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.
22 * Jalview - A Sequence Alignment Editor and Viewer
23 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
25 * This program is free software; you can redistribute it and/or
26 * modify it under the terms of the GNU General Public License
27 * as published by the Free Software Foundation; either version 2
28 * of the License, or (at your option) any later version.
30 * This program is distributed in the hope that it will be useful,
31 * but WITHOUT ANY WARRANTY; without even the implied warranty of
32 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
33 * GNU General Public License for more details.
35 * You should have received a copy of the GNU General Public License
36 * along with this program; if not, write to the Free Software
37 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
41 import jalview.analysis.AlignmentUtils;
42 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
43 import jalview.analysis.NJTree;
44 import jalview.api.AlignViewportI;
45 import jalview.api.AlignmentViewPanel;
46 import jalview.api.FeatureColourI;
47 import jalview.api.FeatureSettingsModelI;
48 import jalview.api.FeaturesDisplayedI;
49 import jalview.api.ViewStyleI;
50 import jalview.bin.Cache;
51 import jalview.commands.CommandI;
52 import jalview.datamodel.AlignedCodonFrame;
53 import jalview.datamodel.Alignment;
54 import jalview.datamodel.AlignmentI;
55 import jalview.datamodel.ColumnSelection;
56 import jalview.datamodel.PDBEntry;
57 import jalview.datamodel.SearchResults;
58 import jalview.datamodel.Sequence;
59 import jalview.datamodel.SequenceGroup;
60 import jalview.datamodel.SequenceI;
61 import jalview.schemes.ColourSchemeProperty;
62 import jalview.schemes.UserColourScheme;
63 import jalview.structure.CommandListener;
64 import jalview.structure.SelectionSource;
65 import jalview.structure.StructureSelectionManager;
66 import jalview.structure.VamsasSource;
67 import jalview.util.MessageManager;
68 import jalview.viewmodel.AlignmentViewport;
69 import jalview.ws.params.AutoCalcSetting;
71 import java.awt.Container;
72 import java.awt.Dimension;
74 import java.awt.Rectangle;
75 import java.util.ArrayList;
76 import java.util.Hashtable;
77 import java.util.List;
78 import java.util.Vector;
80 import javax.swing.JInternalFrame;
81 import javax.swing.JOptionPane;
87 * @version $Revision: 1.141 $
89 public class AlignViewport extends AlignmentViewport implements
90 SelectionSource, CommandListener
94 NJTree currentTree = null;
96 boolean cursorMode = false;
98 boolean antiAlias = false;
100 private Rectangle explodedGeometry;
105 * Flag set true on the view that should 'gather' multiple views of the same
106 * sequence set id when a project is reloaded. Set false on all views when
107 * they are 'exploded' into separate windows. Set true on the current view
108 * when 'Gather' is performed, and also on the first tab when the first new
111 private boolean gatherViewsHere = false;
113 private AnnotationColumnChooser annotationColumnSelectionState;
116 * Creates a new AlignViewport object.
121 public AlignViewport(AlignmentI al)
128 * Create a new AlignViewport object with a specific sequence set ID
132 * (may be null - but potential for ambiguous constructor exception)
134 public AlignViewport(AlignmentI al, String seqsetid)
136 this(al, seqsetid, null);
139 public AlignViewport(AlignmentI al, String seqsetid, String viewid)
141 sequenceSetID = seqsetid;
143 // TODO remove these once 2.4.VAMSAS release finished
144 if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
146 Cache.log.debug("Setting viewport's sequence set id : "
149 if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
151 Cache.log.debug("Setting viewport's view id : " + viewId);
158 * Create a new AlignViewport with hidden regions
162 * @param hiddenColumns
165 public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
168 if (hiddenColumns != null)
170 colSel = hiddenColumns;
176 * New viewport with hidden columns and an existing sequence set id
179 * @param hiddenColumns
183 public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
186 this(al, hiddenColumns, seqsetid, null);
190 * New viewport with hidden columns and an existing sequence set id and viewid
193 * @param hiddenColumns
199 public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
200 String seqsetid, String viewid)
202 sequenceSetID = seqsetid;
204 // TODO remove these once 2.4.VAMSAS release finished
205 if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
207 Cache.log.debug("Setting viewport's sequence set id : "
210 if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
212 Cache.log.debug("Setting viewport's view id : " + viewId);
215 if (hiddenColumns != null)
217 colSel = hiddenColumns;
223 * Apply any settings saved in user preferences
225 private void applyViewProperties()
227 antiAlias = Cache.getDefault("ANTI_ALIAS", false);
229 viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
230 setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
232 setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
233 setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false));
234 autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
236 setPadGaps(Cache.getDefault("PAD_GAPS", true));
237 setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
238 setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
239 viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true));
240 viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false));
241 viewStyle.setShowUnconserved(Cache
242 .getDefault("SHOW_UNCONSERVED", false));
243 sortByTree = Cache.getDefault("SORT_BY_TREE", false);
244 followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
245 sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault(
246 Preferences.SORT_ANNOTATIONS,
247 SequenceAnnotationOrder.NONE.name()));
248 showAutocalculatedAbove = Cache.getDefault(
249 Preferences.SHOW_AUTOCALC_ABOVE, false);
250 viewStyle.setScaleProteinAsCdna(Cache.getDefault(
251 Preferences.SCALE_PROTEIN_TO_CDNA, true));
257 this.endRes = alignment.getWidth() - 1;
259 this.endSeq = alignment.getHeight() - 1;
260 applyViewProperties();
262 String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
263 String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
264 String fontSize = Cache.getDefault("FONT_SIZE", "10");
268 if (fontStyle.equals("bold"))
272 else if (fontStyle.equals("italic"))
277 setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
280 .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
282 // We must set conservation and consensus before setting colour,
283 // as Blosum and Clustal require this to be done
284 if (hconsensus == null && !isDataset)
286 if (!alignment.isNucleotide())
288 showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
289 showQuality = Cache.getDefault("SHOW_QUALITY", true);
290 showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
293 showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
295 showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
296 normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
298 showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
299 showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
301 initAutoAnnotation();
302 String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
303 : Preferences.DEFAULT_COLOUR_PROT;
304 String propertyValue = Cache.getProperty(colourProperty);
305 if (propertyValue == null)
307 // fall back on this property for backwards compatibility
308 propertyValue = Cache.getProperty(Preferences.DEFAULT_COLOUR);
310 if (propertyValue != null)
312 globalColourScheme = ColourSchemeProperty.getColour(alignment,
315 if (globalColourScheme instanceof UserColourScheme)
317 globalColourScheme = UserDefinedColours.loadDefaultColours();
318 ((UserColourScheme) globalColourScheme).setThreshold(0,
319 isIgnoreGapsConsensus());
322 if (globalColourScheme != null)
324 globalColourScheme.setConsensus(hconsensus);
330 * get the consensus sequence as displayed under the PID consensus annotation
333 * @return consensus sequence as a new sequence object
335 public SequenceI getConsensusSeq()
337 if (consensus == null)
339 updateConsensus(null);
341 if (consensus == null)
345 StringBuffer seqs = new StringBuffer();
346 for (int i = 0; i < consensus.annotations.length; i++)
348 if (consensus.annotations[i] != null)
350 if (consensus.annotations[i].description.charAt(0) == '[')
352 seqs.append(consensus.annotations[i].description.charAt(1));
356 seqs.append(consensus.annotations[i].displayCharacter);
361 SequenceI sq = new Sequence("Consensus", seqs.toString());
362 sq.setDescription("Percentage Identity Consensus "
363 + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
367 boolean validCharWidth;
370 * update view settings with the given font. You may need to call
371 * alignPanel.fontChanged to update the layout geometry
374 * when true, charWidth/height is set according to font mentrics
376 public void setFont(Font f, boolean setGrid)
380 Container c = new Container();
382 java.awt.FontMetrics fm = c.getFontMetrics(font);
383 int w = viewStyle.getCharWidth(), ww = fm.charWidth('M'), h = viewStyle
387 setCharHeight(fm.getHeight());
390 viewStyle.setFontName(font.getName());
391 viewStyle.setFontStyle(font.getStyle());
392 viewStyle.setFontSize(font.getSize());
394 validCharWidth = true;
398 public void setViewStyle(ViewStyleI settingsForView)
400 super.setViewStyle(settingsForView);
401 setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
402 viewStyle.getFontSize()), false);
409 * @return DOCUMENT ME!
411 public Font getFont()
422 public void setAlignment(AlignmentI align)
424 replaceMappings(align);
425 this.alignment = align;
429 * Replace any codon mappings for this viewport with those for the given
434 public void replaceMappings(AlignmentI align)
438 * Deregister current mappings (if any)
440 deregisterMappings();
443 * Register new mappings (if any)
447 StructureSelectionManager ssm = StructureSelectionManager
448 .getStructureSelectionManager(Desktop.instance);
449 ssm.registerMappings(align.getCodonFrames());
453 * replace mappings on our alignment
455 if (alignment != null && align != null)
457 alignment.setCodonFrames(align.getCodonFrames());
461 protected void deregisterMappings()
463 AlignmentI al = getAlignment();
466 List<AlignedCodonFrame> mappings = al.getCodonFrames();
467 if (mappings != null)
469 StructureSelectionManager ssm = StructureSelectionManager
470 .getStructureSelectionManager(Desktop.instance);
471 for (AlignedCodonFrame acf : mappings)
473 if (noReferencesTo(acf))
475 ssm.deregisterMapping(acf);
485 * @return DOCUMENT ME!
488 public char getGapCharacter()
490 return getAlignment().getGapCharacter();
499 public void setGapCharacter(char gap)
501 if (getAlignment() != null)
503 getAlignment().setGapCharacter(gap);
513 public void setCurrentTree(NJTree tree)
521 * @return DOCUMENT ME!
523 public NJTree getCurrentTree()
529 * returns the visible column regions of the alignment
531 * @param selectedRegionOnly
532 * true to just return the contigs intersecting with the selected
536 public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
538 int[] viscontigs = null;
539 int start = 0, end = 0;
540 if (selectedRegionOnly && selectionGroup != null)
542 start = selectionGroup.getStartRes();
543 end = selectionGroup.getEndRes() + 1;
547 end = alignment.getWidth();
549 viscontigs = colSel.getVisibleContigs(start, end);
554 * get hash of undo and redo list for the alignment
556 * @return long[] { historyList.hashCode, redoList.hashCode };
558 public long[] getUndoRedoHash()
561 if (historyList == null || redoList == null)
563 return new long[] { -1, -1 };
565 return new long[] { historyList.hashCode(), this.redoList.hashCode() };
569 * test if a particular set of hashcodes are different to the hashcodes for
570 * the undo and redo list.
573 * the stored set of hashcodes as returned by getUndoRedoHash
574 * @return true if the hashcodes differ (ie the alignment has been edited) or
575 * the stored hashcode array differs in size
577 public boolean isUndoRedoHashModified(long[] undoredo)
579 if (undoredo == null)
583 long[] cstate = getUndoRedoHash();
584 if (cstate.length != undoredo.length)
589 for (int i = 0; i < cstate.length; i++)
591 if (cstate[i] != undoredo[i])
599 public boolean followSelection = true;
602 * @return true if view selection should always follow the selections
603 * broadcast by other selection sources
605 public boolean getFollowSelection()
607 return followSelection;
611 * Send the current selection to be broadcast to any selection listeners.
614 public void sendSelection()
616 jalview.structure.StructureSelectionManager
617 .getStructureSelectionManager(Desktop.instance).sendSelection(
618 new SequenceGroup(getSelectionGroup()),
619 new ColumnSelection(getColumnSelection()), this);
623 * return the alignPanel containing the given viewport. Use this to get the
624 * components currently handling the given viewport.
627 * @return null or an alignPanel guaranteed to have non-null alignFrame
630 public AlignmentPanel getAlignPanel()
632 AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this
633 .getSequenceSetId());
634 for (int p = 0; aps != null && p < aps.length; p++)
636 if (aps[p].av == this)
644 public boolean getSortByTree()
649 public void setSortByTree(boolean sort)
655 * Returns the (Desktop) instance of the StructureSelectionManager
658 public StructureSelectionManager getStructureSelectionManager()
660 return StructureSelectionManager
661 .getStructureSelectionManager(Desktop.instance);
667 * @return an array of SequenceI arrays, one for each PDBEntry, listing which
668 * sequences in the alignment hold a reference to it
670 public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
672 List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
673 for (PDBEntry pdb : pdbEntries)
675 List<SequenceI> choosenSeqs = new ArrayList<SequenceI>();
676 for (SequenceI sq : alignment.getSequences())
678 Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence().getAllPDBEntries();
679 if (pdbRefEntries == null)
683 for (PDBEntry pdbRefEntry : pdbRefEntries)
685 if (pdbRefEntry.getId().equals(pdb.getId()))
687 if (pdbRefEntry.getChainCode() != null
688 && pdb.getChainCode() != null)
690 if (pdbRefEntry.getChainCode().equalsIgnoreCase(
692 && !choosenSeqs.contains(sq))
700 if (!choosenSeqs.contains(sq))
710 seqvectors.add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
712 return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
716 public boolean isNormaliseSequenceLogo()
718 return normaliseSequenceLogo;
721 public void setNormaliseSequenceLogo(boolean state)
723 normaliseSequenceLogo = state;
728 * @return true if alignment characters should be displayed
731 public boolean isValidCharWidth()
733 return validCharWidth;
736 private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
738 public AutoCalcSetting getCalcIdSettingsFor(String calcId)
740 return calcIdParams.get(calcId);
743 public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings,
746 calcIdParams.put(calcId, settings);
747 // TODO: create a restart list to trigger any calculations that need to be
748 // restarted after load
749 // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
752 Cache.log.debug("trigger update for " + calcId);
757 * Method called when another alignment's edit (or possibly other) command is
760 * To allow for sequence mappings (e.g. protein to cDNA), we have to first
761 * 'unwind' the command on the source sequences (in simulation, not in fact),
762 * and then for each edit in turn:
764 * <li>compute the equivalent edit on the mapped sequences</li>
765 * <li>apply the mapped edit</li>
766 * <li>'apply' the source edit to the working copy of the source sequences</li>
774 public void mirrorCommand(CommandI command, boolean undo,
775 StructureSelectionManager ssm, VamsasSource source)
778 * Do nothing unless we are a 'complement' of the source. May replace this
779 * with direct calls not via SSM.
781 if (source instanceof AlignViewportI
782 && ((AlignViewportI) source).getCodingComplement() == this)
791 CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
793 if (mappedCommand != null)
795 AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments();
796 mappedCommand.doCommand(views);
797 getAlignPanel().alignmentChanged();
802 * Add the sequences from the given alignment to this viewport. Optionally,
803 * may give the user the option to open a new frame, or split panel, with cDNA
804 * and protein linked.
809 public void addAlignment(AlignmentI toAdd, String title)
811 // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different
813 // JBPComment: title is a largely redundant parameter at the moment
814 // JBPComment: this really should be an 'insert/pre/append' controller
815 // JBPComment: but the DNA/Protein check makes it a bit more complex
817 // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with
819 // TODO: create undo object for this JAL-1101
822 * Ensure datasets are created for the new alignment as
823 * mappings operate on dataset sequences
825 toAdd.setDataset(null);
828 * Check if any added sequence could be the object of a mapping or
829 * cross-reference; if so, make the mapping explicit
831 getAlignment().realiseMappings(toAdd.getSequences());
834 * If any cDNA/protein mappings exist or can be made between the alignments,
835 * offer to open a split frame with linked alignments
837 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
839 if (AlignmentUtils.isMappable(toAdd, getAlignment()))
841 if (openLinkedAlignment(toAdd, title))
849 * No mappings, or offer declined - add sequences to this alignment
851 // TODO: JAL-407 regardless of above - identical sequences (based on ID and
852 // provenance) should share the same dataset sequence
854 AlignmentI al = getAlignment();
855 String gap = String.valueOf(al.getGapCharacter());
856 for (int i = 0; i < toAdd.getHeight(); i++)
858 SequenceI seq = toAdd.getSequenceAt(i);
861 * - 'align' any mapped sequences as per existing
862 * e.g. cdna to genome, domain hit to protein sequence
863 * very experimental! (need a separate menu option for this)
864 * - only add mapped sequences ('select targets from a dataset')
866 if (true /*AlignmentUtils.alignSequenceAs(seq, al, gap, true, true)*/)
872 setEndSeq(getAlignment().getHeight());
873 firePropertyChange("alignment", null, getAlignment().getSequences());
877 * Show a dialog with the option to open and link (cDNA <-> protein) as a new
878 * alignment, either as a standalone alignment or in a split frame. Returns
879 * true if the new alignment was opened, false if not, because the user
880 * declined the offer.
885 protected boolean openLinkedAlignment(AlignmentI al, String title)
887 String[] options = new String[] {
888 MessageManager.getString("action.no"),
889 MessageManager.getString("label.split_window"),
890 MessageManager.getString("label.new_window"), };
891 final String question = JvSwingUtils.wrapTooltip(true,
892 MessageManager.getString("label.open_split_window?"));
893 int response = JOptionPane.showOptionDialog(Desktop.desktop, question,
894 MessageManager.getString("label.open_split_window"),
895 JOptionPane.DEFAULT_OPTION, JOptionPane.PLAIN_MESSAGE, null,
896 options, options[0]);
898 if (response != 1 && response != 2)
902 final boolean openSplitPane = (response == 1);
903 final boolean openInNewWindow = (response == 2);
906 * Identify protein and dna alignments. Make a copy of this one if opening
907 * in a new split pane.
909 AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment())
911 AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
912 final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
915 * Map sequences. At least one should get mapped as we have already passed
916 * the test for 'mappability'. Any mappings made will be added to the
917 * protein alignment. Note creating dataset sequences on the new alignment
918 * is a pre-requisite for building mappings.
921 AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna);
924 * Create the AlignFrame for the added alignment. If it is protein, mappings
925 * are registered with StructureSelectionManager as a side-effect.
927 AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
928 AlignFrame.DEFAULT_HEIGHT);
929 newAlignFrame.setTitle(title);
930 newAlignFrame.statusBar.setText(MessageManager.formatMessage(
931 "label.successfully_loaded_file", new Object[] { title }));
933 // TODO if we want this (e.g. to enable reload of the alignment from file),
934 // we will need to add parameters to the stack.
935 // if (!protocol.equals(AppletFormatAdapter.PASTE))
937 // alignFrame.setFileName(file, format);
942 Desktop.addInternalFrame(newAlignFrame, title,
943 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
948 newAlignFrame.setMaximum(jalview.bin.Cache.getDefault(
949 "SHOW_FULLSCREEN", false));
950 } catch (java.beans.PropertyVetoException ex)
956 al.alignAs(thisAlignment);
957 protein = openSplitFrame(newAlignFrame, thisAlignment);
964 * Helper method to open a new SplitFrame holding linked dna and protein
967 * @param newAlignFrame
968 * containing a new alignment to be shown
970 * cdna/protein complement alignment to show in the other split half
971 * @return the protein alignment in the split frame
973 protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
974 AlignmentI complement)
977 * Make a new frame with a copy of the alignment we are adding to. If this
978 * is protein, the mappings to cDNA will be registered with
979 * StructureSelectionManager as a side-effect.
981 AlignFrame copyMe = new AlignFrame(complement,
982 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
983 copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
985 AlignmentI al = newAlignFrame.viewport.getAlignment();
986 final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
988 final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe;
989 cdnaFrame.setVisible(true);
990 proteinFrame.setVisible(true);
991 String linkedTitle = MessageManager
992 .getString("label.linked_view_title");
995 * Open in split pane. DNA sequence above, protein below.
997 JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
998 Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
1000 return proteinFrame.viewport.getAlignment();
1003 public AnnotationColumnChooser getAnnotationColumnSelectionState()
1005 return annotationColumnSelectionState;
1008 public void setAnnotationColumnSelectionState(
1009 AnnotationColumnChooser currentAnnotationColumnSelectionState)
1011 this.annotationColumnSelectionState = currentAnnotationColumnSelectionState;
1015 public void setIdWidth(int i)
1017 super.setIdWidth(i);
1018 AlignmentPanel ap = getAlignPanel();
1021 // modify GUI elements to reflect geometry change
1022 Dimension idw = getAlignPanel().getIdPanel().getIdCanvas()
1023 .getPreferredSize();
1025 getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw);
1029 public Rectangle getExplodedGeometry()
1031 return explodedGeometry;
1034 public void setExplodedGeometry(Rectangle explodedPosition)
1036 this.explodedGeometry = explodedPosition;
1039 public boolean isGatherViewsHere()
1041 return gatherViewsHere;
1044 public void setGatherViewsHere(boolean gatherViewsHere)
1046 this.gatherViewsHere = gatherViewsHere;
1050 * If this viewport has a (Protein/cDNA) complement, then scroll the
1051 * complementary alignment to match this one.
1053 public void scrollComplementaryAlignment()
1056 * Populate a SearchResults object with the mapped location to scroll to. If
1057 * there is no complement, or it is not following highlights, or no mapping
1058 * is found, the result will be empty.
1060 SearchResults sr = new SearchResults();
1061 int verticalOffset = findComplementScrollTarget(sr);
1064 // TODO would like next line without cast but needs more refactoring...
1065 final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
1067 complementPanel.setDontScrollComplement(true);
1068 complementPanel.scrollToCentre(sr, verticalOffset);
1073 * Answers true if no alignment holds a reference to the given mapping
1078 protected boolean noReferencesTo(AlignedCodonFrame acf)
1080 AlignFrame[] frames = Desktop.getAlignFrames();
1085 for (AlignFrame af : frames)
1089 for (AlignmentViewPanel ap : af.getAlignPanels())
1091 AlignmentI al = ap.getAlignment();
1092 if (al != null && al.getCodonFrames().contains(acf))
1103 * Applies the supplied feature settings descriptor to currently known
1104 * features. This supports an 'initial configuration' of feature colouring
1105 * based on a preset or user favourite. This may then be modified in the usual
1106 * way using the Feature Settings dialogue.
1108 * @param featureSettings
1111 public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
1113 if (featureSettings == null)
1118 FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
1119 .getFeatureRenderer();
1120 fr.findAllFeatures(true);
1121 List<String> renderOrder = fr.getRenderOrder();
1122 FeaturesDisplayedI displayed = fr.getFeaturesDisplayed();
1124 // TODO this clears displayed.featuresRegistered - do we care?
1127 * set feature colour if specified by feature settings
1128 * set visibility of all features
1130 for (String type : renderOrder)
1132 FeatureColourI preferredColour = featureSettings
1133 .getFeatureColour(type);
1134 if (preferredColour != null)
1136 fr.setColour(type, preferredColour);
1138 if (featureSettings.isFeatureDisplayed(type))
1140 displayed.setVisible(type);
1145 * set visibility of feature groups
1147 for (String group : fr.getFeatureGroups())
1149 fr.setGroupVisibility(group, featureSettings.isGroupDisplayed(group));
1153 * order the features
1155 if (featureSettings.optimiseOrder())
1157 // TODO not supported (yet?)
1161 fr.orderFeatures(featureSettings);
1163 fr.setTransparency(featureSettings.getTransparency());