 if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
131 Cache.log.debug("Setting viewport's sequence set id : "
134 if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
136 Cache.log.debug("Setting viewport's view id : " + viewId);
143 * Create a new AlignViewport with hidden regions
147 * @param hiddenColumns
150 public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
153 if (hiddenColumns != null)
155 colSel = hiddenColumns;
161 * New viewport with hidden columns and an existing sequence set id
164 * @param hiddenColumns
168 public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
171 this(al, hiddenColumns, seqsetid, null);
175 * New viewport with hidden columns and an existing sequence set id and viewid
178 * @param hiddenColumns
184 public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
185 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)
192 Cache.log.debug("Setting viewport's sequence set id : "
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 colSel = 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(Cache
227 .getDefault("SHOW_UNCONSERVED", false));
228 sortByTree = Cache.getDefault("SORT_BY_TREE", false);
229 followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
230 sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault(
231 Preferences.SORT_ANNOTATIONS,
232 SequenceAnnotationOrder.NONE.name()));
233 showAutocalculatedAbove = Cache.getDefault(
234 Preferences.SHOW_AUTOCALC_ABOVE, false);
235 viewStyle.setScaleProteinAsCdna(Cache.getDefault(
236 Preferences.SCALE_PROTEIN_TO_CDNA, true));
241 ranges = new ViewportRanges(this.alignment);
242 applyViewProperties();
244 String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
245 String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
246 String fontSize = Cache.getDefault("FONT_SIZE", "10");
250 if (fontStyle.equals("bold"))
254 else if (fontStyle.equals("italic"))
259 setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
262 .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
264 // We must set conservation and consensus before setting colour,
265 // as Blosum and Clustal require this to be done
266 if (hconsensus == null && !isDataset)
268 if (!alignment.isNucleotide())
270 showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
271 showQuality = Cache.getDefault("SHOW_QUALITY", true);
272 showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
275 showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
277 showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
278 normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
280 showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
281 showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
283 initAutoAnnotation();
284 String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
285 : Preferences.DEFAULT_COLOUR_PROT;
286 String schemeName = Cache.getProperty(colourProperty);
287 if (schemeName == null)
289 // only DEFAULT_COLOUR available in Jalview before 2.9
290 schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
291 ResidueColourScheme.NONE);
293 ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(
294 alignment, schemeName);
295 residueShading = new ResidueShader(colourScheme);
297 if (colourScheme instanceof UserColourScheme)
299 residueShading = new ResidueShader(
300 UserDefinedColours.loadDefaultColours());
301 residueShading.setThreshold(0, isIgnoreGapsConsensus());
304 if (residueShading != null)
306 residueShading.setConsensus(hconsensus);
311 * get the consensus sequence as displayed under the PID consensus annotation
314 * @return consensus sequence as a new sequence object
316 public SequenceI getConsensusSeq()
318 if (consensus == null)
320 updateConsensus(null);
322 if (consensus == null)
326 StringBuffer seqs = new StringBuffer();
327 for (int i = 0; i < consensus.annotations.length; i++)
329 if (consensus.annotations[i] != null)
331 if (consensus.annotations[i].description.charAt(0) == '[')
333 seqs.append(consensus.annotations[i].description.charAt(1));
337 seqs.append(consensus.annotations[i].displayCharacter);
342 SequenceI sq = new Sequence("Consensus", seqs.toString());
343 sq.setDescription("Percentage Identity Consensus "
344 + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
348 boolean validCharWidth;
351 * update view settings with the given font. You may need to call
352 * alignPanel.fontChanged to update the layout geometry
355 * when true, charWidth/height is set according to font mentrics
357 public void setFont(Font f, boolean setGrid)
361 Container c = new Container();
363 java.awt.FontMetrics fm = c.getFontMetrics(font);
364 int w = viewStyle.getCharWidth(), ww = fm.charWidth('M'), h = viewStyle
368 setCharHeight(fm.getHeight());
371 viewStyle.setFontName(font.getName());
372 viewStyle.setFontStyle(font.getStyle());
373 viewStyle.setFontSize(font.getSize());
375 validCharWidth = true;
379 public void setViewStyle(ViewStyleI settingsForView)
381 super.setViewStyle(settingsForView);
382 setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
383 viewStyle.getFontSize()), false);
389 * @return DOCUMENT ME!
391 public Font getFont()
403 public void setAlignment(AlignmentI align)
405 replaceMappings(align);
406 super.setAlignment(align);
410 * Replace any codon mappings for this viewport with those for the given
415 public void replaceMappings(AlignmentI align)
419 * Deregister current mappings (if any)
421 deregisterMappings();
424 * Register new mappings (if any)
428 StructureSelectionManager ssm = StructureSelectionManager
429 .getStructureSelectionManager(Desktop.instance);
430 ssm.registerMappings(align.getCodonFrames());
434 * replace mappings on our alignment
436 if (alignment != null && align != null)
438 alignment.setCodonFrames(align.getCodonFrames());
442 protected void deregisterMappings()
444 AlignmentI al = getAlignment();
447 List<AlignedCodonFrame> mappings = al.getCodonFrames();
448 if (mappings != null)
450 StructureSelectionManager ssm = StructureSelectionManager
451 .getStructureSelectionManager(Desktop.instance);
452 for (AlignedCodonFrame acf : mappings)
454 if (noReferencesTo(acf))
456 ssm.deregisterMapping(acf);
466 * @return DOCUMENT ME!
469 public char getGapCharacter()
471 return getAlignment().getGapCharacter();
480 public void setGapCharacter(char gap)
482 if (getAlignment() != null)
484 getAlignment().setGapCharacter(gap);
494 public void setCurrentTree(NJTree tree)
502 * @return DOCUMENT ME!
504 public NJTree getCurrentTree()
510 * returns the visible column regions of the alignment
512 * @param selectedRegionOnly
513 * true to just return the contigs intersecting with the selected
517 public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
519 int[] viscontigs = null;
520 int start = 0, end = 0;
521 if (selectedRegionOnly && selectionGroup != null)
523 start = selectionGroup.getStartRes();
524 end = selectionGroup.getEndRes() + 1;
528 end = alignment.getWidth();
530 viscontigs = colSel.getVisibleContigs(start, end);
535 * get hash of undo and redo list for the alignment
537 * @return long[] { historyList.hashCode, redoList.hashCode };
539 public long[] getUndoRedoHash()
542 if (historyList == null || redoList == null)
544 return new long[] { -1, -1 };
546 return new long[] { historyList.hashCode(), this.redoList.hashCode() };
550 * test if a particular set of hashcodes are different to the hashcodes for
551 * the undo and redo list.
554 * the stored set of hashcodes as returned by getUndoRedoHash
555 * @return true if the hashcodes differ (ie the alignment has been edited) or
556 * the stored hashcode array differs in size
558 public boolean isUndoRedoHashModified(long[] undoredo)
560 if (undoredo == null)
564 long[] cstate = getUndoRedoHash();
565 if (cstate.length != undoredo.length)
570 for (int i = 0; i < cstate.length; i++)
572 if (cstate[i] != undoredo[i])
580 public boolean followSelection = true;
583 * @return true if view selection should always follow the selections
584 * broadcast by other selection sources
586 public boolean getFollowSelection()
588 return followSelection;
592 * Send the current selection to be broadcast to any selection listeners.
595 public void sendSelection()
597 jalview.structure.StructureSelectionManager
598 .getStructureSelectionManager(Desktop.instance).sendSelection(
599 new SequenceGroup(getSelectionGroup()),
600 new ColumnSelection(getColumnSelection()), this);
604 * return the alignPanel containing the given viewport. Use this to get the
605 * components currently handling the given viewport.
608 * @return null or an alignPanel guaranteed to have non-null alignFrame
611 public AlignmentPanel getAlignPanel()
613 AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this
614 .getSequenceSetId());
615 for (int p = 0; aps != null && p < aps.length; p++)
617 if (aps[p].av == this)
625 public boolean getSortByTree()
630 public void setSortByTree(boolean sort)
636 * Returns the (Desktop) instance of the StructureSelectionManager
639 public StructureSelectionManager getStructureSelectionManager()
641 return StructureSelectionManager
642 .getStructureSelectionManager(Desktop.instance);
648 * @return an array of SequenceI arrays, one for each PDBEntry, listing which
649 * sequences in the alignment hold a reference to it
651 public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
653 List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
654 for (PDBEntry pdb : pdbEntries)
656 List<SequenceI> choosenSeqs = new ArrayList<SequenceI>();
657 for (SequenceI sq : alignment.getSequences())
659 Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence()
661 if (pdbRefEntries == null)
665 for (PDBEntry pdbRefEntry : pdbRefEntries)
667 if (pdbRefEntry.getId().equals(pdb.getId()))
669 if (pdbRefEntry.getChainCode() != null
670 && pdb.getChainCode() != null)
672 if (pdbRefEntry.getChainCode().equalsIgnoreCase(
674 && !choosenSeqs.contains(sq))
682 if (!choosenSeqs.contains(sq))
693 .add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
695 return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
699 public boolean isNormaliseSequenceLogo()
701 return normaliseSequenceLogo;
704 public void setNormaliseSequenceLogo(boolean state)
706 normaliseSequenceLogo = state;
711 * @return true if alignment characters should be displayed
714 public boolean isValidCharWidth()
716 return validCharWidth;
719 private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
721 public AutoCalcSetting getCalcIdSettingsFor(String calcId)
723 return calcIdParams.get(calcId);
726 public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings,
729 calcIdParams.put(calcId, settings);
730 // TODO: create a restart list to trigger any calculations that need to be
731 // restarted after load
732 // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
735 Cache.log.debug("trigger update for " + calcId);
740 * Method called when another alignment's edit (or possibly other) command is
743 * To allow for sequence mappings (e.g. protein to cDNA), we have to first
744 * 'unwind' the command on the source sequences (in simulation, not in fact),
745 * and then for each edit in turn:
747 * <li>compute the equivalent edit on the mapped sequences</li>
748 * <li>apply the mapped edit</li>
749 * <li>'apply' the source edit to the working copy of the source sequences</li>
757 public void mirrorCommand(CommandI command, boolean undo,
758 StructureSelectionManager ssm, VamsasSource source)
761 * Do nothing unless we are a 'complement' of the source. May replace this
762 * with direct calls not via SSM.
764 if (source instanceof AlignViewportI
765 && ((AlignViewportI) source).getCodingComplement() == this)
774 CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
776 if (mappedCommand != null)
778 AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments();
779 mappedCommand.doCommand(views);
780 getAlignPanel().alignmentChanged();
785 * Add the sequences from the given alignment to this viewport. Optionally,
786 * may give the user the option to open a new frame, or split panel, with cDNA
787 * and protein linked.
792 public void addAlignment(AlignmentI toAdd, String title)
794 // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different
796 // JBPComment: title is a largely redundant parameter at the moment
797 // JBPComment: this really should be an 'insert/pre/append' controller
798 // JBPComment: but the DNA/Protein check makes it a bit more complex
800 // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with
802 // TODO: create undo object for this JAL-1101
805 * Ensure datasets are created for the new alignment as
806 * mappings operate on dataset sequences
808 toAdd.setDataset(null);
811 * Check if any added sequence could be the object of a mapping or
812 * cross-reference; if so, make the mapping explicit
814 getAlignment().realiseMappings(toAdd.getSequences());
817 * If any cDNA/protein mappings exist or can be made between the alignments,
818 * offer to open a split frame with linked alignments
820 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
822 if (AlignmentUtils.isMappable(toAdd, getAlignment()))
824 if (openLinkedAlignment(toAdd, title))
832 * No mappings, or offer declined - add sequences to this alignment
834 // TODO: JAL-407 regardless of above - identical sequences (based on ID and
835 // provenance) should share the same dataset sequence
837 AlignmentI al = getAlignment();
838 String gap = String.valueOf(al.getGapCharacter());
839 for (int i = 0; i < toAdd.getHeight(); i++)
841 SequenceI seq = toAdd.getSequenceAt(i);
844 * - 'align' any mapped sequences as per existing
845 * e.g. cdna to genome, domain hit to protein sequence
846 * very experimental! (need a separate menu option for this)
847 * - only add mapped sequences ('select targets from a dataset')
849 if (true /*AlignmentUtils.alignSequenceAs(seq, al, gap, true, true)*/)
855 ranges.setEndSeq(getAlignment().getHeight());
856 firePropertyChange("alignment", null, getAlignment().getSequences());
860 * Show a dialog with the option to open and link (cDNA <-> protein) as a new
861 * alignment, either as a standalone alignment or in a split frame. Returns
862 * true if the new alignment was opened, false if not, because the user
863 * declined the offer.
868 protected boolean openLinkedAlignment(AlignmentI al, String title)
870 String[] options = new String[] {
871 MessageManager.getString("action.no"),
872 MessageManager.getString("label.split_window"),
873 MessageManager.getString("label.new_window"), };
874 final String question = JvSwingUtils.wrapTooltip(true,
875 MessageManager.getString("label.open_split_window?"));
876 int response = JvOptionPane.showOptionDialog(Desktop.desktop, question,
877 MessageManager.getString("label.open_split_window"),
878 JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
879 options, options[0]);
881 if (response != 1 && response != 2)
885 final boolean openSplitPane = (response == 1);
886 final boolean openInNewWindow = (response == 2);
889 * Identify protein and dna alignments. Make a copy of this one if opening
890 * in a new split pane.
892 AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment())
894 AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
895 final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
898 * Map sequences. At least one should get mapped as we have already passed
899 * the test for 'mappability'. Any mappings made will be added to the
900 * protein alignment. Note creating dataset sequences on the new alignment
901 * is a pre-requisite for building mappings.
904 AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna);
907 * Create the AlignFrame for the added alignment. If it is protein, mappings
908 * are registered with StructureSelectionManager as a side-effect.
910 AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
911 AlignFrame.DEFAULT_HEIGHT);
912 newAlignFrame.setTitle(title);
913 newAlignFrame.statusBar.setText(MessageManager.formatMessage(
914 "label.successfully_loaded_file", new Object[] { title }));
916 // TODO if we want this (e.g. to enable reload of the alignment from file),
917 // we will need to add parameters to the stack.
918 // if (!protocol.equals(DataSourceType.PASTE))
920 // alignFrame.setFileName(file, format);
925 Desktop.addInternalFrame(newAlignFrame, title,
926 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
931 newAlignFrame.setMaximum(jalview.bin.Cache.getDefault(
932 "SHOW_FULLSCREEN", false));
933 } catch (java.beans.PropertyVetoException ex)
939 al.alignAs(thisAlignment);
940 protein = openSplitFrame(newAlignFrame, thisAlignment);
947 * Helper method to open a new SplitFrame holding linked dna and protein
950 * @param newAlignFrame
951 * containing a new alignment to be shown
953 * cdna/protein complement alignment to show in the other split half
954 * @return the protein alignment in the split frame
956 protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
957 AlignmentI complement)
960 * Make a new frame with a copy of the alignment we are adding to. If this
961 * is protein, the mappings to cDNA will be registered with
962 * StructureSelectionManager as a side-effect.
964 AlignFrame copyMe = new AlignFrame(complement,
965 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
966 copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
968 AlignmentI al = newAlignFrame.viewport.getAlignment();
969 final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
971 final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe;
972 cdnaFrame.setVisible(true);
973 proteinFrame.setVisible(true);
974 String linkedTitle = MessageManager
975 .getString("label.linked_view_title");
978 * Open in split pane. DNA sequence above, protein below.
980 JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
981 Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
983 return proteinFrame.viewport.getAlignment();
986 public AnnotationColumnChooser getAnnotationColumnSelectionState()
988 return annotationColumnSelectionState;
991 public void setAnnotationColumnSelectionState(
992 AnnotationColumnChooser currentAnnotationColumnSelectionState)
994 this.annotationColumnSelectionState = currentAnnotationColumnSelectionState;
998 public void setIdWidth(int i)
1000 super.setIdWidth(i);
1001 AlignmentPanel ap = getAlignPanel();
1004 // modify GUI elements to reflect geometry change
1005 Dimension idw = getAlignPanel().getIdPanel().getIdCanvas()
1006 .getPreferredSize();
1008 getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw);
1012 public Rectangle getExplodedGeometry()
1014 return explodedGeometry;
1017 public void setExplodedGeometry(Rectangle explodedPosition)
1019 this.explodedGeometry = explodedPosition;
1022 public boolean isGatherViewsHere()
1024 return gatherViewsHere;
1027 public void setGatherViewsHere(boolean gatherViewsHere)
1029 this.gatherViewsHere = gatherViewsHere;
1033 * If this viewport has a (Protein/cDNA) complement, then scroll the
1034 * complementary alignment to match this one.
1036 public void scrollComplementaryAlignment()
1039 * Populate a SearchResults object with the mapped location to scroll to. If
1040 * there is no complement, or it is not following highlights, or no mapping
1041 * is found, the result will be empty.
1043 SearchResultsI sr = new SearchResults();
1044 int verticalOffset = findComplementScrollTarget(sr);
1047 // TODO would like next line without cast but needs more refactoring...
1048 final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
1050 complementPanel.setDontScrollComplement(true);
1051 complementPanel.scrollToCentre(sr, verticalOffset);
1056 * Answers true if no alignment holds a reference to the given mapping
1061 protected boolean noReferencesTo(AlignedCodonFrame acf)
1063 AlignFrame[] frames = Desktop.getAlignFrames();
1068 for (AlignFrame af : frames)
1072 for (AlignmentViewPanel ap : af.getAlignPanels())
1074 AlignmentI al = ap.getAlignment();
1075 if (al != null && al.getCodonFrames().contains(acf))
1086 * Applies the supplied feature settings descriptor to currently known
1087 * features. This supports an 'initial configuration' of feature colouring
1088 * based on a preset or user favourite. This may then be modified in the usual
1089 * way using the Feature Settings dialogue.
1091 * @param featureSettings
1094 public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
1096 if (featureSettings == null)
1101 FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
1102 .getFeatureRenderer();
1103 fr.findAllFeatures(true);
1104 List<String> renderOrder = fr.getRenderOrder();
1105 FeaturesDisplayedI displayed = fr.getFeaturesDisplayed();
1107 // TODO this clears displayed.featuresRegistered - do we care?
1110 * set feature colour if specified by feature settings
1111 * set visibility of all features
1113 for (String type : renderOrder)
1115 FeatureColourI preferredColour = featureSettings
1116 .getFeatureColour(type);
1117 if (preferredColour != null)
1119 fr.setColour(type, preferredColour);
1121 if (featureSettings.isFeatureDisplayed(type))
1123 displayed.setVisible(type);
1128 * set visibility of feature groups
1130 for (String group : fr.getFeatureGroups())
1132 fr.setGroupVisibility(group, featureSettings.isGroupDisplayed(group));
1136 * order the features
1138 if (featureSettings.optimiseOrder())
1140 // TODO not supported (yet?)
1144 fr.orderFeatures(featureSettings);
1146 fr.setTransparency(featureSettings.getTransparency());