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.Sequence;
43 import jalview.datamodel.SequenceGroup;
44 import jalview.datamodel.SequenceI;
45 import jalview.renderer.ResidueShader;
46 import jalview.schemes.ColourSchemeI;
47 import jalview.schemes.ColourSchemeProperty;
48 import jalview.schemes.ResidueColourScheme;
49 import jalview.schemes.UserColourScheme;
50 import jalview.structure.SelectionSource;
51 import jalview.structure.StructureSelectionManager;
52 import jalview.structure.VamsasSource;
53 import jalview.util.MessageManager;
54 import jalview.viewmodel.AlignmentViewport;
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 TreeModel 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)
128 sequenceSetID = seqsetid;
130 // TODO remove these once 2.4.VAMSAS release finished
131 if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
133 Cache.log.debug("Setting viewport's sequence set id : "
136 if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
138 Cache.log.debug("Setting viewport's view id : " + viewId);
145 * Create a new AlignViewport with hidden regions
149 * @param hiddenColumns
152 public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns)
155 if (hiddenColumns != null)
157 al.setHiddenColumns(hiddenColumns);
163 * New viewport with hidden columns and an existing sequence set id
166 * @param hiddenColumns
170 public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
173 this(al, hiddenColumns, seqsetid, null);
177 * New viewport with hidden columns and an existing sequence set id and viewid
180 * @param hiddenColumns
186 public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
187 String seqsetid, String viewid)
190 sequenceSetID = seqsetid;
192 // TODO remove these once 2.4.VAMSAS release finished
193 if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
195 Cache.log.debug("Setting viewport's sequence set id : "
198 if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
200 Cache.log.debug("Setting viewport's view id : " + viewId);
203 if (hiddenColumns != null)
205 al.setHiddenColumns(hiddenColumns);
211 * Apply any settings saved in user preferences
213 private void applyViewProperties()
215 antiAlias = Cache.getDefault("ANTI_ALIAS", false);
217 viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
218 setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
220 setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
221 setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false));
222 autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
224 setPadGaps(Cache.getDefault("PAD_GAPS", true));
225 setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
226 setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
227 viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true));
228 viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false));
229 viewStyle.setShowUnconserved(Cache
230 .getDefault("SHOW_UNCONSERVED", false));
231 sortByTree = Cache.getDefault("SORT_BY_TREE", false);
232 followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
233 sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault(
234 Preferences.SORT_ANNOTATIONS,
235 SequenceAnnotationOrder.NONE.name()));
236 showAutocalculatedAbove = Cache.getDefault(
237 Preferences.SHOW_AUTOCALC_ABOVE, false);
238 viewStyle.setScaleProteinAsCdna(Cache.getDefault(
239 Preferences.SCALE_PROTEIN_TO_CDNA, true));
244 applyViewProperties();
246 String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
247 String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
248 String fontSize = Cache.getDefault("FONT_SIZE", "10");
252 if (fontStyle.equals("bold"))
256 else if (fontStyle.equals("italic"))
261 setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
264 .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
266 // We must set conservation and consensus before setting colour,
267 // as Blosum and Clustal require this to be done
268 if (hconsensus == null && !isDataset)
270 if (!alignment.isNucleotide())
272 showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
273 showQuality = Cache.getDefault("SHOW_QUALITY", true);
274 showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
277 showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
279 showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
280 normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
282 showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
283 showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
285 showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
287 initAutoAnnotation();
290 String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
291 : Preferences.DEFAULT_COLOUR_PROT;
292 String schemeName = Cache.getProperty(colourProperty);
293 if (schemeName == null)
295 // only DEFAULT_COLOUR available in Jalview before 2.9
296 schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
297 ResidueColourScheme.NONE);
299 ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(
300 alignment, schemeName);
301 residueShading = new ResidueShader(colourScheme);
303 if (colourScheme instanceof UserColourScheme)
305 residueShading = new ResidueShader(
306 UserDefinedColours.loadDefaultColours());
307 residueShading.setThreshold(0, isIgnoreGapsConsensus());
310 if (residueShading != null)
312 residueShading.setConsensus(hconsensus);
317 * get the consensus sequence as displayed under the PID consensus annotation
320 * @return consensus sequence as a new sequence object
322 public SequenceI getConsensusSeq()
324 if (consensus == null)
326 updateConsensus(null);
328 if (consensus == null)
332 StringBuffer seqs = new StringBuffer();
333 for (int i = 0; i < consensus.annotations.length; i++)
335 if (consensus.annotations[i] != null)
337 if (consensus.annotations[i].description.charAt(0) == '[')
339 seqs.append(consensus.annotations[i].description.charAt(1));
343 seqs.append(consensus.annotations[i].displayCharacter);
348 SequenceI sq = new Sequence("Consensus", seqs.toString());
349 sq.setDescription("Percentage Identity Consensus "
350 + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
354 boolean validCharWidth;
360 public void setFont(Font f, boolean setGrid)
364 Container c = new Container();
368 FontMetrics fm = c.getFontMetrics(font);
369 int ww = fm.charWidth('M');
370 setCharHeight(fm.getHeight());
373 viewStyle.setFontName(font.getName());
374 viewStyle.setFontStyle(font.getStyle());
375 viewStyle.setFontSize(font.getSize());
377 validCharWidth = true;
381 public void setViewStyle(ViewStyleI settingsForView)
383 super.setViewStyle(settingsForView);
384 setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
385 viewStyle.getFontSize()), false);
391 * @return DOCUMENT ME!
393 public Font getFont()
405 public void setAlignment(AlignmentI align)
407 replaceMappings(align);
408 super.setAlignment(align);
412 * Replace any codon mappings for this viewport with those for the given
417 public void replaceMappings(AlignmentI align)
421 * Deregister current mappings (if any)
423 deregisterMappings();
426 * Register new mappings (if any)
430 StructureSelectionManager ssm = StructureSelectionManager
431 .getStructureSelectionManager(Desktop.instance);
432 ssm.registerMappings(align.getCodonFrames());
436 * replace mappings on our alignment
438 if (alignment != null && align != null)
440 alignment.setCodonFrames(align.getCodonFrames());
444 protected void deregisterMappings()
446 AlignmentI al = getAlignment();
449 List<AlignedCodonFrame> mappings = al.getCodonFrames();
450 if (mappings != null)
452 StructureSelectionManager ssm = StructureSelectionManager
453 .getStructureSelectionManager(Desktop.instance);
454 for (AlignedCodonFrame acf : mappings)
456 if (noReferencesTo(acf))
458 ssm.deregisterMapping(acf);
468 * @return DOCUMENT ME!
471 public char getGapCharacter()
473 return getAlignment().getGapCharacter();
482 public void setGapCharacter(char gap)
484 if (getAlignment() != null)
486 getAlignment().setGapCharacter(gap);
496 public void setCurrentTree(TreeModel tree)
504 * @return DOCUMENT ME!
506 public TreeModel getCurrentTree()
512 * returns the visible column regions of the alignment
514 * @param selectedRegionOnly
515 * true to just return the contigs intersecting with the selected
519 public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
521 int[] viscontigs = null;
522 int start = 0, end = 0;
523 if (selectedRegionOnly && selectionGroup != null)
525 start = selectionGroup.getStartRes();
526 end = selectionGroup.getEndRes() + 1;
530 end = alignment.getWidth();
532 viscontigs = alignment.getHiddenColumns().getVisibleContigs(start, end);
537 * get hash of undo and redo list for the alignment
539 * @return long[] { historyList.hashCode, redoList.hashCode };
541 public long[] getUndoRedoHash()
544 if (historyList == null || redoList == null)
546 return new long[] { -1, -1 };
548 return new long[] { historyList.hashCode(), this.redoList.hashCode() };
552 * test if a particular set of hashcodes are different to the hashcodes for
553 * the undo and redo list.
556 * the stored set of hashcodes as returned by getUndoRedoHash
557 * @return true if the hashcodes differ (ie the alignment has been edited) or
558 * the stored hashcode array differs in size
560 public boolean isUndoRedoHashModified(long[] undoredo)
562 if (undoredo == null)
566 long[] cstate = getUndoRedoHash();
567 if (cstate.length != undoredo.length)
572 for (int i = 0; i < cstate.length; i++)
574 if (cstate[i] != undoredo[i])
582 public boolean followSelection = true;
585 * @return true if view selection should always follow the selections
586 * broadcast by other selection sources
588 public boolean getFollowSelection()
590 return followSelection;
594 * Send the current selection to be broadcast to any selection listeners.
597 public void sendSelection()
599 jalview.structure.StructureSelectionManager
600 .getStructureSelectionManager(Desktop.instance).sendSelection(
601 new SequenceGroup(getSelectionGroup()),
602 new ColumnSelection(getColumnSelection()),
603 new HiddenColumns(getAlignment().getHiddenColumns()),
608 * return the alignPanel containing the given viewport. Use this to get the
609 * components currently handling the given viewport.
612 * @return null or an alignPanel guaranteed to have non-null alignFrame
615 public AlignmentPanel getAlignPanel()
617 AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this
618 .getSequenceSetId());
619 for (int p = 0; aps != null && p < aps.length; p++)
621 if (aps[p].av == this)
629 public boolean getSortByTree()
634 public void setSortByTree(boolean sort)
640 * Returns the (Desktop) instance of the StructureSelectionManager
643 public StructureSelectionManager getStructureSelectionManager()
645 return StructureSelectionManager
646 .getStructureSelectionManager(Desktop.instance);
652 * @return an array of SequenceI arrays, one for each PDBEntry, listing which
653 * sequences in the alignment hold a reference to it
655 public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
657 List<SequenceI[]> seqvectors = new ArrayList<>();
658 for (PDBEntry pdb : pdbEntries)
660 List<SequenceI> choosenSeqs = new ArrayList<>();
661 for (SequenceI sq : alignment.getSequences())
663 Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence()
665 if (pdbRefEntries == null)
669 for (PDBEntry pdbRefEntry : pdbRefEntries)
671 if (pdbRefEntry.getId().equals(pdb.getId()))
673 if (pdbRefEntry.getChainCode() != null
674 && pdb.getChainCode() != null)
676 if (pdbRefEntry.getChainCode().equalsIgnoreCase(
678 && !choosenSeqs.contains(sq))
686 if (!choosenSeqs.contains(sq))
697 .add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
699 return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
703 public boolean isNormaliseSequenceLogo()
705 return normaliseSequenceLogo;
709 public void setNormaliseSequenceLogo(boolean state)
711 normaliseSequenceLogo = state;
714 public void setNormaliseHMMSequenceLogo(boolean state)
716 normaliseHMMSequenceLogo = state;
721 * @return true if alignment characters should be displayed
724 public boolean isValidCharWidth()
726 return validCharWidth;
729 private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
731 public AutoCalcSetting getCalcIdSettingsFor(String calcId)
733 return calcIdParams.get(calcId);
736 public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings,
739 calcIdParams.put(calcId, settings);
740 // TODO: create a restart list to trigger any calculations that need to be
741 // restarted after load
742 // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
745 Cache.log.debug("trigger update for " + calcId);
750 * Method called when another alignment's edit (or possibly other) command is
753 * To allow for sequence mappings (e.g. protein to cDNA), we have to first
754 * 'unwind' the command on the source sequences (in simulation, not in fact),
755 * and then for each edit in turn:
757 * <li>compute the equivalent edit on the mapped sequences</li>
758 * <li>apply the mapped edit</li>
759 * <li>'apply' the source edit to the working copy of the source sequences</li>
767 public void mirrorCommand(CommandI command, boolean undo,
768 StructureSelectionManager ssm, VamsasSource source)
771 * Do nothing unless we are a 'complement' of the source. May replace this
772 * with direct calls not via SSM.
774 if (source instanceof AlignViewportI
775 && ((AlignViewportI) source).getCodingComplement() == this)
784 CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
786 if (mappedCommand != null)
788 AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments();
789 mappedCommand.doCommand(views);
790 getAlignPanel().alignmentChanged();
795 * Add the sequences from the given alignment to this viewport. Optionally,
796 * may give the user the option to open a new frame, or split panel, with cDNA
797 * and protein linked.
802 public void addAlignment(AlignmentI toAdd, String title)
804 // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different
806 // JBPComment: title is a largely redundant parameter at the moment
807 // JBPComment: this really should be an 'insert/pre/append' controller
808 // JBPComment: but the DNA/Protein check makes it a bit more complex
810 // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with
812 // TODO: create undo object for this JAL-1101
815 * Ensure datasets are created for the new alignment as
816 * mappings operate on dataset sequences
818 toAdd.setDataset(null);
821 * Check if any added sequence could be the object of a mapping or
822 * cross-reference; if so, make the mapping explicit
824 getAlignment().realiseMappings(toAdd.getSequences());
827 * If any cDNA/protein mappings exist or can be made between the alignments,
828 * offer to open a split frame with linked alignments
830 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
832 if (AlignmentUtils.isMappable(toAdd, getAlignment()))
834 if (openLinkedAlignment(toAdd, title))
842 * No mappings, or offer declined - add sequences to this alignment
844 // TODO: JAL-407 regardless of above - identical sequences (based on ID and
845 // provenance) should share the same dataset sequence
847 AlignmentI al = getAlignment();
848 String gap = String.valueOf(al.getGapCharacter());
849 for (int i = 0; i < toAdd.getHeight(); i++)
851 SequenceI seq = toAdd.getSequenceAt(i);
854 * - 'align' any mapped sequences as per existing
855 * e.g. cdna to genome, domain hit to protein sequence
856 * very experimental! (need a separate menu option for this)
857 * - only add mapped sequences ('select targets from a dataset')
859 if (true /*AlignmentUtils.alignSequenceAs(seq, al, gap, true, true)*/)
865 ranges.setEndSeq(getAlignment().getHeight());
866 firePropertyChange("alignment", null, getAlignment().getSequences());
870 * Show a dialog with the option to open and link (cDNA <-> protein) as a new
871 * alignment, either as a standalone alignment or in a split frame. Returns
872 * true if the new alignment was opened, false if not, because the user
873 * declined the offer.
878 protected boolean openLinkedAlignment(AlignmentI al, String title)
880 String[] options = new String[] {
881 MessageManager.getString("action.no"),
882 MessageManager.getString("label.split_window"),
883 MessageManager.getString("label.new_window"), };
884 final String question = JvSwingUtils.wrapTooltip(true,
885 MessageManager.getString("label.open_split_window?"));
886 int response = JvOptionPane.showOptionDialog(Desktop.desktop, question,
887 MessageManager.getString("label.open_split_window"),
888 JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
889 options, options[0]);
891 if (response != 1 && response != 2)
895 final boolean openSplitPane = (response == 1);
896 final boolean openInNewWindow = (response == 2);
899 * Identify protein and dna alignments. Make a copy of this one if opening
900 * in a new split pane.
902 AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment())
904 AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
905 final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
908 * Map sequences. At least one should get mapped as we have already passed
909 * the test for 'mappability'. Any mappings made will be added to the
910 * protein alignment. Note creating dataset sequences on the new alignment
911 * is a pre-requisite for building mappings.
914 AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna);
917 * Create the AlignFrame for the added alignment. If it is protein, mappings
918 * are registered with StructureSelectionManager as a side-effect.
920 AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
921 AlignFrame.DEFAULT_HEIGHT);
922 newAlignFrame.setTitle(title);
923 newAlignFrame.statusBar.setText(MessageManager.formatMessage(
924 "label.successfully_loaded_file", new Object[] { title }));
926 // TODO if we want this (e.g. to enable reload of the alignment from file),
927 // we will need to add parameters to the stack.
928 // if (!protocol.equals(DataSourceType.PASTE))
930 // alignFrame.setFileName(file, format);
935 Desktop.addInternalFrame(newAlignFrame, title,
936 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
941 newAlignFrame.setMaximum(jalview.bin.Cache.getDefault(
942 "SHOW_FULLSCREEN", false));
943 } catch (java.beans.PropertyVetoException ex)
949 al.alignAs(thisAlignment);
950 protein = openSplitFrame(newAlignFrame, thisAlignment);
957 * Helper method to open a new SplitFrame holding linked dna and protein
960 * @param newAlignFrame
961 * containing a new alignment to be shown
963 * cdna/protein complement alignment to show in the other split half
964 * @return the protein alignment in the split frame
966 protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
967 AlignmentI complement)
970 * Make a new frame with a copy of the alignment we are adding to. If this
971 * is protein, the mappings to cDNA will be registered with
972 * StructureSelectionManager as a side-effect.
974 AlignFrame copyMe = new AlignFrame(complement,
975 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
976 copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
978 AlignmentI al = newAlignFrame.viewport.getAlignment();
979 final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
981 final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe;
982 cdnaFrame.setVisible(true);
983 proteinFrame.setVisible(true);
984 String linkedTitle = MessageManager
985 .getString("label.linked_view_title");
988 * Open in split pane. DNA sequence above, protein below.
990 JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
991 Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
993 return proteinFrame.viewport.getAlignment();
996 public AnnotationColumnChooser getAnnotationColumnSelectionState()
998 return annotationColumnSelectionState;
1001 public void setAnnotationColumnSelectionState(
1002 AnnotationColumnChooser currentAnnotationColumnSelectionState)
1004 this.annotationColumnSelectionState = currentAnnotationColumnSelectionState;
1008 public void setIdWidth(int i)
1010 super.setIdWidth(i);
1011 AlignmentPanel ap = getAlignPanel();
1014 // modify GUI elements to reflect geometry change
1015 Dimension idw = getAlignPanel().getIdPanel().getIdCanvas()
1016 .getPreferredSize();
1018 getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw);
1022 public Rectangle getExplodedGeometry()
1024 return explodedGeometry;
1027 public void setExplodedGeometry(Rectangle explodedPosition)
1029 this.explodedGeometry = explodedPosition;
1032 public boolean isGatherViewsHere()
1034 return gatherViewsHere;
1037 public void setGatherViewsHere(boolean gatherViewsHere)
1039 this.gatherViewsHere = gatherViewsHere;
1043 * If this viewport has a (Protein/cDNA) complement, then scroll the
1044 * complementary alignment to match this one.
1046 public void scrollComplementaryAlignment()
1049 * Populate a SearchResults object with the mapped location to scroll to. If
1050 * there is no complement, or it is not following highlights, or no mapping
1051 * is found, the result will be empty.
1053 SearchResultsI sr = new SearchResults();
1054 int verticalOffset = findComplementScrollTarget(sr);
1057 // TODO would like next line without cast but needs more refactoring...
1058 final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
1060 complementPanel.setToScrollComplementPanel(false);
1061 complementPanel.scrollToCentre(sr, verticalOffset);
1062 complementPanel.setToScrollComplementPanel(true);
1067 * Answers true if no alignment holds a reference to the given mapping
1072 protected boolean noReferencesTo(AlignedCodonFrame acf)
1074 AlignFrame[] frames = Desktop.getAlignFrames();
1079 for (AlignFrame af : frames)
1083 for (AlignmentViewPanel ap : af.getAlignPanels())
1085 AlignmentI al = ap.getAlignment();
1086 if (al != null && al.getCodonFrames().contains(acf))
1097 * Applies the supplied feature settings descriptor to currently known
1098 * features. This supports an 'initial configuration' of feature colouring
1099 * based on a preset or user favourite. This may then be modified in the usual
1100 * way using the Feature Settings dialogue.
1102 * @param featureSettings
1105 public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
1107 if (featureSettings == null)
1112 FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
1113 .getFeatureRenderer();
1114 fr.findAllFeatures(true);
1115 List<String> renderOrder = fr.getRenderOrder();
1116 FeaturesDisplayedI displayed = fr.getFeaturesDisplayed();
1118 // TODO this clears displayed.featuresRegistered - do we care?
1121 * set feature colour if specified by feature settings
1122 * set visibility of all features
1124 for (String type : renderOrder)
1126 FeatureColourI preferredColour = featureSettings
1127 .getFeatureColour(type);
1128 if (preferredColour != null)
1130 fr.setColour(type, preferredColour);
1132 if (featureSettings.isFeatureDisplayed(type))
1134 displayed.setVisible(type);
1139 * set visibility of feature groups
1141 for (String group : fr.getFeatureGroups())
1143 fr.setGroupVisibility(group, featureSettings.isGroupDisplayed(group));
1147 * order the features
1149 if (featureSettings.optimiseOrder())
1151 // TODO not supported (yet?)
1155 fr.orderFeatures(featureSettings);
1157 fr.setTransparency(featureSettings.getTransparency());
1161 public boolean isNormaliseHMMSequenceLogo()
1163 return normaliseHMMSequenceLogo;