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.FontMetrics;
61 import java.awt.Rectangle;
62 import java.util.ArrayList;
63 import java.util.Hashtable;
64 import java.util.List;
65 import java.util.Vector;
67 import javax.swing.JInternalFrame;
73 * @version $Revision: 1.141 $
75 public class AlignViewport extends AlignmentViewport implements
80 NJTree currentTree = null;
82 boolean cursorMode = false;
84 boolean antiAlias = false;
86 private Rectangle explodedGeometry;
91 * Flag set true on the view that should 'gather' multiple views of the same
92 * sequence set id when a project is reloaded. Set false on all views when
93 * they are 'exploded' into separate windows. Set true on the current view
94 * when 'Gather' is performed, and also on the first tab when the first new
97 private boolean gatherViewsHere = false;
99 private AnnotationColumnChooser annotationColumnSelectionState;
102 * Creates a new AlignViewport object.
107 public AlignViewport(AlignmentI al)
114 * Create a new AlignViewport object with a specific sequence set ID
118 * (may be null - but potential for ambiguous constructor exception)
120 public AlignViewport(AlignmentI al, String seqsetid)
122 this(al, seqsetid, null);
125 public AlignViewport(AlignmentI al, String seqsetid, String viewid)
127 sequenceSetID = seqsetid;
129 // TODO remove these once 2.4.VAMSAS release finished
130 if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
132 Cache.log.debug("Setting viewport's sequence set id : "
135 if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
137 Cache.log.debug("Setting viewport's view id : " + viewId);
144 * Create a new AlignViewport with hidden regions
148 * @param hiddenColumns
151 public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
154 if (hiddenColumns != null)
156 colSel = hiddenColumns;
162 * New viewport with hidden columns and an existing sequence set id
165 * @param hiddenColumns
169 public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
172 this(al, hiddenColumns, seqsetid, null);
176 * New viewport with hidden columns and an existing sequence set id and viewid
179 * @param hiddenColumns
185 public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
186 String seqsetid, String viewid)
188 sequenceSetID = seqsetid;
190 // TODO remove these once 2.4.VAMSAS release finished
191 if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
193 Cache.log.debug("Setting viewport's sequence set id : "
196 if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
198 Cache.log.debug("Setting viewport's view id : " + viewId);
201 if (hiddenColumns != null)
203 colSel = hiddenColumns;
209 * Apply any settings saved in user preferences
211 private void applyViewProperties()
213 antiAlias = Cache.getDefault("ANTI_ALIAS", false);
215 viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
216 setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
218 setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
219 setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false));
220 autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
222 setPadGaps(Cache.getDefault("PAD_GAPS", true));
223 setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
224 setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
225 viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true));
226 viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false));
227 viewStyle.setShowUnconserved(Cache
228 .getDefault("SHOW_UNCONSERVED", false));
229 sortByTree = Cache.getDefault("SORT_BY_TREE", false);
230 followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
231 sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault(
232 Preferences.SORT_ANNOTATIONS,
233 SequenceAnnotationOrder.NONE.name()));
234 showAutocalculatedAbove = Cache.getDefault(
235 Preferences.SHOW_AUTOCALC_ABOVE, false);
236 viewStyle.setScaleProteinAsCdna(Cache.getDefault(
237 Preferences.SCALE_PROTEIN_TO_CDNA, true));
242 ranges = new ViewportRanges(this.alignment);
243 applyViewProperties();
245 String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
246 String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
247 String fontSize = Cache.getDefault("FONT_SIZE", "10");
251 if (fontStyle.equals("bold"))
255 else if (fontStyle.equals("italic"))
260 setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
263 .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
265 // We must set conservation and consensus before setting colour,
266 // as Blosum and Clustal require this to be done
267 if (hconsensus == null && !isDataset)
269 if (!alignment.isNucleotide())
271 showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
272 showQuality = Cache.getDefault("SHOW_QUALITY", true);
273 showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
276 showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
278 showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
279 normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
281 showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
282 showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
284 initAutoAnnotation();
285 String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
286 : Preferences.DEFAULT_COLOUR_PROT;
287 String schemeName = Cache.getProperty(colourProperty);
288 if (schemeName == null)
290 // only DEFAULT_COLOUR available in Jalview before 2.9
291 schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
292 ResidueColourScheme.NONE);
294 ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(
295 alignment, schemeName);
296 residueShading = new ResidueShader(colourScheme);
298 if (colourScheme instanceof UserColourScheme)
300 residueShading = new ResidueShader(
301 UserDefinedColours.loadDefaultColours());
302 residueShading.setThreshold(0, isIgnoreGapsConsensus());
305 if (residueShading != null)
307 residueShading.setConsensus(hconsensus);
312 * get the consensus sequence as displayed under the PID consensus annotation
315 * @return consensus sequence as a new sequence object
317 public SequenceI getConsensusSeq()
319 if (consensus == null)
321 updateConsensus(null);
323 if (consensus == null)
327 StringBuffer seqs = new StringBuffer();
328 for (int i = 0; i < consensus.annotations.length; i++)
330 if (consensus.annotations[i] != null)
332 if (consensus.annotations[i].description.charAt(0) == '[')
334 seqs.append(consensus.annotations[i].description.charAt(1));
338 seqs.append(consensus.annotations[i].displayCharacter);
343 SequenceI sq = new Sequence("Consensus", seqs.toString());
344 sq.setDescription("Percentage Identity Consensus "
345 + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
349 boolean validCharWidth;
355 public void setFont(Font f, boolean setGrid)
359 Container c = new Container();
363 FontMetrics fm = c.getFontMetrics(font);
364 int ww = fm.charWidth('M');
365 setCharHeight(fm.getHeight());
368 viewStyle.setFontName(font.getName());
369 viewStyle.setFontStyle(font.getStyle());
370 viewStyle.setFontSize(font.getSize());
372 validCharWidth = true;
376 public void setViewStyle(ViewStyleI settingsForView)
378 super.setViewStyle(settingsForView);
379 setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
380 viewStyle.getFontSize()), false);
386 * @return DOCUMENT ME!
388 public Font getFont()
400 public void setAlignment(AlignmentI align)
402 replaceMappings(align);
403 super.setAlignment(align);
407 * Replace any codon mappings for this viewport with those for the given
412 public void replaceMappings(AlignmentI align)
416 * Deregister current mappings (if any)
418 deregisterMappings();
421 * Register new mappings (if any)
425 StructureSelectionManager ssm = StructureSelectionManager
426 .getStructureSelectionManager(Desktop.instance);
427 ssm.registerMappings(align.getCodonFrames());
431 * replace mappings on our alignment
433 if (alignment != null && align != null)
435 alignment.setCodonFrames(align.getCodonFrames());
439 protected void deregisterMappings()
441 AlignmentI al = getAlignment();
444 List<AlignedCodonFrame> mappings = al.getCodonFrames();
445 if (mappings != null)
447 StructureSelectionManager ssm = StructureSelectionManager
448 .getStructureSelectionManager(Desktop.instance);
449 for (AlignedCodonFrame acf : mappings)
451 if (noReferencesTo(acf))
453 ssm.deregisterMapping(acf);
463 * @return DOCUMENT ME!
466 public char getGapCharacter()
468 return getAlignment().getGapCharacter();
477 public void setGapCharacter(char gap)
479 if (getAlignment() != null)
481 getAlignment().setGapCharacter(gap);
491 public void setCurrentTree(NJTree tree)
499 * @return DOCUMENT ME!
501 public NJTree getCurrentTree()
507 * returns the visible column regions of the alignment
509 * @param selectedRegionOnly
510 * true to just return the contigs intersecting with the selected
514 public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
516 int[] viscontigs = null;
517 int start = 0, end = 0;
518 if (selectedRegionOnly && selectionGroup != null)
520 start = selectionGroup.getStartRes();
521 end = selectionGroup.getEndRes() + 1;
525 end = alignment.getWidth();
527 viscontigs = colSel.getVisibleContigs(start, end);
532 * get hash of undo and redo list for the alignment
534 * @return long[] { historyList.hashCode, redoList.hashCode };
536 public long[] getUndoRedoHash()
539 if (historyList == null || redoList == null)
541 return new long[] { -1, -1 };
543 return new long[] { historyList.hashCode(), this.redoList.hashCode() };
547 * test if a particular set of hashcodes are different to the hashcodes for
548 * the undo and redo list.
551 * the stored set of hashcodes as returned by getUndoRedoHash
552 * @return true if the hashcodes differ (ie the alignment has been edited) or
553 * the stored hashcode array differs in size
555 public boolean isUndoRedoHashModified(long[] undoredo)
557 if (undoredo == null)
561 long[] cstate = getUndoRedoHash();
562 if (cstate.length != undoredo.length)
567 for (int i = 0; i < cstate.length; i++)
569 if (cstate[i] != undoredo[i])
577 public boolean followSelection = true;
580 * @return true if view selection should always follow the selections
581 * broadcast by other selection sources
583 public boolean getFollowSelection()
585 return followSelection;
589 * Send the current selection to be broadcast to any selection listeners.
592 public void sendSelection()
594 jalview.structure.StructureSelectionManager
595 .getStructureSelectionManager(Desktop.instance).sendSelection(
596 new SequenceGroup(getSelectionGroup()),
597 new ColumnSelection(getColumnSelection()), this);
601 * return the alignPanel containing the given viewport. Use this to get the
602 * components currently handling the given viewport.
605 * @return null or an alignPanel guaranteed to have non-null alignFrame
608 public AlignmentPanel getAlignPanel()
610 AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this
611 .getSequenceSetId());
612 for (int p = 0; aps != null && p < aps.length; p++)
614 if (aps[p].av == this)
622 public boolean getSortByTree()
627 public void setSortByTree(boolean sort)
633 * Returns the (Desktop) instance of the StructureSelectionManager
636 public StructureSelectionManager getStructureSelectionManager()
638 return StructureSelectionManager
639 .getStructureSelectionManager(Desktop.instance);
645 * @return an array of SequenceI arrays, one for each PDBEntry, listing which
646 * sequences in the alignment hold a reference to it
648 public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
650 List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
651 for (PDBEntry pdb : pdbEntries)
653 List<SequenceI> choosenSeqs = new ArrayList<SequenceI>();
654 for (SequenceI sq : alignment.getSequences())
656 Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence()
658 if (pdbRefEntries == null)
662 for (PDBEntry pdbRefEntry : pdbRefEntries)
664 if (pdbRefEntry.getId().equals(pdb.getId()))
666 if (pdbRefEntry.getChainCode() != null
667 && pdb.getChainCode() != null)
669 if (pdbRefEntry.getChainCode().equalsIgnoreCase(
671 && !choosenSeqs.contains(sq))
679 if (!choosenSeqs.contains(sq))
690 .add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
692 return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
696 public boolean isNormaliseSequenceLogo()
698 return normaliseSequenceLogo;
701 public void setNormaliseSequenceLogo(boolean state)
703 normaliseSequenceLogo = state;
708 * @return true if alignment characters should be displayed
711 public boolean isValidCharWidth()
713 return validCharWidth;
716 private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
718 public AutoCalcSetting getCalcIdSettingsFor(String calcId)
720 return calcIdParams.get(calcId);
723 public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings,
726 calcIdParams.put(calcId, settings);
727 // TODO: create a restart list to trigger any calculations that need to be
728 // restarted after load
729 // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
732 Cache.log.debug("trigger update for " + calcId);
737 * Method called when another alignment's edit (or possibly other) command is
740 * To allow for sequence mappings (e.g. protein to cDNA), we have to first
741 * 'unwind' the command on the source sequences (in simulation, not in fact),
742 * and then for each edit in turn:
744 * <li>compute the equivalent edit on the mapped sequences</li>
745 * <li>apply the mapped edit</li>
746 * <li>'apply' the source edit to the working copy of the source sequences</li>
754 public void mirrorCommand(CommandI command, boolean undo,
755 StructureSelectionManager ssm, VamsasSource source)
758 * Do nothing unless we are a 'complement' of the source. May replace this
759 * with direct calls not via SSM.
761 if (source instanceof AlignViewportI
762 && ((AlignViewportI) source).getCodingComplement() == this)
771 CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
773 if (mappedCommand != null)
775 AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments();
776 mappedCommand.doCommand(views);
777 getAlignPanel().alignmentChanged();
782 * Add the sequences from the given alignment to this viewport. Optionally,
783 * may give the user the option to open a new frame, or split panel, with cDNA
784 * and protein linked.
789 public void addAlignment(AlignmentI toAdd, String title)
791 // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different
793 // JBPComment: title is a largely redundant parameter at the moment
794 // JBPComment: this really should be an 'insert/pre/append' controller
795 // JBPComment: but the DNA/Protein check makes it a bit more complex
797 // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with
799 // TODO: create undo object for this JAL-1101
802 * Ensure datasets are created for the new alignment as
803 * mappings operate on dataset sequences
805 toAdd.setDataset(null);
808 * Check if any added sequence could be the object of a mapping or
809 * cross-reference; if so, make the mapping explicit
811 getAlignment().realiseMappings(toAdd.getSequences());
814 * If any cDNA/protein mappings exist or can be made between the alignments,
815 * offer to open a split frame with linked alignments
817 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
819 if (AlignmentUtils.isMappable(toAdd, getAlignment()))
821 if (openLinkedAlignment(toAdd, title))
829 * No mappings, or offer declined - add sequences to this alignment
831 // TODO: JAL-407 regardless of above - identical sequences (based on ID and
832 // provenance) should share the same dataset sequence
834 AlignmentI al = getAlignment();
835 String gap = String.valueOf(al.getGapCharacter());
836 for (int i = 0; i < toAdd.getHeight(); i++)
838 SequenceI seq = toAdd.getSequenceAt(i);
841 * - 'align' any mapped sequences as per existing
842 * e.g. cdna to genome, domain hit to protein sequence
843 * very experimental! (need a separate menu option for this)
844 * - only add mapped sequences ('select targets from a dataset')
846 if (true /*AlignmentUtils.alignSequenceAs(seq, al, gap, true, true)*/)
852 ranges.setEndSeq(getAlignment().getHeight());
853 firePropertyChange("alignment", null, getAlignment().getSequences());
857 * Show a dialog with the option to open and link (cDNA <-> protein) as a new
858 * alignment, either as a standalone alignment or in a split frame. Returns
859 * true if the new alignment was opened, false if not, because the user
860 * declined the offer.
865 protected boolean openLinkedAlignment(AlignmentI al, String title)
867 String[] options = new String[] {
868 MessageManager.getString("action.no"),
869 MessageManager.getString("label.split_window"),
870 MessageManager.getString("label.new_window"), };
871 final String question = JvSwingUtils.wrapTooltip(true,
872 MessageManager.getString("label.open_split_window?"));
873 int response = JvOptionPane.showOptionDialog(Desktop.desktop, question,
874 MessageManager.getString("label.open_split_window"),
875 JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
876 options, options[0]);
878 if (response != 1 && response != 2)
882 final boolean openSplitPane = (response == 1);
883 final boolean openInNewWindow = (response == 2);
886 * Identify protein and dna alignments. Make a copy of this one if opening
887 * in a new split pane.
889 AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment())
891 AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
892 final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
895 * Map sequences. At least one should get mapped as we have already passed
896 * the test for 'mappability'. Any mappings made will be added to the
897 * protein alignment. Note creating dataset sequences on the new alignment
898 * is a pre-requisite for building mappings.
901 AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna);
904 * Create the AlignFrame for the added alignment. If it is protein, mappings
905 * are registered with StructureSelectionManager as a side-effect.
907 AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
908 AlignFrame.DEFAULT_HEIGHT);
909 newAlignFrame.setTitle(title);
910 newAlignFrame.statusBar.setText(MessageManager.formatMessage(
911 "label.successfully_loaded_file", new Object[] { title }));
913 // TODO if we want this (e.g. to enable reload of the alignment from file),
914 // we will need to add parameters to the stack.
915 // if (!protocol.equals(DataSourceType.PASTE))
917 // alignFrame.setFileName(file, format);
922 Desktop.addInternalFrame(newAlignFrame, title,
923 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
928 newAlignFrame.setMaximum(jalview.bin.Cache.getDefault(
929 "SHOW_FULLSCREEN", false));
930 } catch (java.beans.PropertyVetoException ex)
936 al.alignAs(thisAlignment);
937 protein = openSplitFrame(newAlignFrame, thisAlignment);
944 * Helper method to open a new SplitFrame holding linked dna and protein
947 * @param newAlignFrame
948 * containing a new alignment to be shown
950 * cdna/protein complement alignment to show in the other split half
951 * @return the protein alignment in the split frame
953 protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
954 AlignmentI complement)
957 * Make a new frame with a copy of the alignment we are adding to. If this
958 * is protein, the mappings to cDNA will be registered with
959 * StructureSelectionManager as a side-effect.
961 AlignFrame copyMe = new AlignFrame(complement,
962 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
963 copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
965 AlignmentI al = newAlignFrame.viewport.getAlignment();
966 final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
968 final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe;
969 cdnaFrame.setVisible(true);
970 proteinFrame.setVisible(true);
971 String linkedTitle = MessageManager
972 .getString("label.linked_view_title");
975 * Open in split pane. DNA sequence above, protein below.
977 JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
978 Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
980 return proteinFrame.viewport.getAlignment();
983 public AnnotationColumnChooser getAnnotationColumnSelectionState()
985 return annotationColumnSelectionState;
988 public void setAnnotationColumnSelectionState(
989 AnnotationColumnChooser currentAnnotationColumnSelectionState)
991 this.annotationColumnSelectionState = currentAnnotationColumnSelectionState;
995 public void setIdWidth(int i)
998 AlignmentPanel ap = getAlignPanel();
1001 // modify GUI elements to reflect geometry change
1002 Dimension idw = getAlignPanel().getIdPanel().getIdCanvas()
1003 .getPreferredSize();
1005 getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw);
1009 public Rectangle getExplodedGeometry()
1011 return explodedGeometry;
1014 public void setExplodedGeometry(Rectangle explodedPosition)
1016 this.explodedGeometry = explodedPosition;
1019 public boolean isGatherViewsHere()
1021 return gatherViewsHere;
1024 public void setGatherViewsHere(boolean gatherViewsHere)
1026 this.gatherViewsHere = gatherViewsHere;
1030 * If this viewport has a (Protein/cDNA) complement, then scroll the
1031 * complementary alignment to match this one.
1033 public void scrollComplementaryAlignment()
1036 * Populate a SearchResults object with the mapped location to scroll to. If
1037 * there is no complement, or it is not following highlights, or no mapping
1038 * is found, the result will be empty.
1040 SearchResultsI sr = new SearchResults();
1041 int verticalOffset = findComplementScrollTarget(sr);
1044 // TODO would like next line without cast but needs more refactoring...
1045 final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
1047 complementPanel.setDontScrollComplement(true);
1048 complementPanel.scrollToCentre(sr, verticalOffset);
1053 * Answers true if no alignment holds a reference to the given mapping
1058 protected boolean noReferencesTo(AlignedCodonFrame acf)
1060 AlignFrame[] frames = Desktop.getAlignFrames();
1065 for (AlignFrame af : frames)
1069 for (AlignmentViewPanel ap : af.getAlignPanels())
1071 AlignmentI al = ap.getAlignment();
1072 if (al != null && al.getCodonFrames().contains(acf))
1083 * Applies the supplied feature settings descriptor to currently known
1084 * features. This supports an 'initial configuration' of feature colouring
1085 * based on a preset or user favourite. This may then be modified in the usual
1086 * way using the Feature Settings dialogue.
1088 * @param featureSettings
1091 public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
1093 if (featureSettings == null)
1098 FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
1099 .getFeatureRenderer();
1100 fr.findAllFeatures(true);
1101 List<String> renderOrder = fr.getRenderOrder();
1102 FeaturesDisplayedI displayed = fr.getFeaturesDisplayed();
1104 // TODO this clears displayed.featuresRegistered - do we care?
1107 * set feature colour if specified by feature settings
1108 * set visibility of all features
1110 for (String type : renderOrder)
1112 FeatureColourI preferredColour = featureSettings
1113 .getFeatureColour(type);
1114 if (preferredColour != null)
1116 fr.setColour(type, preferredColour);
1118 if (featureSettings.isFeatureDisplayed(type))
1120 displayed.setVisible(type);
1125 * set visibility of feature groups
1127 for (String group : fr.getFeatureGroups())
1129 fr.setGroupVisibility(group, featureSettings.isGroupDisplayed(group));
1133 * order the features
1135 if (featureSettings.optimiseOrder())
1137 // TODO not supported (yet?)
1141 fr.orderFeatures(featureSettings);
1143 fr.setTransparency(featureSettings.getTransparency());