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 java.awt.Container;
42 import java.awt.Dimension;
44 import java.awt.Rectangle;
45 import java.util.ArrayList;
46 import java.util.Hashtable;
47 import java.util.List;
49 import java.util.Vector;
51 import javax.swing.JInternalFrame;
52 import javax.swing.JOptionPane;
54 import jalview.analysis.AlignmentUtils;
55 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
56 import jalview.analysis.NJTree;
57 import jalview.api.AlignViewportI;
58 import jalview.api.FeatureRenderer;
59 import jalview.api.ViewStyleI;
60 import jalview.bin.Cache;
61 import jalview.commands.CommandI;
62 import jalview.datamodel.AlignedCodonFrame;
63 import jalview.datamodel.Alignment;
64 import jalview.datamodel.AlignmentI;
65 import jalview.datamodel.ColumnSelection;
66 import jalview.datamodel.PDBEntry;
67 import jalview.datamodel.SearchResults;
68 import jalview.datamodel.Sequence;
69 import jalview.datamodel.SequenceGroup;
70 import jalview.datamodel.SequenceI;
71 import jalview.schemes.ColourSchemeProperty;
72 import jalview.schemes.UserColourScheme;
73 import jalview.structure.CommandListener;
74 import jalview.structure.SelectionSource;
75 import jalview.structure.StructureSelectionManager;
76 import jalview.structure.VamsasSource;
77 import jalview.util.MessageManager;
78 import jalview.viewmodel.AlignmentViewport;
79 import jalview.ws.params.AutoCalcSetting;
85 * @version $Revision: 1.141 $
87 public class AlignViewport extends AlignmentViewport implements
88 SelectionSource, CommandListener
92 NJTree currentTree = null;
94 boolean cursorMode = false;
96 boolean antiAlias = false;
98 private Rectangle explodedGeometry;
100 private FeatureRenderer featureRenderer;
102 private boolean includeHiddenRegion = true;
106 * Flag set true on the view that should 'gather' multiple views of the same
107 * sequence set id when a project is reloaded. Set false on all views when
108 * they are 'exploded' into separate windows. Set true on the current view
109 * when 'Gather' is performed, and also on the first tab when the first new
112 private boolean gatherViewsHere = false;
114 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);
408 * @return DOCUMENT ME!
410 public Font getFont()
421 public void setAlignment(AlignmentI align)
423 if (alignment != null && alignment.getCodonFrames() != null)
425 StructureSelectionManager.getStructureSelectionManager(
426 Desktop.instance).removeMappings(alignment.getCodonFrames());
428 this.alignment = align;
429 if (alignment != null && alignment.getCodonFrames() != null)
431 StructureSelectionManager.getStructureSelectionManager(
432 Desktop.instance).addMappings(alignment.getCodonFrames());
439 * @return DOCUMENT ME!
441 public char getGapCharacter()
443 return getAlignment().getGapCharacter();
452 public void setGapCharacter(char gap)
454 if (getAlignment() != null)
456 getAlignment().setGapCharacter(gap);
463 * @return DOCUMENT ME!
465 public ColumnSelection getColumnSelection()
476 public void setCurrentTree(NJTree tree)
484 * @return DOCUMENT ME!
486 public NJTree getCurrentTree()
492 * returns the visible column regions of the alignment
494 * @param selectedRegionOnly
495 * true to just return the contigs intersecting with the selected
499 public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
501 int[] viscontigs = null;
502 int start = 0, end = 0;
503 if (selectedRegionOnly && selectionGroup != null)
505 start = selectionGroup.getStartRes();
506 end = selectionGroup.getEndRes() + 1;
510 end = alignment.getWidth();
512 viscontigs = colSel.getVisibleContigs(start, end);
517 * get hash of undo and redo list for the alignment
519 * @return long[] { historyList.hashCode, redoList.hashCode };
521 public long[] getUndoRedoHash()
524 if (historyList == null || redoList == null)
530 { historyList.hashCode(), this.redoList.hashCode() };
534 * test if a particular set of hashcodes are different to the hashcodes for
535 * the undo and redo list.
538 * the stored set of hashcodes as returned by getUndoRedoHash
539 * @return true if the hashcodes differ (ie the alignment has been edited) or
540 * the stored hashcode array differs in size
542 public boolean isUndoRedoHashModified(long[] undoredo)
544 if (undoredo == null)
548 long[] cstate = getUndoRedoHash();
549 if (cstate.length != undoredo.length)
554 for (int i = 0; i < cstate.length; i++)
556 if (cstate[i] != undoredo[i])
564 public boolean followSelection = true;
567 * @return true if view selection should always follow the selections
568 * broadcast by other selection sources
570 public boolean getFollowSelection()
572 return followSelection;
576 * Send the current selection to be broadcast to any selection listeners.
578 public void sendSelection()
580 jalview.structure.StructureSelectionManager
581 .getStructureSelectionManager(Desktop.instance).sendSelection(
582 new SequenceGroup(getSelectionGroup()),
583 new ColumnSelection(getColumnSelection()), this);
587 * return the alignPanel containing the given viewport. Use this to get the
588 * components currently handling the given viewport.
591 * @return null or an alignPanel guaranteed to have non-null alignFrame
594 public AlignmentPanel getAlignPanel()
596 AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this
597 .getSequenceSetId());
598 for (int p = 0; aps != null && p < aps.length; p++)
600 if (aps[p].av == this)
608 public boolean getSortByTree()
613 public void setSortByTree(boolean sort)
619 * synthesize a column selection if none exists so it covers the given
620 * selection group. if wholewidth is false, no column selection is made if the
621 * selection group covers the whole alignment width.
626 public void expandColSelection(SequenceGroup sg, boolean wholewidth)
630 && (sgs = sg.getStartRes()) >= 0
631 && sg.getStartRes() <= (sge = sg.getEndRes())
632 && (colSel == null || colSel.getSelected() == null || colSel
633 .getSelected().size() == 0))
635 if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
642 colSel = new ColumnSelection();
644 for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
646 colSel.addElement(cspos);
652 * Returns the (Desktop) instance of the StructureSelectionManager
655 public StructureSelectionManager getStructureSelectionManager()
657 return StructureSelectionManager
658 .getStructureSelectionManager(Desktop.instance);
664 * @return an array of SequenceI arrays, one for each PDBEntry, listing which
665 * sequences in the alignment hold a reference to it
667 public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
669 List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
670 for (PDBEntry pdb : pdbEntries)
672 List<SequenceI> seqs = new ArrayList<SequenceI>();
673 for (SequenceI sq : alignment.getSequences())
675 Vector<PDBEntry> pdbs = sq
676 .getDatasetSequence().getPDBId();
681 for (PDBEntry p1 : pdbs)
683 if (p1.getId().equals(pdb.getId()))
685 if (!seqs.contains(sq))
693 seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
695 return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
698 public boolean isNormaliseSequenceLogo()
700 return normaliseSequenceLogo;
703 public void setNormaliseSequenceLogo(boolean state)
705 normaliseSequenceLogo = state;
710 * @return true if alignment characters should be displayed
712 public boolean isValidCharWidth()
714 return validCharWidth;
717 private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
719 public AutoCalcSetting getCalcIdSettingsFor(String calcId)
721 return calcIdParams.get(calcId);
724 public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings,
727 calcIdParams.put(calcId, settings);
728 // TODO: create a restart list to trigger any calculations that need to be
729 // restarted after load
730 // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
733 Cache.log.debug("trigger update for " + calcId);
738 * Method called when another alignment's edit (or possibly other) command is
741 * To allow for sequence mappings (e.g. protein to cDNA), we have to first
742 * 'unwind' the command on the source sequences (in simulation, not in fact),
743 * and then for each edit in turn:
745 * <li>compute the equivalent edit on the mapped sequences</li>
746 * <li>apply the mapped edit</li>
747 * <li>'apply' the source edit to the working copy of the source sequences</li>
755 public void mirrorCommand(CommandI command, boolean undo,
756 StructureSelectionManager ssm, VamsasSource source)
759 * Do nothing unless we are a 'complement' of the source. May replace this
760 * with direct calls not via SSM.
762 if (source instanceof AlignViewportI
763 && ((AlignViewportI) source).getCodingComplement() == this)
772 CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
774 if (mappedCommand != null)
776 AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments();
777 mappedCommand.doCommand(views);
778 getAlignPanel().alignmentChanged();
783 * Add the sequences from the given alignment to this viewport. Optionally,
784 * may give the user the option to open a new frame, or split panel, with cDNA
785 * and protein linked.
790 public void addAlignment(AlignmentI al, String title)
792 // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different
794 // JBPComment: title is a largely redundant parameter at the moment
795 // JBPComment: this really should be an 'insert/pre/append' controller
796 // JBPComment: but the DNA/Protein check makes it a bit more complex
798 // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with
800 // TODO: create undo object for this JAL-1101
803 * If any cDNA/protein mappings can be made between the alignments, offer to
804 * open a linked alignment with split frame option.
806 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, false))
808 if (AlignmentUtils.isMappable(al, getAlignment()))
810 if (openLinkedAlignment(al, title))
818 * No mappings, or offer declined - add sequences to this alignment
820 // TODO: JAL-407 regardless of above - identical sequences (based on ID and
821 // provenance) should share the same dataset sequence
823 for (int i = 0; i < al.getHeight(); i++)
825 getAlignment().addSequence(al.getSequenceAt(i));
828 setEndSeq(getAlignment().getHeight());
829 firePropertyChange("alignment", null, getAlignment().getSequences());
833 * Show a dialog with the option to open and link (cDNA <-> protein) as a new
834 * alignment, either as a standalone alignment or in a split frame. Returns
835 * true if the new alignment was opened, false if not, because the user
836 * declined the offer.
841 protected boolean openLinkedAlignment(AlignmentI al, String title)
843 String[] options = new String[]
844 { MessageManager.getString("action.no"),
845 MessageManager.getString("label.split_window"),
846 MessageManager.getString("label.new_window"), };
847 final String question = JvSwingUtils.wrapTooltip(true,
848 MessageManager.getString("label.open_split_window?"));
849 int response = JOptionPane.showOptionDialog(Desktop.desktop, question,
850 MessageManager.getString("label.open_split_window"),
851 JOptionPane.DEFAULT_OPTION, JOptionPane.PLAIN_MESSAGE, null,
852 options, options[0]);
854 if (response != 1 && response != 2)
858 final boolean openSplitPane = (response == 1);
859 final boolean openInNewWindow = (response == 2);
862 * Identify protein and dna alignments. Make a copy of this one if opening
863 * in a new split pane.
865 AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment())
867 AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
868 final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
871 * Map sequences. At least one should get mapped as we have already passed
872 * the test for 'mappability'. Any mappings made will be added to the
873 * protein alignment. Note creating dataset sequences on the new alignment
874 * is a pre-requisite for building mappings.
877 AlignmentUtils.mapProteinToCdna(protein, cdna);
880 * Create the AlignFrame for the added alignment. Note this will include the
881 * cDNA consensus annotation if it is protein (because the alignment holds
882 * mappings to nucleotide)
884 AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
885 AlignFrame.DEFAULT_HEIGHT);
886 newAlignFrame.setTitle(title);
887 newAlignFrame.statusBar.setText(MessageManager.formatMessage(
888 "label.successfully_loaded_file", new Object[]
891 // TODO if we want this (e.g. to enable reload of the alignment from file),
892 // we will need to add parameters to the stack.
893 // if (!protocol.equals(AppletFormatAdapter.PASTE))
895 // alignFrame.setFileName(file, format);
900 Desktop.addInternalFrame(newAlignFrame, title,
901 AlignFrame.DEFAULT_WIDTH,
902 AlignFrame.DEFAULT_HEIGHT);
907 newAlignFrame.setMaximum(jalview.bin.Cache.getDefault(
910 } catch (java.beans.PropertyVetoException ex)
916 protein = openSplitFrame(newAlignFrame, thisAlignment,
917 protein.getCodonFrames());
921 * Register the mappings (held on the protein alignment) with the
922 * StructureSelectionManager (for mouseover linking).
924 final StructureSelectionManager ssm = StructureSelectionManager
925 .getStructureSelectionManager(Desktop.instance);
926 ssm.addMappings(protein.getCodonFrames());
932 * Helper method to open a new SplitFrame holding linked dna and protein
935 * @param newAlignFrame
936 * containing a new alignment to be shown
938 * cdna/protein complement alignment to show in the other split half
940 * @return the protein alignment in the split frame
942 protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
943 AlignmentI complement, Set<AlignedCodonFrame> mappings)
946 * Make a new frame with a copy of the alignment we are adding to. If this
947 * is protein, the new frame will have a cDNA consensus annotation row
950 AlignFrame copyMe = new AlignFrame(complement,
951 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
952 copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
954 AlignmentI al = newAlignFrame.viewport.getAlignment();
955 final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
957 final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame
959 AlignmentI protein = proteinFrame.viewport.getAlignment();
960 protein.setCodonFrames(mappings);
962 cdnaFrame.setVisible(true);
963 proteinFrame.setVisible(true);
964 String linkedTitle = MessageManager
965 .getString("label.linked_view_title");
968 * Open in split pane. DNA sequence above, protein below.
970 JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
971 Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
976 public AnnotationColumnChooser getAnnotationColumnSelectionState()
978 return annotationColumnSelectionState;
981 public void setAnnotationColumnSelectionState(
982 AnnotationColumnChooser currentAnnotationColumnSelectionState)
984 this.annotationColumnSelectionState = currentAnnotationColumnSelectionState;
988 public void setIdWidth(int i)
991 AlignmentPanel ap = getAlignPanel();
994 // modify GUI elements to reflect geometry change
995 Dimension idw = getAlignPanel().getIdPanel().getIdCanvas()
998 getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw);
1002 public Rectangle getExplodedGeometry()
1004 return explodedGeometry;
1007 public void setExplodedGeometry(Rectangle explodedPosition)
1009 this.explodedGeometry = explodedPosition;
1012 public boolean isGatherViewsHere()
1014 return gatherViewsHere;
1017 public void setGatherViewsHere(boolean gatherViewsHere)
1019 this.gatherViewsHere = gatherViewsHere;
1023 * If this viewport has a (Protein/cDNA) complement, then scroll the
1024 * complementary alignment to match this one.
1026 public void scrollComplementaryAlignment()
1029 * Populate a SearchResults object with the mapped location to scroll to. If
1030 * there is no complement, or it is not following highlights, or no mapping
1031 * is found, the result will be empty.
1033 SearchResults sr = new SearchResults();
1034 int seqOffset = findComplementScrollTarget(sr);
1037 // TODO would like next line without cast but needs more refactoring...
1038 final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement()).getAlignPanel();
1039 complementPanel.setFollowingComplementScroll(true);
1040 complementPanel.scrollToCentre(sr, seqOffset);
1045 public FeatureRenderer getFeatureRenderer()
1047 return featureRenderer;
1051 public void setFeatureRenderer(FeatureRenderer featureRenderer)
1053 this.featureRenderer = featureRenderer;
1056 public boolean isIncludeHiddenRegion()
1058 return includeHiddenRegion;
1061 public void setIncludeHiddenRegion(boolean includeHiddenRegion)
1063 this.includeHiddenRegion = includeHiddenRegion;