2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 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.AAFrequency;
24 import jalview.analysis.AlignmentSorter;
25 import jalview.analysis.AlignmentUtils;
26 import jalview.analysis.AlignmentUtils.MappingResult;
27 import jalview.analysis.Conservation;
28 import jalview.analysis.CrossRef;
29 import jalview.analysis.Dna;
30 import jalview.analysis.ParseProperties;
31 import jalview.analysis.SequenceIdMatcher;
32 import jalview.api.AlignViewControllerGuiI;
33 import jalview.api.AlignViewControllerI;
34 import jalview.api.AlignViewportI;
35 import jalview.api.AlignmentViewPanel;
36 import jalview.api.analysis.ScoreModelI;
37 import jalview.bin.Cache;
38 import jalview.commands.CommandI;
39 import jalview.commands.EditCommand;
40 import jalview.commands.EditCommand.Action;
41 import jalview.commands.OrderCommand;
42 import jalview.commands.RemoveGapColCommand;
43 import jalview.commands.RemoveGapsCommand;
44 import jalview.commands.SlideSequencesCommand;
45 import jalview.commands.TrimRegionCommand;
46 import jalview.datamodel.AlignedCodonFrame;
47 import jalview.datamodel.Alignment;
48 import jalview.datamodel.AlignmentAnnotation;
49 import jalview.datamodel.AlignmentI;
50 import jalview.datamodel.AlignmentOrder;
51 import jalview.datamodel.AlignmentView;
52 import jalview.datamodel.ColumnSelection;
53 import jalview.datamodel.PDBEntry;
54 import jalview.datamodel.SeqCigar;
55 import jalview.datamodel.Sequence;
56 import jalview.datamodel.SequenceGroup;
57 import jalview.datamodel.SequenceI;
58 import jalview.io.AlignmentProperties;
59 import jalview.io.AnnotationFile;
60 import jalview.io.FeaturesFile;
61 import jalview.io.FileLoader;
62 import jalview.io.FormatAdapter;
63 import jalview.io.HTMLOutput;
64 import jalview.io.IdentifyFile;
65 import jalview.io.JalviewFileChooser;
66 import jalview.io.JalviewFileView;
67 import jalview.io.JnetAnnotationMaker;
68 import jalview.io.NewickFile;
69 import jalview.io.TCoffeeScoreFile;
70 import jalview.jbgui.GAlignFrame;
71 import jalview.schemes.Blosum62ColourScheme;
72 import jalview.schemes.BuriedColourScheme;
73 import jalview.schemes.ClustalxColourScheme;
74 import jalview.schemes.ColourSchemeI;
75 import jalview.schemes.ColourSchemeProperty;
76 import jalview.schemes.HelixColourScheme;
77 import jalview.schemes.HydrophobicColourScheme;
78 import jalview.schemes.NucleotideColourScheme;
79 import jalview.schemes.PIDColourScheme;
80 import jalview.schemes.PurinePyrimidineColourScheme;
81 import jalview.schemes.RNAHelicesColourChooser;
82 import jalview.schemes.ResidueProperties;
83 import jalview.schemes.StrandColourScheme;
84 import jalview.schemes.TCoffeeColourScheme;
85 import jalview.schemes.TaylorColourScheme;
86 import jalview.schemes.TurnColourScheme;
87 import jalview.schemes.UserColourScheme;
88 import jalview.schemes.ZappoColourScheme;
89 import jalview.structure.StructureSelectionManager;
90 import jalview.util.MessageManager;
91 import jalview.ws.jws1.Discoverer;
92 import jalview.ws.jws2.Jws2Discoverer;
93 import jalview.ws.jws2.jabaws2.Jws2Instance;
94 import jalview.ws.seqfetcher.DbSourceProxy;
96 import java.awt.BorderLayout;
97 import java.awt.Component;
98 import java.awt.GridLayout;
99 import java.awt.Rectangle;
100 import java.awt.Toolkit;
101 import java.awt.datatransfer.Clipboard;
102 import java.awt.datatransfer.DataFlavor;
103 import java.awt.datatransfer.StringSelection;
104 import java.awt.datatransfer.Transferable;
105 import java.awt.dnd.DnDConstants;
106 import java.awt.dnd.DropTargetDragEvent;
107 import java.awt.dnd.DropTargetDropEvent;
108 import java.awt.dnd.DropTargetEvent;
109 import java.awt.dnd.DropTargetListener;
110 import java.awt.event.ActionEvent;
111 import java.awt.event.ActionListener;
112 import java.awt.event.KeyAdapter;
113 import java.awt.event.KeyEvent;
114 import java.awt.event.MouseAdapter;
115 import java.awt.event.MouseEvent;
116 import java.awt.print.PageFormat;
117 import java.awt.print.PrinterJob;
118 import java.beans.PropertyChangeEvent;
121 import java.util.ArrayList;
122 import java.util.Arrays;
123 import java.util.Enumeration;
124 import java.util.Hashtable;
125 import java.util.List;
126 import java.util.Vector;
128 import javax.swing.JButton;
129 import javax.swing.JCheckBoxMenuItem;
130 import javax.swing.JEditorPane;
131 import javax.swing.JInternalFrame;
132 import javax.swing.JLabel;
133 import javax.swing.JLayeredPane;
134 import javax.swing.JMenu;
135 import javax.swing.JMenuItem;
136 import javax.swing.JOptionPane;
137 import javax.swing.JPanel;
138 import javax.swing.JProgressBar;
139 import javax.swing.JRadioButtonMenuItem;
140 import javax.swing.JScrollPane;
141 import javax.swing.SwingUtilities;
147 * @version $Revision$
149 public class AlignFrame extends GAlignFrame implements DropTargetListener,
150 IProgressIndicator, AlignViewControllerGuiI
154 public static final int DEFAULT_WIDTH = 700;
157 public static final int DEFAULT_HEIGHT = 500;
159 public AlignmentPanel alignPanel;
161 AlignViewport viewport;
163 public AlignViewControllerI avc;
165 List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
168 * Last format used to load or save alignments in this window
170 String currentFileFormat = null;
173 * Current filename for this alignment
175 String fileName = null;
178 * Creates a new AlignFrame object with specific width and height.
184 public AlignFrame(AlignmentI al, int width, int height)
186 this(al, null, width, height);
190 * Creates a new AlignFrame object with specific width, height and
196 * @param sequenceSetId
198 public AlignFrame(AlignmentI al, int width, int height,
199 String sequenceSetId)
201 this(al, null, width, height, sequenceSetId);
205 * Creates a new AlignFrame object with specific width, height and
211 * @param sequenceSetId
214 public AlignFrame(AlignmentI al, int width, int height,
215 String sequenceSetId, String viewId)
217 this(al, null, width, height, sequenceSetId, viewId);
221 * new alignment window with hidden columns
225 * @param hiddenColumns
226 * ColumnSelection or null
228 * Width of alignment frame
232 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
233 int width, int height)
235 this(al, hiddenColumns, width, height, null);
239 * Create alignment frame for al with hiddenColumns, a specific width and
240 * height, and specific sequenceId
243 * @param hiddenColumns
246 * @param sequenceSetId
249 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
250 int width, int height, String sequenceSetId)
252 this(al, hiddenColumns, width, height, sequenceSetId, null);
256 * Create alignment frame for al with hiddenColumns, a specific width and
257 * height, and specific sequenceId
260 * @param hiddenColumns
263 * @param sequenceSetId
268 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
269 int width, int height, String sequenceSetId, String viewId)
271 setSize(width, height);
273 if (al.getDataset() == null)
278 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
280 alignPanel = new AlignmentPanel(this, viewport);
283 addAlignmentPanel(alignPanel, true);
288 * Make a new AlignFrame from existing alignmentPanels
295 public AlignFrame(AlignmentPanel ap)
299 addAlignmentPanel(ap, false);
304 * initalise the alignframe from the underlying viewport data and the
309 avc = new jalview.controller.AlignViewController(this, viewport,
311 if (viewport.getAlignmentConservationAnnotation() == null)
313 BLOSUM62Colour.setEnabled(false);
314 conservationMenuItem.setEnabled(false);
315 modifyConservation.setEnabled(false);
316 // PIDColour.setEnabled(false);
317 // abovePIDThreshold.setEnabled(false);
318 // modifyPID.setEnabled(false);
321 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
324 if (sortby.equals("Id"))
326 sortIDMenuItem_actionPerformed(null);
328 else if (sortby.equals("Pairwise Identity"))
330 sortPairwiseMenuItem_actionPerformed(null);
333 if (Desktop.desktop != null)
335 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
336 addServiceListeners();
337 setGUINucleotide(viewport.getAlignment().isNucleotide());
340 setMenusFromViewport(viewport);
341 buildSortByAnnotationScoresMenu();
344 if (viewport.wrapAlignment)
346 wrapMenuItem_actionPerformed(null);
349 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
351 this.overviewMenuItem_actionPerformed(null);
359 * Change the filename and format for the alignment, and enable the 'reload'
360 * button functionality.
367 public void setFileName(String file, String format)
370 currentFileFormat = format;
371 reload.setEnabled(true);
374 void addKeyListener()
376 addKeyListener(new KeyAdapter()
379 public void keyPressed(KeyEvent evt)
381 if (viewport.cursorMode
382 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
383 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
384 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
385 && Character.isDigit(evt.getKeyChar()))
387 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
390 switch (evt.getKeyCode())
393 case 27: // escape key
394 deselectAllSequenceMenuItem_actionPerformed(null);
398 case KeyEvent.VK_DOWN:
399 if (evt.isAltDown() || !viewport.cursorMode)
401 moveSelectedSequences(false);
403 if (viewport.cursorMode)
405 alignPanel.seqPanel.moveCursor(0, 1);
410 if (evt.isAltDown() || !viewport.cursorMode)
412 moveSelectedSequences(true);
414 if (viewport.cursorMode)
416 alignPanel.seqPanel.moveCursor(0, -1);
421 case KeyEvent.VK_LEFT:
422 if (evt.isAltDown() || !viewport.cursorMode)
424 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
428 alignPanel.seqPanel.moveCursor(-1, 0);
433 case KeyEvent.VK_RIGHT:
434 if (evt.isAltDown() || !viewport.cursorMode)
436 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
440 alignPanel.seqPanel.moveCursor(1, 0);
444 case KeyEvent.VK_SPACE:
445 if (viewport.cursorMode)
447 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
448 || evt.isShiftDown() || evt.isAltDown());
452 // case KeyEvent.VK_A:
453 // if (viewport.cursorMode)
455 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
456 // //System.out.println("A");
460 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
461 * System.out.println("closing bracket"); } break;
463 case KeyEvent.VK_DELETE:
464 case KeyEvent.VK_BACK_SPACE:
465 if (!viewport.cursorMode)
467 cut_actionPerformed(null);
471 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
472 || evt.isShiftDown() || evt.isAltDown());
478 if (viewport.cursorMode)
480 alignPanel.seqPanel.setCursorRow();
484 if (viewport.cursorMode && !evt.isControlDown())
486 alignPanel.seqPanel.setCursorColumn();
490 if (viewport.cursorMode)
492 alignPanel.seqPanel.setCursorPosition();
496 case KeyEvent.VK_ENTER:
497 case KeyEvent.VK_COMMA:
498 if (viewport.cursorMode)
500 alignPanel.seqPanel.setCursorRowAndColumn();
505 if (viewport.cursorMode)
507 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
511 if (viewport.cursorMode)
513 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
518 viewport.cursorMode = !viewport.cursorMode;
519 statusBar.setText(MessageManager.formatMessage(
520 "label.keyboard_editing_mode", new String[]
521 { (viewport.cursorMode ? "on" : "off") }));
522 if (viewport.cursorMode)
524 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
525 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
527 alignPanel.seqPanel.seqCanvas.repaint();
533 Help.showHelpWindow();
534 } catch (Exception ex)
536 ex.printStackTrace();
541 boolean toggleSeqs = !evt.isControlDown();
542 boolean toggleCols = !evt.isShiftDown();
543 toggleHiddenRegions(toggleSeqs, toggleCols);
546 case KeyEvent.VK_PAGE_UP:
547 if (viewport.wrapAlignment)
549 alignPanel.scrollUp(true);
553 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
554 - viewport.endSeq + viewport.startSeq);
557 case KeyEvent.VK_PAGE_DOWN:
558 if (viewport.wrapAlignment)
560 alignPanel.scrollUp(false);
564 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
565 + viewport.endSeq - viewport.startSeq);
572 public void keyReleased(KeyEvent evt)
574 switch (evt.getKeyCode())
576 case KeyEvent.VK_LEFT:
577 if (evt.isAltDown() || !viewport.cursorMode)
579 viewport.firePropertyChange("alignment", null, viewport
580 .getAlignment().getSequences());
584 case KeyEvent.VK_RIGHT:
585 if (evt.isAltDown() || !viewport.cursorMode)
587 viewport.firePropertyChange("alignment", null, viewport
588 .getAlignment().getSequences());
596 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
598 ap.alignFrame = this;
599 avc = new jalview.controller.AlignViewController(this, viewport,
604 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
606 int aSize = alignPanels.size();
608 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
610 if (aSize == 1 && ap.av.viewName == null)
612 this.getContentPane().add(ap, BorderLayout.CENTER);
618 setInitialTabVisible();
621 expandViews.setEnabled(true);
622 gatherViews.setEnabled(true);
623 tabbedPane.addTab(ap.av.viewName, ap);
625 ap.setVisible(false);
630 if (ap.av.isPadGaps())
632 ap.av.getAlignment().padGaps();
634 ap.av.updateConservation(ap);
635 ap.av.updateConsensus(ap);
636 ap.av.updateStrucConsensus(ap);
640 public void setInitialTabVisible()
642 expandViews.setEnabled(true);
643 gatherViews.setEnabled(true);
644 tabbedPane.setVisible(true);
645 AlignmentPanel first = alignPanels.get(0);
646 tabbedPane.addTab(first.av.viewName, first);
647 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
650 public AlignViewport getViewport()
655 /* Set up intrinsic listeners for dynamically generated GUI bits. */
656 private void addServiceListeners()
658 final java.beans.PropertyChangeListener thisListener;
659 Desktop.instance.addJalviewPropertyChangeListener("services",
660 thisListener = new java.beans.PropertyChangeListener()
663 public void propertyChange(PropertyChangeEvent evt)
665 // // System.out.println("Discoverer property change.");
666 // if (evt.getPropertyName().equals("services"))
668 SwingUtilities.invokeLater(new Runnable()
675 .println("Rebuild WS Menu for service change");
676 BuildWebServiceMenu();
683 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
686 public void internalFrameClosed(
687 javax.swing.event.InternalFrameEvent evt)
689 System.out.println("deregistering discoverer listener");
690 Desktop.instance.removeJalviewPropertyChangeListener("services",
692 closeMenuItem_actionPerformed(true);
695 // Finally, build the menu once to get current service state
696 new Thread(new Runnable()
701 BuildWebServiceMenu();
706 public void setGUINucleotide(boolean nucleotide)
708 showTranslation.setVisible(nucleotide);
709 cdna.setVisible(!nucleotide);
710 conservationMenuItem.setEnabled(!nucleotide);
711 modifyConservation.setEnabled(!nucleotide);
712 showGroupConservation.setEnabled(!nucleotide);
713 rnahelicesColour.setEnabled(nucleotide);
714 purinePyrimidineColour.setEnabled(nucleotide);
718 * Builds codon mappings from this (protein) alignment to any compatible
719 * nucleotide alignments. Mappings are built between sequences with the same
720 * name and compatible lengths. Also makes the cDNA alignment a
721 * CommandListener for the protein alignment so that edits are mirrored.
724 protected void linkCdna_actionPerformed()
727 int alreadyLinkedCount = 0;
728 final AlignmentI thisAlignment = this.alignPanel.getAlignment();
730 for (AlignFrame af : Desktop.getAlignFrames())
732 if (af.alignPanel != null)
734 final AlignmentI thatAlignment = af.alignPanel.getAlignment();
735 if (thatAlignment.isNucleotide())
737 MappingResult mapped = AlignmentUtils.mapProteinToCdna(
738 thisAlignment, thatAlignment);
739 if (mapped == MappingResult.AlreadyMapped)
741 alreadyLinkedCount++;
743 else if (mapped == MappingResult.Mapped)
745 final StructureSelectionManager ssm = StructureSelectionManager
746 .getStructureSelectionManager(Desktop.instance);
747 ssm.addMappings(thisAlignment.getCodonFrames());
748 // enable the next line to enable linked editing
749 // ssm.addCommandListener(af.getViewport());
756 if (linkedCount == 0 && alreadyLinkedCount == 0)
758 msg = MessageManager.getString("label.no_cdna");
760 else if (linkedCount > 0)
762 msg = MessageManager.formatMessage("label.linked_cdna", linkedCount);
766 msg = MessageManager.formatMessage("label.cdna_all_linked",
773 * Align any linked cDNA to match the alignment of this (protein) alignment.
774 * Any mapped sequence regions will be realigned, unmapped sequences are not
778 protected void alignCdna_actionPerformed()
782 final AlignmentI thisAlignment = this.alignPanel.getAlignment();
783 for (AlignFrame af : Desktop.getAlignFrames())
785 if (af.alignPanel != null)
787 final AlignmentI thatAlignment = af.alignPanel.getAlignment();
788 if (thatAlignment.isNucleotide())
790 int seqsAligned = thatAlignment.alignAs(thisAlignment);
791 seqCount += seqsAligned;
794 af.alignPanel.alignmentChanged();
800 setStatus(MessageManager.formatMessage("label.cdna_aligned", seqCount,
804 * set up menus for the current viewport. This may be called after any
805 * operation that affects the data in the current view (selection changed,
806 * etc) to update the menus to reflect the new state.
808 public void setMenusForViewport()
810 setMenusFromViewport(viewport);
814 * Need to call this method when tabs are selected for multiple views, or when
815 * loading from Jalview2XML.java
820 void setMenusFromViewport(AlignViewport av)
822 padGapsMenuitem.setSelected(av.isPadGaps());
823 colourTextMenuItem.setSelected(av.showColourText);
824 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
825 conservationMenuItem.setSelected(av.getConservationSelected());
826 seqLimits.setSelected(av.getShowJVSuffix());
827 idRightAlign.setSelected(av.rightAlignIds);
828 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
829 renderGapsMenuItem.setSelected(av.renderGaps);
830 wrapMenuItem.setSelected(av.wrapAlignment);
831 scaleAbove.setVisible(av.wrapAlignment);
832 scaleLeft.setVisible(av.wrapAlignment);
833 scaleRight.setVisible(av.wrapAlignment);
834 annotationPanelMenuItem.setState(av.showAnnotation);
836 * Show/hide annotations only enabled if annotation panel is shown
838 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
839 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
840 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
841 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
842 viewBoxesMenuItem.setSelected(av.showBoxes);
843 viewTextMenuItem.setSelected(av.showText);
844 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
845 showGroupConsensus.setSelected(av.isShowGroupConsensus());
846 showGroupConservation.setSelected(av.isShowGroupConservation());
847 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
848 showSequenceLogo.setSelected(av.isShowSequenceLogo());
849 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
851 setColourSelected(ColourSchemeProperty.getColourName(av
852 .getGlobalColourScheme()));
854 showSeqFeatures.setSelected(av.showSequenceFeatures);
855 hiddenMarkers.setState(av.showHiddenMarkers);
856 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
857 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
858 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
859 autoCalculate.setSelected(av.autoCalculateConsensus);
860 sortByTree.setSelected(av.sortByTree);
861 listenToViewSelections.setSelected(av.followSelection);
862 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
864 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
865 setShowProductsEnabled();
869 // methods for implementing IProgressIndicator
870 // need to refactor to a reusable stub class
871 Hashtable progressBars, progressBarHandlers;
876 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
879 public void setProgressBar(String message, long id)
881 if (progressBars == null)
883 progressBars = new Hashtable();
884 progressBarHandlers = new Hashtable();
887 JPanel progressPanel;
888 Long lId = new Long(id);
889 GridLayout layout = (GridLayout) statusPanel.getLayout();
890 if (progressBars.get(lId) != null)
892 progressPanel = (JPanel) progressBars.get(new Long(id));
893 statusPanel.remove(progressPanel);
894 progressBars.remove(lId);
895 progressPanel = null;
898 statusBar.setText(message);
900 if (progressBarHandlers.contains(lId))
902 progressBarHandlers.remove(lId);
904 layout.setRows(layout.getRows() - 1);
908 progressPanel = new JPanel(new BorderLayout(10, 5));
910 JProgressBar progressBar = new JProgressBar();
911 progressBar.setIndeterminate(true);
913 progressPanel.add(new JLabel(message), BorderLayout.WEST);
914 progressPanel.add(progressBar, BorderLayout.CENTER);
916 layout.setRows(layout.getRows() + 1);
917 statusPanel.add(progressPanel);
919 progressBars.put(lId, progressPanel);
922 // setMenusForViewport();
927 public void registerHandler(final long id,
928 final IProgressIndicatorHandler handler)
930 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
932 throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
934 progressBarHandlers.put(new Long(id), handler);
935 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
936 if (handler.canCancel())
938 JButton cancel = new JButton(
939 MessageManager.getString("action.cancel"));
940 final IProgressIndicator us = this;
941 cancel.addActionListener(new ActionListener()
945 public void actionPerformed(ActionEvent e)
947 handler.cancelActivity(id);
948 us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
951 progressPanel.add(cancel, BorderLayout.EAST);
957 * @return true if any progress bars are still active
960 public boolean operationInProgress()
962 if (progressBars != null && progressBars.size() > 0)
970 public void setStatus(String text)
972 statusBar.setText(text);
976 * Added so Castor Mapping file can obtain Jalview Version
978 public String getVersion()
980 return jalview.bin.Cache.getProperty("VERSION");
983 public FeatureRenderer getFeatureRenderer()
985 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
989 public void fetchSequence_actionPerformed(ActionEvent e)
991 new SequenceFetcher(this);
995 public void addFromFile_actionPerformed(ActionEvent e)
997 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1001 public void reload_actionPerformed(ActionEvent e)
1003 if (fileName != null)
1005 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1006 // originating file's format
1007 // TODO: work out how to recover feature settings for correct view(s) when
1008 // file is reloaded.
1009 if (currentFileFormat.equals("Jalview"))
1011 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1012 for (int i = 0; i < frames.length; i++)
1014 if (frames[i] instanceof AlignFrame && frames[i] != this
1015 && ((AlignFrame) frames[i]).fileName != null
1016 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1020 frames[i].setSelected(true);
1021 Desktop.instance.closeAssociatedWindows();
1022 } catch (java.beans.PropertyVetoException ex)
1028 Desktop.instance.closeAssociatedWindows();
1030 FileLoader loader = new FileLoader();
1031 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1032 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1036 Rectangle bounds = this.getBounds();
1038 FileLoader loader = new FileLoader();
1039 String protocol = fileName.startsWith("http:") ? "URL" : "File";
1040 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1041 protocol, currentFileFormat);
1043 newframe.setBounds(bounds);
1044 if (featureSettings != null && featureSettings.isShowing())
1046 final Rectangle fspos = featureSettings.frame.getBounds();
1047 // TODO: need a 'show feature settings' function that takes bounds -
1048 // need to refactor Desktop.addFrame
1049 newframe.featureSettings_actionPerformed(null);
1050 final FeatureSettings nfs = newframe.featureSettings;
1051 SwingUtilities.invokeLater(new Runnable()
1056 nfs.frame.setBounds(fspos);
1059 this.featureSettings.close();
1060 this.featureSettings = null;
1062 this.closeMenuItem_actionPerformed(true);
1068 public void addFromText_actionPerformed(ActionEvent e)
1070 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
1074 public void addFromURL_actionPerformed(ActionEvent e)
1076 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1080 public void save_actionPerformed(ActionEvent e)
1082 if (fileName == null
1083 || (currentFileFormat == null || !jalview.io.FormatAdapter
1084 .isValidIOFormat(currentFileFormat, true))
1085 || fileName.startsWith("http"))
1087 saveAs_actionPerformed(null);
1091 saveAlignment(fileName, currentFileFormat);
1102 public void saveAs_actionPerformed(ActionEvent e)
1104 JalviewFileChooser chooser = new JalviewFileChooser(
1105 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1106 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1107 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1108 currentFileFormat, false);
1110 chooser.setFileView(new JalviewFileView());
1111 chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
1112 chooser.setToolTipText(MessageManager.getString("action.save"));
1114 int value = chooser.showSaveDialog(this);
1116 if (value == JalviewFileChooser.APPROVE_OPTION)
1118 currentFileFormat = chooser.getSelectedFormat();
1119 while (currentFileFormat == null)
1122 .showInternalMessageDialog(
1125 .getString("label.select_file_format_before_saving"),
1127 .getString("label.file_format_not_specified"),
1128 JOptionPane.WARNING_MESSAGE);
1129 currentFileFormat = chooser.getSelectedFormat();
1130 value = chooser.showSaveDialog(this);
1131 if (value != JalviewFileChooser.APPROVE_OPTION)
1137 fileName = chooser.getSelectedFile().getPath();
1139 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1142 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1143 if (currentFileFormat.indexOf(" ") > -1)
1145 currentFileFormat = currentFileFormat.substring(0,
1146 currentFileFormat.indexOf(" "));
1148 saveAlignment(fileName, currentFileFormat);
1152 public boolean saveAlignment(String file, String format)
1154 boolean success = true;
1156 if (format.equalsIgnoreCase("Jalview"))
1158 String shortName = title;
1160 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1162 shortName = shortName.substring(shortName
1163 .lastIndexOf(java.io.File.separatorChar) + 1);
1166 success = new Jalview2XML().SaveAlignment(this, file, shortName);
1168 statusBar.setText(MessageManager.formatMessage(
1169 "label.successfully_saved_to_file_in_format", new String[]
1170 { fileName, format }));
1175 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1177 warningMessage("Cannot save file " + fileName + " using format "
1178 + format, "Alignment output format not supported");
1179 saveAs_actionPerformed(null);
1180 // JBPNote need to have a raise_gui flag here
1184 String[] omitHidden = null;
1186 if (viewport.hasHiddenColumns())
1188 int reply = JOptionPane
1189 .showInternalConfirmDialog(
1192 .getString("label.alignment_contains_hidden_columns"),
1194 .getString("action.save_omit_hidden_columns"),
1195 JOptionPane.YES_NO_OPTION,
1196 JOptionPane.QUESTION_MESSAGE);
1198 if (reply == JOptionPane.YES_OPTION)
1200 omitHidden = viewport.getViewAsString(false);
1203 FormatAdapter f = new FormatAdapter();
1204 String output = f.formatSequences(format,
1205 viewport.getAlignment(), // class cast exceptions will
1206 // occur in the distant future
1207 omitHidden, f.getCacheSuffixDefault(format),
1208 viewport.getColumnSelection());
1218 java.io.PrintWriter out = new java.io.PrintWriter(
1219 new java.io.FileWriter(file));
1223 this.setTitle(file);
1224 statusBar.setText(MessageManager.formatMessage(
1225 "label.successfully_saved_to_file_in_format",
1227 { fileName, format }));
1228 } catch (Exception ex)
1231 ex.printStackTrace();
1238 JOptionPane.showInternalMessageDialog(this, MessageManager
1239 .formatMessage("label.couldnt_save_file", new String[]
1240 { fileName }), MessageManager
1241 .getString("label.error_saving_file"),
1242 JOptionPane.WARNING_MESSAGE);
1248 private void warningMessage(String warning, String title)
1250 if (new jalview.util.Platform().isHeadless())
1252 System.err.println("Warning: " + title + "\nWarning: " + warning);
1257 JOptionPane.showInternalMessageDialog(this, warning, title,
1258 JOptionPane.WARNING_MESSAGE);
1270 protected void outputText_actionPerformed(ActionEvent e)
1272 String[] omitHidden = null;
1274 if (viewport.hasHiddenColumns())
1276 int reply = JOptionPane
1277 .showInternalConfirmDialog(
1280 .getString("label.alignment_contains_hidden_columns"),
1282 .getString("action.save_omit_hidden_columns"),
1283 JOptionPane.YES_NO_OPTION,
1284 JOptionPane.QUESTION_MESSAGE);
1286 if (reply == JOptionPane.YES_OPTION)
1288 omitHidden = viewport.getViewAsString(false);
1292 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1293 cap.setForInput(null);
1297 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1298 viewport.getAlignment(), omitHidden,
1299 viewport.getColumnSelection()));
1300 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1301 "label.alignment_output_command", new String[]
1302 { e.getActionCommand() }), 600, 500);
1303 } catch (OutOfMemoryError oom)
1305 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1318 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1320 new HTMLOutput(alignPanel,
1321 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1322 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1325 public void createImageMap(File file, String image)
1327 alignPanel.makePNGImageMap(file, image);
1337 public void createPNG(File f)
1339 alignPanel.makePNG(f);
1349 public void createEPS(File f)
1351 alignPanel.makeEPS(f);
1354 public void createSVG(File f)
1356 alignPanel.makeSVG(f);
1359 public void pageSetup_actionPerformed(ActionEvent e)
1361 PrinterJob printJob = PrinterJob.getPrinterJob();
1362 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1372 public void printMenuItem_actionPerformed(ActionEvent e)
1374 // Putting in a thread avoids Swing painting problems
1375 PrintThread thread = new PrintThread(alignPanel);
1380 public void exportFeatures_actionPerformed(ActionEvent e)
1382 new AnnotationExporter().exportFeatures(alignPanel);
1386 public void exportAnnotations_actionPerformed(ActionEvent e)
1388 new AnnotationExporter().exportAnnotations(alignPanel,
1389 viewport.showAnnotation ? viewport.getAlignment()
1390 .getAlignmentAnnotation() : null, viewport
1391 .getAlignment().getGroups(), ((Alignment) viewport
1392 .getAlignment()).alignmentProperties);
1396 public void associatedData_actionPerformed(ActionEvent e)
1398 // Pick the tree file
1399 JalviewFileChooser chooser = new JalviewFileChooser(
1400 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1401 chooser.setFileView(new JalviewFileView());
1402 chooser.setDialogTitle(MessageManager
1403 .getString("label.load_jalview_annotations"));
1404 chooser.setToolTipText(MessageManager
1405 .getString("label.load_jalview_annotations"));
1407 int value = chooser.showOpenDialog(null);
1409 if (value == JalviewFileChooser.APPROVE_OPTION)
1411 String choice = chooser.getSelectedFile().getPath();
1412 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1413 loadJalviewDataFile(choice, null, null, null);
1419 * Close the current view or all views in the alignment frame. If the frame
1420 * only contains one view then the alignment will be removed from memory.
1422 * @param closeAllTabs
1425 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1427 if (alignPanels != null && alignPanels.size() < 2)
1429 closeAllTabs = true;
1434 if (alignPanels != null)
1438 if (this.isClosed())
1440 // really close all the windows - otherwise wait till
1441 // setClosed(true) is called
1442 for (int i = 0; i < alignPanels.size(); i++)
1444 AlignmentPanel ap = alignPanels.get(i);
1451 closeView(alignPanel);
1457 this.setClosed(true);
1459 } catch (Exception ex)
1461 ex.printStackTrace();
1466 * close alignPanel2 and shuffle tabs appropriately.
1468 * @param alignPanel2
1470 public void closeView(AlignmentPanel alignPanel2)
1472 int index = tabbedPane.getSelectedIndex();
1473 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1474 alignPanels.remove(alignPanel2);
1476 // if (viewport == alignPanel2.av)
1480 alignPanel2.closePanel();
1483 tabbedPane.removeTabAt(closedindex);
1484 tabbedPane.validate();
1486 if (index > closedindex || index == tabbedPane.getTabCount())
1488 // modify currently selected tab index if necessary.
1492 this.tabSelectionChanged(index);
1498 void updateEditMenuBar()
1501 if (viewport.getHistoryList().size() > 0)
1503 undoMenuItem.setEnabled(true);
1504 CommandI command = viewport.getHistoryList().peek();
1505 undoMenuItem.setText(MessageManager.formatMessage(
1506 "label.undo_command", new String[]
1507 { command.getDescription() }));
1511 undoMenuItem.setEnabled(false);
1512 undoMenuItem.setText(MessageManager.getString("action.undo"));
1515 if (viewport.getRedoList().size() > 0)
1517 redoMenuItem.setEnabled(true);
1519 CommandI command = viewport.getRedoList().peek();
1520 redoMenuItem.setText(MessageManager.formatMessage(
1521 "label.redo_command", new String[]
1522 { command.getDescription() }));
1526 redoMenuItem.setEnabled(false);
1527 redoMenuItem.setText(MessageManager.getString("action.redo"));
1531 public void addHistoryItem(CommandI command)
1533 if (command.getSize() > 0)
1535 viewport.addToHistoryList(command);
1536 viewport.clearRedoList();
1537 updateEditMenuBar();
1538 viewport.updateHiddenColumns();
1539 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1540 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1541 // viewport.getColumnSelection()
1542 // .getHiddenColumns().size() > 0);
1548 * @return alignment objects for all views
1550 AlignmentI[] getViewAlignments()
1552 if (alignPanels != null)
1554 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1556 for (AlignmentPanel ap : alignPanels)
1558 als[i++] = ap.av.getAlignment();
1562 if (viewport != null)
1564 return new AlignmentI[]
1565 { viewport.getAlignment() };
1577 protected void undoMenuItem_actionPerformed(ActionEvent e)
1579 if (viewport.getHistoryList().isEmpty())
1583 CommandI command = viewport.getHistoryList().pop();
1584 viewport.addToRedoList(command);
1585 // TODO: execute command before adding to redo list / broadcasting?
1586 command.undoCommand(getViewAlignments());
1588 AlignViewport originalSource = getOriginatingSource(command);
1589 updateEditMenuBar();
1591 if (originalSource != null)
1593 if (originalSource != viewport)
1596 .warn("Implementation worry: mismatch of viewport origin for undo");
1598 originalSource.updateHiddenColumns();
1599 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1601 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1602 // viewport.getColumnSelection()
1603 // .getHiddenColumns().size() > 0);
1604 originalSource.firePropertyChange("alignment", null, originalSource
1605 .getAlignment().getSequences());
1616 protected void redoMenuItem_actionPerformed(ActionEvent e)
1618 if (viewport.getRedoList().size() < 1)
1623 CommandI command = viewport.getRedoList().pop();
1624 viewport.addToHistoryList(command);
1625 command.doCommand(getViewAlignments());
1627 AlignViewport originalSource = getOriginatingSource(command);
1628 updateEditMenuBar();
1630 if (originalSource != null)
1633 if (originalSource != viewport)
1636 .warn("Implementation worry: mismatch of viewport origin for redo");
1638 originalSource.updateHiddenColumns();
1639 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1641 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1642 // viewport.getColumnSelection()
1643 // .getHiddenColumns().size() > 0);
1644 originalSource.firePropertyChange("alignment", null, originalSource
1645 .getAlignment().getSequences());
1649 AlignViewport getOriginatingSource(CommandI command)
1651 AlignViewport originalSource = null;
1652 // For sequence removal and addition, we need to fire
1653 // the property change event FROM the viewport where the
1654 // original alignment was altered
1655 AlignmentI al = null;
1656 if (command instanceof EditCommand)
1658 EditCommand editCommand = (EditCommand) command;
1659 al = editCommand.getAlignment();
1660 Vector comps = (Vector) PaintRefresher.components.get(viewport
1661 .getSequenceSetId());
1663 for (int i = 0; i < comps.size(); i++)
1665 if (comps.elementAt(i) instanceof AlignmentPanel)
1667 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1669 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1676 if (originalSource == null)
1678 // The original view is closed, we must validate
1679 // the current view against the closed view first
1682 PaintRefresher.validateSequences(al, viewport.getAlignment());
1685 originalSource = viewport;
1688 return originalSource;
1697 public void moveSelectedSequences(boolean up)
1699 SequenceGroup sg = viewport.getSelectionGroup();
1705 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1706 viewport.getHiddenRepSequences(), up);
1707 alignPanel.paintAlignment(true);
1709 final AlignViewportI slave = viewport.getSlave();
1712 final SequenceGroup selectionGroup = viewport.getSlave()
1713 .getSelectionGroup();
1714 if (selectionGroup != null)
1718 .moveSelectedSequencesByOne(
1719 viewport.getSlave().getSelectionGroup(),
1720 viewport.getSlave().getHiddenRepSequences(), up);
1725 synchronized void slideSequences(boolean right, int size)
1727 List<SequenceI> sg = new Vector();
1728 if (viewport.cursorMode)
1730 sg.add(viewport.getAlignment().getSequenceAt(
1731 alignPanel.seqPanel.seqCanvas.cursorY));
1733 else if (viewport.getSelectionGroup() != null
1734 && viewport.getSelectionGroup().getSize() != viewport
1735 .getAlignment().getHeight())
1737 sg = viewport.getSelectionGroup().getSequences(
1738 viewport.getHiddenRepSequences());
1746 Vector invertGroup = new Vector();
1748 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1750 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1752 invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1756 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1758 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1759 for (int i = 0; i < invertGroup.size(); i++)
1761 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1764 SlideSequencesCommand ssc;
1767 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1768 size, viewport.getGapCharacter());
1772 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1773 size, viewport.getGapCharacter());
1776 int groupAdjustment = 0;
1777 if (ssc.getGapsInsertedBegin() && right)
1779 if (viewport.cursorMode)
1781 alignPanel.seqPanel.moveCursor(size, 0);
1785 groupAdjustment = size;
1788 else if (!ssc.getGapsInsertedBegin() && !right)
1790 if (viewport.cursorMode)
1792 alignPanel.seqPanel.moveCursor(-size, 0);
1796 groupAdjustment = -size;
1800 if (groupAdjustment != 0)
1802 viewport.getSelectionGroup().setStartRes(
1803 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1804 viewport.getSelectionGroup().setEndRes(
1805 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1808 boolean appendHistoryItem = false;
1809 if (viewport.getHistoryList() != null
1810 && viewport.getHistoryList().size() > 0
1811 && viewport.getHistoryList().peek() instanceof SlideSequencesCommand)
1813 appendHistoryItem = ssc
1814 .appendSlideCommand((SlideSequencesCommand) viewport
1819 if (!appendHistoryItem)
1821 addHistoryItem(ssc);
1834 protected void copy_actionPerformed(ActionEvent e)
1837 if (viewport.getSelectionGroup() == null)
1841 // TODO: preserve the ordering of displayed alignment annotation in any
1842 // internal paste (particularly sequence associated annotation)
1843 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1844 String[] omitHidden = null;
1846 if (viewport.hasHiddenColumns())
1848 omitHidden = viewport.getViewAsString(true);
1851 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1854 StringSelection ss = new StringSelection(output);
1858 jalview.gui.Desktop.internalCopy = true;
1859 // Its really worth setting the clipboard contents
1860 // to empty before setting the large StringSelection!!
1861 Toolkit.getDefaultToolkit().getSystemClipboard()
1862 .setContents(new StringSelection(""), null);
1864 Toolkit.getDefaultToolkit().getSystemClipboard()
1865 .setContents(ss, Desktop.instance);
1866 } catch (OutOfMemoryError er)
1868 new OOMWarning("copying region", er);
1872 Vector hiddenColumns = null;
1873 if (viewport.hasHiddenColumns())
1875 hiddenColumns = new Vector();
1876 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1877 .getSelectionGroup().getEndRes();
1878 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1881 int[] region = (int[]) viewport.getColumnSelection()
1882 .getHiddenColumns().elementAt(i);
1883 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1885 hiddenColumns.addElement(new int[]
1886 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1891 Desktop.jalviewClipboard = new Object[]
1892 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1893 statusBar.setText(MessageManager.formatMessage(
1894 "label.copied_sequences_to_clipboard", new String[]
1895 { Integer.valueOf(seqs.length).toString() }));
1905 protected void pasteNew_actionPerformed(ActionEvent e)
1917 protected void pasteThis_actionPerformed(ActionEvent e)
1923 * Paste contents of Jalview clipboard
1925 * @param newAlignment
1926 * true to paste to a new alignment, otherwise add to this.
1928 void paste(boolean newAlignment)
1930 boolean externalPaste = true;
1933 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1934 Transferable contents = c.getContents(this);
1936 if (contents == null)
1944 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1945 if (str.length() < 1)
1950 format = new IdentifyFile().Identify(str, "Paste");
1952 } catch (OutOfMemoryError er)
1954 new OOMWarning("Out of memory pasting sequences!!", er);
1958 SequenceI[] sequences;
1959 boolean annotationAdded = false;
1960 AlignmentI alignment = null;
1962 if (Desktop.jalviewClipboard != null)
1964 // The clipboard was filled from within Jalview, we must use the
1966 // And dataset from the copied alignment
1967 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1968 // be doubly sure that we create *new* sequence objects.
1969 sequences = new SequenceI[newseq.length];
1970 for (int i = 0; i < newseq.length; i++)
1972 sequences[i] = new Sequence(newseq[i]);
1974 alignment = new Alignment(sequences);
1975 externalPaste = false;
1979 // parse the clipboard as an alignment.
1980 alignment = new FormatAdapter().readFile(str, "Paste", format);
1981 sequences = alignment.getSequencesArray();
1985 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1991 if (Desktop.jalviewClipboard != null)
1993 // dataset is inherited
1994 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1998 // new dataset is constructed
1999 alignment.setDataset(null);
2001 alwidth = alignment.getWidth() + 1;
2005 AlignmentI pastedal = alignment; // preserve pasted alignment object
2006 // Add pasted sequences and dataset into existing alignment.
2007 alignment = viewport.getAlignment();
2008 alwidth = alignment.getWidth() + 1;
2009 // decide if we need to import sequences from an existing dataset
2010 boolean importDs = Desktop.jalviewClipboard != null
2011 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2012 // importDs==true instructs us to copy over new dataset sequences from
2013 // an existing alignment
2014 Vector newDs = (importDs) ? new Vector() : null; // used to create
2015 // minimum dataset set
2017 for (int i = 0; i < sequences.length; i++)
2021 newDs.addElement(null);
2023 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2025 if (importDs && ds != null)
2027 if (!newDs.contains(ds))
2029 newDs.setElementAt(ds, i);
2030 ds = new Sequence(ds);
2031 // update with new dataset sequence
2032 sequences[i].setDatasetSequence(ds);
2036 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2041 // copy and derive new dataset sequence
2042 sequences[i] = sequences[i].deriveSequence();
2043 alignment.getDataset().addSequence(
2044 sequences[i].getDatasetSequence());
2045 // TODO: avoid creation of duplicate dataset sequences with a
2046 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2048 alignment.addSequence(sequences[i]); // merges dataset
2052 newDs.clear(); // tidy up
2054 if (alignment.getAlignmentAnnotation() != null)
2056 for (AlignmentAnnotation alan : alignment
2057 .getAlignmentAnnotation())
2059 if (alan.graphGroup > fgroup)
2061 fgroup = alan.graphGroup;
2065 if (pastedal.getAlignmentAnnotation() != null)
2067 // Add any annotation attached to alignment.
2068 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2069 for (int i = 0; i < alann.length; i++)
2071 annotationAdded = true;
2072 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2074 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2075 if (newann.graphGroup > -1)
2077 if (newGraphGroups.size() <= newann.graphGroup
2078 || newGraphGroups.get(newann.graphGroup) == null)
2080 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2082 newGraphGroups.add(q, null);
2084 newGraphGroups.set(newann.graphGroup, new Integer(
2087 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2091 newann.padAnnotation(alwidth);
2092 alignment.addAnnotation(newann);
2102 addHistoryItem(new EditCommand(
2103 MessageManager.getString("label.add_sequences"),
2105 sequences, 0, alignment.getWidth(), alignment));
2107 // Add any annotations attached to sequences
2108 for (int i = 0; i < sequences.length; i++)
2110 if (sequences[i].getAnnotation() != null)
2112 AlignmentAnnotation newann;
2113 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2115 annotationAdded = true;
2116 newann = sequences[i].getAnnotation()[a];
2117 newann.adjustForAlignment();
2118 newann.padAnnotation(alwidth);
2119 if (newann.graphGroup > -1)
2121 if (newann.graphGroup > -1)
2123 if (newGraphGroups.size() <= newann.graphGroup
2124 || newGraphGroups.get(newann.graphGroup) == null)
2126 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2128 newGraphGroups.add(q, null);
2130 newGraphGroups.set(newann.graphGroup, new Integer(
2133 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2137 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2142 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2149 // propagate alignment changed.
2150 viewport.setEndSeq(alignment.getHeight());
2151 if (annotationAdded)
2153 // Duplicate sequence annotation in all views.
2154 AlignmentI[] alview = this.getViewAlignments();
2155 for (int i = 0; i < sequences.length; i++)
2157 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2162 for (int avnum = 0; avnum < alview.length; avnum++)
2164 if (alview[avnum] != alignment)
2166 // duplicate in a view other than the one with input focus
2167 int avwidth = alview[avnum].getWidth() + 1;
2168 // this relies on sann being preserved after we
2169 // modify the sequence's annotation array for each duplication
2170 for (int a = 0; a < sann.length; a++)
2172 AlignmentAnnotation newann = new AlignmentAnnotation(
2174 sequences[i].addAlignmentAnnotation(newann);
2175 newann.padAnnotation(avwidth);
2176 alview[avnum].addAnnotation(newann); // annotation was
2177 // duplicated earlier
2178 // TODO JAL-1145 graphGroups are not updated for sequence
2179 // annotation added to several views. This may cause
2181 alview[avnum].setAnnotationIndex(newann, a);
2186 buildSortByAnnotationScoresMenu();
2188 viewport.firePropertyChange("alignment", null,
2189 alignment.getSequences());
2190 if (alignPanels != null)
2192 for (AlignmentPanel ap : alignPanels)
2194 ap.validateAnnotationDimensions(false);
2199 alignPanel.validateAnnotationDimensions(false);
2205 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2207 String newtitle = new String("Copied sequences");
2209 if (Desktop.jalviewClipboard != null
2210 && Desktop.jalviewClipboard[2] != null)
2212 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2213 for (int i = 0; i < hc.size(); i++)
2215 int[] region = (int[]) hc.elementAt(i);
2216 af.viewport.hideColumns(region[0], region[1]);
2220 // >>>This is a fix for the moment, until a better solution is
2222 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2224 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2226 // TODO: maintain provenance of an alignment, rather than just make the
2227 // title a concatenation of operations.
2230 if (title.startsWith("Copied sequences"))
2236 newtitle = newtitle.concat("- from " + title);
2241 newtitle = new String("Pasted sequences");
2244 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2249 } catch (Exception ex)
2251 ex.printStackTrace();
2252 System.out.println("Exception whilst pasting: " + ex);
2253 // could be anything being pasted in here
2259 protected void expand_newalign(ActionEvent e)
2263 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2264 .getAlignment(), -1);
2265 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2267 String newtitle = new String("Flanking alignment");
2269 if (Desktop.jalviewClipboard != null
2270 && Desktop.jalviewClipboard[2] != null)
2272 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2273 for (int i = 0; i < hc.size(); i++)
2275 int[] region = (int[]) hc.elementAt(i);
2276 af.viewport.hideColumns(region[0], region[1]);
2280 // >>>This is a fix for the moment, until a better solution is
2282 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2284 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2286 // TODO: maintain provenance of an alignment, rather than just make the
2287 // title a concatenation of operations.
2289 if (title.startsWith("Copied sequences"))
2295 newtitle = newtitle.concat("- from " + title);
2299 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2301 } catch (Exception ex)
2303 ex.printStackTrace();
2304 System.out.println("Exception whilst pasting: " + ex);
2305 // could be anything being pasted in here
2306 } catch (OutOfMemoryError oom)
2308 new OOMWarning("Viewing flanking region of alignment", oom);
2319 protected void cut_actionPerformed(ActionEvent e)
2321 copy_actionPerformed(null);
2322 delete_actionPerformed(null);
2332 protected void delete_actionPerformed(ActionEvent evt)
2335 SequenceGroup sg = viewport.getSelectionGroup();
2341 List<SequenceI> seqs = new ArrayList<SequenceI>(sg.getSize());
2343 for (int i = 0; i < sg.getSize(); i++)
2345 seq = sg.getSequenceAt(i);
2349 // If the cut affects all sequences, warn, remove highlighted columns
2350 if (sg.getSize() == viewport.getAlignment().getHeight())
2352 int confirm = JOptionPane.showConfirmDialog(this,
2353 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2354 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2355 JOptionPane.OK_CANCEL_OPTION);
2357 if (confirm == JOptionPane.CANCEL_OPTION
2358 || confirm == JOptionPane.CLOSED_OPTION)
2362 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2363 sg.getEndRes() + 1);
2366 SequenceI[] cut = new SequenceI[seqs.size()];
2367 for (int i = 0; i < seqs.size(); i++)
2369 cut[i] = seqs.get(i);
2373 * //ADD HISTORY ITEM
2375 addHistoryItem(new EditCommand(
2376 MessageManager.getString("label.cut_sequences"), Action.CUT,
2377 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2378 viewport.getAlignment()));
2380 viewport.setSelectionGroup(null);
2381 viewport.sendSelection();
2382 viewport.getAlignment().deleteGroup(sg);
2384 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2386 if (viewport.getAlignment().getHeight() < 1)
2390 this.setClosed(true);
2391 } catch (Exception ex)
2404 protected void deleteGroups_actionPerformed(ActionEvent e)
2406 if (avc.deleteGroups())
2408 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2409 alignPanel.updateAnnotation();
2410 alignPanel.paintAlignment(true);
2421 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2423 SequenceGroup sg = new SequenceGroup();
2425 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2427 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2430 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2431 viewport.setSelectionGroup(sg);
2432 viewport.sendSelection();
2433 alignPanel.paintAlignment(true);
2434 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2444 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2446 if (viewport.cursorMode)
2448 alignPanel.seqPanel.keyboardNo1 = null;
2449 alignPanel.seqPanel.keyboardNo2 = null;
2451 viewport.setSelectionGroup(null);
2452 viewport.getColumnSelection().clear();
2453 viewport.setSelectionGroup(null);
2454 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2455 alignPanel.idPanel.idCanvas.searchResults = null;
2456 alignPanel.paintAlignment(true);
2457 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2458 viewport.sendSelection();
2468 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2470 SequenceGroup sg = viewport.getSelectionGroup();
2474 selectAllSequenceMenuItem_actionPerformed(null);
2479 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2481 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2484 alignPanel.paintAlignment(true);
2485 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2486 viewport.sendSelection();
2490 public void invertColSel_actionPerformed(ActionEvent e)
2492 viewport.invertColumnSelection();
2493 alignPanel.paintAlignment(true);
2494 viewport.sendSelection();
2504 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2506 trimAlignment(true);
2516 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2518 trimAlignment(false);
2521 void trimAlignment(boolean trimLeft)
2523 ColumnSelection colSel = viewport.getColumnSelection();
2526 if (colSel.size() > 0)
2530 column = colSel.getMin();
2534 column = colSel.getMax();
2538 if (viewport.getSelectionGroup() != null)
2540 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2541 viewport.getHiddenRepSequences());
2545 seqs = viewport.getAlignment().getSequencesArray();
2548 TrimRegionCommand trimRegion;
2551 trimRegion = new TrimRegionCommand("Remove Left",
2552 TrimRegionCommand.TRIM_LEFT, seqs, column,
2553 viewport.getAlignment(), viewport.getColumnSelection(),
2554 viewport.getSelectionGroup());
2555 viewport.setStartRes(0);
2559 trimRegion = new TrimRegionCommand("Remove Right",
2560 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2561 viewport.getAlignment(), viewport.getColumnSelection(),
2562 viewport.getSelectionGroup());
2565 statusBar.setText(MessageManager.formatMessage(
2566 "label.removed_columns", new String[]
2567 { Integer.valueOf(trimRegion.getSize()).toString() }));
2569 addHistoryItem(trimRegion);
2571 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2573 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2574 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2576 viewport.getAlignment().deleteGroup(sg);
2580 viewport.firePropertyChange("alignment", null, viewport
2581 .getAlignment().getSequences());
2592 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2594 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2597 if (viewport.getSelectionGroup() != null)
2599 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2600 viewport.getHiddenRepSequences());
2601 start = viewport.getSelectionGroup().getStartRes();
2602 end = viewport.getSelectionGroup().getEndRes();
2606 seqs = viewport.getAlignment().getSequencesArray();
2609 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2610 "Remove Gapped Columns", seqs, start, end,
2611 viewport.getAlignment());
2613 addHistoryItem(removeGapCols);
2615 statusBar.setText(MessageManager.formatMessage(
2616 "label.removed_empty_columns", new String[]
2617 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2619 // This is to maintain viewport position on first residue
2620 // of first sequence
2621 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2622 int startRes = seq.findPosition(viewport.startRes);
2623 // ShiftList shifts;
2624 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2625 // edit.alColumnChanges=shifts.getInverse();
2626 // if (viewport.hasHiddenColumns)
2627 // viewport.getColumnSelection().compensateForEdits(shifts);
2628 viewport.setStartRes(seq.findIndex(startRes) - 1);
2629 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2641 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2643 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2646 if (viewport.getSelectionGroup() != null)
2648 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2649 viewport.getHiddenRepSequences());
2650 start = viewport.getSelectionGroup().getStartRes();
2651 end = viewport.getSelectionGroup().getEndRes();
2655 seqs = viewport.getAlignment().getSequencesArray();
2658 // This is to maintain viewport position on first residue
2659 // of first sequence
2660 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2661 int startRes = seq.findPosition(viewport.startRes);
2663 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2664 viewport.getAlignment()));
2666 viewport.setStartRes(seq.findIndex(startRes) - 1);
2668 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2680 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2682 viewport.setPadGaps(padGapsMenuitem.isSelected());
2683 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2689 // if (justifySeqs>0)
2691 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2704 public void findMenuItem_actionPerformed(ActionEvent e)
2710 * Create a new view of the current alignment.
2713 public void newView_actionPerformed(ActionEvent e)
2720 * @param copyAnnotation
2721 * if true then duplicate all annnotation, groups and settings
2722 * @return new alignment panel, already displayed.
2724 public AlignmentPanel newView(boolean copyAnnotation)
2726 return newView(null, copyAnnotation);
2732 * title of newly created view
2733 * @return new alignment panel, already displayed.
2735 public AlignmentPanel newView(String viewTitle)
2737 return newView(viewTitle, true);
2743 * title of newly created view
2744 * @param copyAnnotation
2745 * if true then duplicate all annnotation, groups and settings
2746 * @return new alignment panel, already displayed.
2748 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2750 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2752 if (!copyAnnotation)
2754 // just remove all the current annotation except for the automatic stuff
2755 newap.av.getAlignment().deleteAllGroups();
2756 for (AlignmentAnnotation alan : newap.av.getAlignment()
2757 .getAlignmentAnnotation())
2759 if (!alan.autoCalculated)
2761 newap.av.getAlignment().deleteAnnotation(alan);
2767 newap.av.gatherViewsHere = false;
2769 if (viewport.viewName == null)
2771 viewport.viewName = "Original";
2774 newap.av.setHistoryList(viewport.getHistoryList());
2775 newap.av.setRedoList(viewport.getRedoList());
2777 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2778 // make sure the new view has a unique name - this is essential for Jalview
2780 boolean addFirstIndex = false;
2781 if (viewTitle == null || viewTitle.trim().length() == 0)
2783 viewTitle = MessageManager.getString("action.view");
2784 addFirstIndex = true;
2788 index = 1;// we count from 1 if given a specific name
2790 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2791 Vector comps = (Vector) PaintRefresher.components.get(viewport
2792 .getSequenceSetId());
2793 Vector existingNames = new Vector();
2794 for (int i = 0; i < comps.size(); i++)
2796 if (comps.elementAt(i) instanceof AlignmentPanel)
2798 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2799 if (!existingNames.contains(ap.av.viewName))
2801 existingNames.addElement(ap.av.viewName);
2806 while (existingNames.contains(newViewName))
2808 newViewName = viewTitle + " " + (++index);
2811 newap.av.viewName = newViewName;
2813 addAlignmentPanel(newap, true);
2814 newap.alignmentChanged();
2816 if (alignPanels.size() == 2)
2818 viewport.gatherViewsHere = true;
2820 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2825 public void expandViews_actionPerformed(ActionEvent e)
2827 Desktop.instance.explodeViews(this);
2831 public void gatherViews_actionPerformed(ActionEvent e)
2833 Desktop.instance.gatherViews(this);
2843 public void font_actionPerformed(ActionEvent e)
2845 new FontChooser(alignPanel);
2855 protected void seqLimit_actionPerformed(ActionEvent e)
2857 viewport.setShowJVSuffix(seqLimits.isSelected());
2859 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2860 .calculateIdWidth());
2861 alignPanel.paintAlignment(true);
2865 public void idRightAlign_actionPerformed(ActionEvent e)
2867 viewport.rightAlignIds = idRightAlign.isSelected();
2868 alignPanel.paintAlignment(true);
2872 public void centreColumnLabels_actionPerformed(ActionEvent e)
2874 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2875 alignPanel.paintAlignment(true);
2881 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2884 protected void followHighlight_actionPerformed()
2886 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2888 alignPanel.scrollToPosition(
2889 alignPanel.seqPanel.seqCanvas.searchResults, false);
2900 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2902 viewport.setColourText(colourTextMenuItem.isSelected());
2903 alignPanel.paintAlignment(true);
2913 public void wrapMenuItem_actionPerformed(ActionEvent e)
2915 scaleAbove.setVisible(wrapMenuItem.isSelected());
2916 scaleLeft.setVisible(wrapMenuItem.isSelected());
2917 scaleRight.setVisible(wrapMenuItem.isSelected());
2918 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2919 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2923 public void showAllSeqs_actionPerformed(ActionEvent e)
2925 viewport.showAllHiddenSeqs();
2929 public void showAllColumns_actionPerformed(ActionEvent e)
2931 viewport.showAllHiddenColumns();
2936 public void hideSelSequences_actionPerformed(ActionEvent e)
2938 viewport.hideAllSelectedSeqs();
2939 alignPanel.paintAlignment(true);
2943 * called by key handler and the hide all/show all menu items
2948 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2951 boolean hide = false;
2952 SequenceGroup sg = viewport.getSelectionGroup();
2953 if (!toggleSeqs && !toggleCols)
2955 // Hide everything by the current selection - this is a hack - we do the
2956 // invert and then hide
2957 // first check that there will be visible columns after the invert.
2958 if ((viewport.getColumnSelection() != null
2959 && viewport.getColumnSelection().getSelected() != null && viewport
2960 .getColumnSelection().getSelected().size() > 0)
2961 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2964 // now invert the sequence set, if required - empty selection implies
2965 // that no hiding is required.
2968 invertSequenceMenuItem_actionPerformed(null);
2969 sg = viewport.getSelectionGroup();
2973 viewport.expandColSelection(sg, true);
2974 // finally invert the column selection and get the new sequence
2976 invertColSel_actionPerformed(null);
2983 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2985 hideSelSequences_actionPerformed(null);
2988 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2991 showAllSeqs_actionPerformed(null);
2997 if (viewport.getColumnSelection().getSelected().size() > 0)
2999 hideSelColumns_actionPerformed(null);
3002 viewport.setSelectionGroup(sg);
3007 showAllColumns_actionPerformed(null);
3016 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3017 * event.ActionEvent)
3020 public void hideAllButSelection_actionPerformed(ActionEvent e)
3022 toggleHiddenRegions(false, false);
3029 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3033 public void hideAllSelection_actionPerformed(ActionEvent e)
3035 SequenceGroup sg = viewport.getSelectionGroup();
3036 viewport.expandColSelection(sg, false);
3037 viewport.hideAllSelectedSeqs();
3038 viewport.hideSelectedColumns();
3039 alignPanel.paintAlignment(true);
3046 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3050 public void showAllhidden_actionPerformed(ActionEvent e)
3052 viewport.showAllHiddenColumns();
3053 viewport.showAllHiddenSeqs();
3054 alignPanel.paintAlignment(true);
3058 public void hideSelColumns_actionPerformed(ActionEvent e)
3060 viewport.hideSelectedColumns();
3061 alignPanel.paintAlignment(true);
3065 public void hiddenMarkers_actionPerformed(ActionEvent e)
3067 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3078 protected void scaleAbove_actionPerformed(ActionEvent e)
3080 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3081 alignPanel.paintAlignment(true);
3091 protected void scaleLeft_actionPerformed(ActionEvent e)
3093 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3094 alignPanel.paintAlignment(true);
3104 protected void scaleRight_actionPerformed(ActionEvent e)
3106 viewport.setScaleRightWrapped(scaleRight.isSelected());
3107 alignPanel.paintAlignment(true);
3117 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3119 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3120 alignPanel.paintAlignment(true);
3130 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3132 viewport.setShowText(viewTextMenuItem.isSelected());
3133 alignPanel.paintAlignment(true);
3143 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3145 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3146 alignPanel.paintAlignment(true);
3149 public FeatureSettings featureSettings;
3152 public void featureSettings_actionPerformed(ActionEvent e)
3154 if (featureSettings != null)
3156 featureSettings.close();
3157 featureSettings = null;
3159 if (!showSeqFeatures.isSelected())
3161 // make sure features are actually displayed
3162 showSeqFeatures.setSelected(true);
3163 showSeqFeatures_actionPerformed(null);
3165 featureSettings = new FeatureSettings(this);
3169 * Set or clear 'Show Sequence Features'
3175 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3177 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3178 alignPanel.paintAlignment(true);
3179 if (alignPanel.getOverviewPanel() != null)
3181 alignPanel.getOverviewPanel().updateOverviewImage();
3186 * Set or clear 'Show Sequence Features'
3192 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3194 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3196 if (viewport.getShowSequenceFeaturesHeight())
3198 // ensure we're actually displaying features
3199 viewport.setShowSequenceFeatures(true);
3200 showSeqFeatures.setSelected(true);
3202 alignPanel.paintAlignment(true);
3203 if (alignPanel.getOverviewPanel() != null)
3205 alignPanel.getOverviewPanel().updateOverviewImage();
3210 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3211 * the annotations panel as a whole.
3213 * The options to show/hide all annotations should be enabled when the panel
3214 * is shown, and disabled when the panel is hidden.
3219 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3221 final boolean setVisible = annotationPanelMenuItem.isSelected();
3222 viewport.setShowAnnotation(setVisible);
3223 alignPanel.setAnnotationVisible(setVisible);
3224 this.showAllSeqAnnotations.setEnabled(setVisible);
3225 this.hideAllSeqAnnotations.setEnabled(setVisible);
3226 this.showAllAlAnnotations.setEnabled(setVisible);
3227 this.hideAllAlAnnotations.setEnabled(setVisible);
3231 public void alignmentProperties()
3233 JEditorPane editPane = new JEditorPane("text/html", "");
3234 editPane.setEditable(false);
3235 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3237 editPane.setText(MessageManager.formatMessage("label.html_content",
3239 { contents.toString() }));
3240 JInternalFrame frame = new JInternalFrame();
3241 frame.getContentPane().add(new JScrollPane(editPane));
3243 Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage(
3244 "label.alignment_properties", new String[]
3245 { getTitle() }), 500, 400);
3255 public void overviewMenuItem_actionPerformed(ActionEvent e)
3257 if (alignPanel.overviewPanel != null)
3262 JInternalFrame frame = new JInternalFrame();
3263 OverviewPanel overview = new OverviewPanel(alignPanel);
3264 frame.setContentPane(overview);
3265 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3266 "label.overview_params", new String[]
3267 { this.getTitle() }), frame.getWidth(), frame.getHeight());
3269 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3270 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3273 public void internalFrameClosed(
3274 javax.swing.event.InternalFrameEvent evt)
3276 alignPanel.setOverviewPanel(null);
3280 alignPanel.setOverviewPanel(overview);
3284 public void textColour_actionPerformed(ActionEvent e)
3286 new TextColourChooser().chooseColour(alignPanel, null);
3296 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3308 public void clustalColour_actionPerformed(ActionEvent e)
3310 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3311 viewport.getHiddenRepSequences()));
3321 public void zappoColour_actionPerformed(ActionEvent e)
3323 changeColour(new ZappoColourScheme());
3333 public void taylorColour_actionPerformed(ActionEvent e)
3335 changeColour(new TaylorColourScheme());
3345 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3347 changeColour(new HydrophobicColourScheme());
3357 public void helixColour_actionPerformed(ActionEvent e)
3359 changeColour(new HelixColourScheme());
3369 public void strandColour_actionPerformed(ActionEvent e)
3371 changeColour(new StrandColourScheme());
3381 public void turnColour_actionPerformed(ActionEvent e)
3383 changeColour(new TurnColourScheme());
3393 public void buriedColour_actionPerformed(ActionEvent e)
3395 changeColour(new BuriedColourScheme());
3405 public void nucleotideColour_actionPerformed(ActionEvent e)
3407 changeColour(new NucleotideColourScheme());
3411 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3413 changeColour(new PurinePyrimidineColourScheme());
3417 * public void covariationColour_actionPerformed(ActionEvent e) {
3419 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3423 public void annotationColour_actionPerformed(ActionEvent e)
3425 new AnnotationColourChooser(viewport, alignPanel);
3429 public void rnahelicesColour_actionPerformed(ActionEvent e)
3431 new RNAHelicesColourChooser(viewport, alignPanel);
3441 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3443 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3452 public void changeColour(ColourSchemeI cs)
3454 // TODO: compare with applet and pull up to model method
3459 if (viewport.getAbovePIDThreshold())
3461 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3463 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3467 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3470 if (viewport.getConservationSelected())
3473 Alignment al = (Alignment) viewport.getAlignment();
3474 Conservation c = new Conservation("All",
3475 ResidueProperties.propHash, 3, al.getSequences(), 0,
3479 c.verdict(false, viewport.getConsPercGaps());
3481 cs.setConservation(c);
3483 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3488 cs.setConservation(null);
3491 cs.setConsensus(viewport.getSequenceConsensusHash());
3494 viewport.setGlobalColourScheme(cs);
3496 if (viewport.getColourAppliesToAllGroups())
3499 for (SequenceGroup sg : viewport.getAlignment().getGroups())
3507 if (cs instanceof ClustalxColourScheme)
3509 sg.cs = new ClustalxColourScheme(sg,
3510 viewport.getHiddenRepSequences());
3512 else if (cs instanceof UserColourScheme)
3514 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3520 sg.cs = cs.getClass().newInstance();
3521 } catch (Exception ex)
3526 if (viewport.getAbovePIDThreshold()
3527 || cs instanceof PIDColourScheme
3528 || cs instanceof Blosum62ColourScheme)
3530 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3532 sg.cs.setConsensus(AAFrequency.calculate(
3533 sg.getSequences(viewport.getHiddenRepSequences()),
3534 sg.getStartRes(), sg.getEndRes() + 1));
3538 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3541 if (viewport.getConservationSelected())
3543 Conservation c = new Conservation("Group",
3544 ResidueProperties.propHash, 3, sg.getSequences(viewport
3545 .getHiddenRepSequences()), sg.getStartRes(),
3546 sg.getEndRes() + 1);
3548 c.verdict(false, viewport.getConsPercGaps());
3549 sg.cs.setConservation(c);
3553 sg.cs.setConservation(null);
3558 if (alignPanel.getOverviewPanel() != null)
3560 alignPanel.getOverviewPanel().updateOverviewImage();
3563 alignPanel.paintAlignment(true);
3573 protected void modifyPID_actionPerformed(ActionEvent e)
3575 if (viewport.getAbovePIDThreshold()
3576 && viewport.getGlobalColourScheme() != null)
3578 SliderPanel.setPIDSliderSource(alignPanel,
3579 viewport.getGlobalColourScheme(), "Background");
3580 SliderPanel.showPIDSlider();
3591 protected void modifyConservation_actionPerformed(ActionEvent e)
3593 if (viewport.getConservationSelected()
3594 && viewport.getGlobalColourScheme() != null)
3596 SliderPanel.setConservationSlider(alignPanel,
3597 viewport.getGlobalColourScheme(), "Background");
3598 SliderPanel.showConservationSlider();
3609 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3611 viewport.setConservationSelected(conservationMenuItem.isSelected());
3613 viewport.setAbovePIDThreshold(false);
3614 abovePIDThreshold.setSelected(false);
3616 changeColour(viewport.getGlobalColourScheme());
3618 modifyConservation_actionPerformed(null);
3628 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3630 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3632 conservationMenuItem.setSelected(false);
3633 viewport.setConservationSelected(false);
3635 changeColour(viewport.getGlobalColourScheme());
3637 modifyPID_actionPerformed(null);
3647 public void userDefinedColour_actionPerformed(ActionEvent e)
3649 if (e.getActionCommand().equals(
3650 MessageManager.getString("action.user_defined")))
3652 new UserDefinedColours(alignPanel, null);
3656 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3657 .getUserColourSchemes().get(e.getActionCommand());
3663 public void updateUserColourMenu()
3666 Component[] menuItems = colourMenu.getMenuComponents();
3667 int i, iSize = menuItems.length;
3668 for (i = 0; i < iSize; i++)
3670 if (menuItems[i].getName() != null
3671 && menuItems[i].getName().equals("USER_DEFINED"))
3673 colourMenu.remove(menuItems[i]);
3677 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3679 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3680 .getUserColourSchemes().keys();
3682 while (userColours.hasMoreElements())
3684 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3685 userColours.nextElement().toString());
3686 radioItem.setName("USER_DEFINED");
3687 radioItem.addMouseListener(new MouseAdapter()
3690 public void mousePressed(MouseEvent evt)
3692 if (evt.isControlDown()
3693 || SwingUtilities.isRightMouseButton(evt))
3695 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3697 int option = JOptionPane.showInternalConfirmDialog(
3698 jalview.gui.Desktop.desktop,
3700 .getString("label.remove_from_default_list"),
3702 .getString("label.remove_user_defined_colour"),
3703 JOptionPane.YES_NO_OPTION);
3704 if (option == JOptionPane.YES_OPTION)
3706 jalview.gui.UserDefinedColours
3707 .removeColourFromDefaults(radioItem.getText());
3708 colourMenu.remove(radioItem);
3712 radioItem.addActionListener(new ActionListener()
3715 public void actionPerformed(ActionEvent evt)
3717 userDefinedColour_actionPerformed(evt);
3724 radioItem.addActionListener(new ActionListener()
3727 public void actionPerformed(ActionEvent evt)
3729 userDefinedColour_actionPerformed(evt);
3733 colourMenu.insert(radioItem, 15);
3734 colours.add(radioItem);
3746 public void PIDColour_actionPerformed(ActionEvent e)
3748 changeColour(new PIDColourScheme());
3758 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3760 changeColour(new Blosum62ColourScheme());
3770 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3772 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3773 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3774 .getAlignment().getSequenceAt(0), null);
3775 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3776 viewport.getAlignment()));
3777 alignPanel.paintAlignment(true);
3787 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3789 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3790 AlignmentSorter.sortByID(viewport.getAlignment());
3791 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3792 viewport.getAlignment()));
3793 alignPanel.paintAlignment(true);
3803 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3805 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3806 AlignmentSorter.sortByLength(viewport.getAlignment());
3807 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3808 viewport.getAlignment()));
3809 alignPanel.paintAlignment(true);
3819 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3821 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3822 AlignmentSorter.sortByGroup(viewport.getAlignment());
3823 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3824 viewport.getAlignment()));
3826 alignPanel.paintAlignment(true);
3836 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3838 new RedundancyPanel(alignPanel, this);
3848 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3850 if ((viewport.getSelectionGroup() == null)
3851 || (viewport.getSelectionGroup().getSize() < 2))
3853 JOptionPane.showInternalMessageDialog(this, MessageManager
3854 .getString("label.you_must_select_least_two_sequences"),
3855 MessageManager.getString("label.invalid_selection"),
3856 JOptionPane.WARNING_MESSAGE);
3860 JInternalFrame frame = new JInternalFrame();
3861 frame.setContentPane(new PairwiseAlignPanel(viewport));
3862 Desktop.addInternalFrame(frame,
3863 MessageManager.getString("action.pairwise_alignment"), 600,
3875 public void PCAMenuItem_actionPerformed(ActionEvent e)
3877 if (((viewport.getSelectionGroup() != null)
3878 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3879 .getSelectionGroup().getSize() > 0))
3880 || (viewport.getAlignment().getHeight() < 4))
3883 .showInternalMessageDialog(
3886 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3888 .getString("label.sequence_selection_insufficient"),
3889 JOptionPane.WARNING_MESSAGE);
3894 new PCAPanel(alignPanel);
3898 public void autoCalculate_actionPerformed(ActionEvent e)
3900 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3901 if (viewport.autoCalculateConsensus)
3903 viewport.firePropertyChange("alignment", null, viewport
3904 .getAlignment().getSequences());
3909 public void sortByTreeOption_actionPerformed(ActionEvent e)
3911 viewport.sortByTree = sortByTree.isSelected();
3915 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3917 viewport.followSelection = listenToViewSelections.isSelected();
3927 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3929 NewTreePanel("AV", "PID", "Average distance tree using PID");
3939 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3941 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3951 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3953 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3963 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3965 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3978 void NewTreePanel(String type, String pwType, String title)
3982 if (viewport.getSelectionGroup() != null
3983 && viewport.getSelectionGroup().getSize() > 0)
3985 if (viewport.getSelectionGroup().getSize() < 3)
3991 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3993 .getString("label.not_enough_sequences"),
3994 JOptionPane.WARNING_MESSAGE);
3998 SequenceGroup sg = viewport.getSelectionGroup();
4000 /* Decide if the selection is a column region */
4001 for (SequenceI _s : sg.getSequences())
4003 if (_s.getLength() < sg.getEndRes())
4009 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
4011 .getString("label.sequences_selection_not_aligned"),
4012 JOptionPane.WARNING_MESSAGE);
4018 title = title + " on region";
4019 tp = new TreePanel(alignPanel, type, pwType);
4023 // are the visible sequences aligned?
4024 if (!viewport.getAlignment().isAligned(false))
4030 .getString("label.sequences_must_be_aligned_before_creating_tree"),
4032 .getString("label.sequences_not_aligned"),
4033 JOptionPane.WARNING_MESSAGE);
4038 if (viewport.getAlignment().getHeight() < 2)
4043 tp = new TreePanel(alignPanel, type, pwType);
4048 if (viewport.viewName != null)
4050 title += viewport.viewName + " of ";
4053 title += this.title;
4055 Desktop.addInternalFrame(tp, title, 600, 500);
4066 public void addSortByOrderMenuItem(String title,
4067 final AlignmentOrder order)
4069 final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new String[]{title}));
4071 item.addActionListener(new java.awt.event.ActionListener()
4074 public void actionPerformed(ActionEvent e)
4076 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4078 // TODO: JBPNote - have to map order entries to curent SequenceI
4080 AlignmentSorter.sortBy(viewport.getAlignment(), order);
4082 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4085 alignPanel.paintAlignment(true);
4091 * Add a new sort by annotation score menu item
4094 * the menu to add the option to
4096 * the label used to retrieve scores for each sequence on the
4099 public void addSortByAnnotScoreMenuItem(JMenu sort,
4100 final String scoreLabel)
4102 final JMenuItem item = new JMenuItem(scoreLabel);
4104 item.addActionListener(new java.awt.event.ActionListener()
4107 public void actionPerformed(ActionEvent e)
4109 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4110 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4111 viewport.getAlignment());// ,viewport.getSelectionGroup());
4112 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4113 viewport.getAlignment()));
4114 alignPanel.paintAlignment(true);
4120 * last hash for alignment's annotation array - used to minimise cost of
4123 protected int _annotationScoreVectorHash;
4126 * search the alignment and rebuild the sort by annotation score submenu the
4127 * last alignment annotation vector hash is stored to minimize cost of
4128 * rebuilding in subsequence calls.
4132 public void buildSortByAnnotationScoresMenu()
4134 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4139 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4141 sortByAnnotScore.removeAll();
4142 // almost certainly a quicker way to do this - but we keep it simple
4143 Hashtable scoreSorts = new Hashtable();
4144 AlignmentAnnotation aann[];
4145 for (SequenceI sqa : viewport.getAlignment().getSequences())
4147 aann = sqa.getAnnotation();
4148 for (int i = 0; aann != null && i < aann.length; i++)
4150 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4152 scoreSorts.put(aann[i].label, aann[i].label);
4156 Enumeration labels = scoreSorts.keys();
4157 while (labels.hasMoreElements())
4159 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4160 (String) labels.nextElement());
4162 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4165 _annotationScoreVectorHash = viewport.getAlignment()
4166 .getAlignmentAnnotation().hashCode();
4171 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4172 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4173 * call. Listeners are added to remove the menu item when the treePanel is
4174 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4178 * Displayed tree window.
4180 * SortBy menu item title.
4183 public void buildTreeMenu()
4185 calculateTree.removeAll();
4186 // build the calculate menu
4188 for (final String type : new String[]
4191 String treecalcnm = MessageManager.getString("label.tree_calc_"
4192 + type.toLowerCase());
4193 for (final Object pwtype : ResidueProperties.scoreMatrices.keySet())
4195 JMenuItem tm = new JMenuItem();
4196 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4197 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4199 String smn = MessageManager.getStringOrReturn(
4200 "label.score_model_", sm.getName());
4201 final String title = MessageManager.formatMessage(
4202 "label.treecalc_title", treecalcnm, smn);
4203 tm.setText(title);//
4204 tm.addActionListener(new java.awt.event.ActionListener()
4207 public void actionPerformed(ActionEvent e)
4209 NewTreePanel(type, (String) pwtype, title);
4212 calculateTree.add(tm);
4217 sortByTreeMenu.removeAll();
4219 Vector comps = (Vector) PaintRefresher.components.get(viewport
4220 .getSequenceSetId());
4221 Vector treePanels = new Vector();
4222 int i, iSize = comps.size();
4223 for (i = 0; i < iSize; i++)
4225 if (comps.elementAt(i) instanceof TreePanel)
4227 treePanels.add(comps.elementAt(i));
4231 iSize = treePanels.size();
4235 sortByTreeMenu.setVisible(false);
4239 sortByTreeMenu.setVisible(true);
4241 for (i = 0; i < treePanels.size(); i++)
4243 final TreePanel tp = (TreePanel) treePanels.elementAt(i);
4244 final JMenuItem item = new JMenuItem(tp.getTitle());
4245 item.addActionListener(new java.awt.event.ActionListener()
4248 public void actionPerformed(ActionEvent e)
4250 tp.sortByTree_actionPerformed();
4251 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4256 sortByTreeMenu.add(item);
4260 public boolean sortBy(AlignmentOrder alorder, String undoname)
4262 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4263 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4264 if (undoname != null)
4266 addHistoryItem(new OrderCommand(undoname, oldOrder,
4267 viewport.getAlignment()));
4269 alignPanel.paintAlignment(true);
4274 * Work out whether the whole set of sequences or just the selected set will
4275 * be submitted for multiple alignment.
4278 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4280 // Now, check we have enough sequences
4281 AlignmentView msa = null;
4283 if ((viewport.getSelectionGroup() != null)
4284 && (viewport.getSelectionGroup().getSize() > 1))
4286 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4287 // some common interface!
4289 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4290 * SequenceI[sz = seqs.getSize(false)];
4292 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4293 * seqs.getSequenceAt(i); }
4295 msa = viewport.getAlignmentView(true);
4297 else if (viewport.getSelectionGroup() != null
4298 && viewport.getSelectionGroup().getSize() == 1)
4300 int option = JOptionPane.showConfirmDialog(this,
4301 MessageManager.getString("warn.oneseq_msainput_selection"),
4302 MessageManager.getString("label.invalid_selection"),
4303 JOptionPane.OK_CANCEL_OPTION);
4304 if (option == JOptionPane.OK_OPTION)
4306 msa = viewport.getAlignmentView(false);
4311 msa = viewport.getAlignmentView(false);
4317 * Decides what is submitted to a secondary structure prediction service: the
4318 * first sequence in the alignment, or in the current selection, or, if the
4319 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4320 * region or the whole alignment. (where the first sequence in the set is the
4321 * one that the prediction will be for).
4323 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4325 AlignmentView seqs = null;
4327 if ((viewport.getSelectionGroup() != null)
4328 && (viewport.getSelectionGroup().getSize() > 0))
4330 seqs = viewport.getAlignmentView(true);
4334 seqs = viewport.getAlignmentView(false);
4336 // limit sequences - JBPNote in future - could spawn multiple prediction
4338 // TODO: viewport.getAlignment().isAligned is a global state - the local
4339 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4340 if (!viewport.getAlignment().isAligned(false))
4342 seqs.setSequences(new SeqCigar[]
4343 { seqs.getSequences()[0] });
4344 // TODO: if seqs.getSequences().length>1 then should really have warned
4358 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
4360 // Pick the tree file
4361 JalviewFileChooser chooser = new JalviewFileChooser(
4362 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4363 chooser.setFileView(new JalviewFileView());
4364 chooser.setDialogTitle(MessageManager
4365 .getString("label.select_newick_like_tree_file"));
4366 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4368 int value = chooser.showOpenDialog(null);
4370 if (value == JalviewFileChooser.APPROVE_OPTION)
4372 String choice = chooser.getSelectedFile().getPath();
4373 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4374 jalview.io.NewickFile fin = null;
4377 fin = new jalview.io.NewickFile(choice, "File");
4378 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4379 } catch (Exception ex)
4386 .getString("label.problem_reading_tree_file"),
4387 JOptionPane.WARNING_MESSAGE);
4388 ex.printStackTrace();
4390 if (fin != null && fin.hasWarningMessage())
4392 JOptionPane.showMessageDialog(Desktop.desktop, fin
4393 .getWarningMessage(), MessageManager
4394 .getString("label.possible_problem_with_tree_file"),
4395 JOptionPane.WARNING_MESSAGE);
4401 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4403 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4406 public TreePanel ShowNewickTree(NewickFile nf, String title)
4408 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4411 public TreePanel ShowNewickTree(NewickFile nf, String title,
4412 AlignmentView input)
4414 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4417 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4418 int h, int x, int y)
4420 return ShowNewickTree(nf, title, null, w, h, x, y);
4424 * Add a treeviewer for the tree extracted from a newick file object to the
4425 * current alignment view
4432 * Associated alignment input data (or null)
4441 * @return TreePanel handle
4443 public TreePanel ShowNewickTree(NewickFile nf, String title,
4444 AlignmentView input, int w, int h, int x, int y)
4446 TreePanel tp = null;
4452 if (nf.getTree() != null)
4454 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4460 tp.setLocation(x, y);
4463 Desktop.addInternalFrame(tp, title, w, h);
4465 } catch (Exception ex)
4467 ex.printStackTrace();
4473 private boolean buildingMenu = false;
4476 * Generates menu items and listener event actions for web service clients
4479 public void BuildWebServiceMenu()
4481 while (buildingMenu)
4485 System.err.println("Waiting for building menu to finish.");
4487 } catch (Exception e)
4492 final AlignFrame me = this;
4493 buildingMenu = true;
4494 new Thread(new Runnable()
4499 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4502 System.err.println("Building ws menu again "
4503 + Thread.currentThread());
4504 // TODO: add support for context dependent disabling of services based
4506 // alignment and current selection
4507 // TODO: add additional serviceHandle parameter to specify abstract
4509 // class independently of AbstractName
4510 // TODO: add in rediscovery GUI function to restart discoverer
4511 // TODO: group services by location as well as function and/or
4513 // object broker mechanism.
4514 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4515 final IProgressIndicator af = me;
4516 final JMenu msawsmenu = new JMenu("Alignment");
4517 final JMenu secstrmenu = new JMenu(
4518 "Secondary Structure Prediction");
4519 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4520 final JMenu analymenu = new JMenu("Analysis");
4521 final JMenu dismenu = new JMenu("Protein Disorder");
4522 // final JMenu msawsmenu = new
4523 // JMenu(MessageManager.getString("label.alignment"));
4524 // final JMenu secstrmenu = new
4525 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4526 // final JMenu seqsrchmenu = new
4527 // JMenu(MessageManager.getString("label.sequence_database_search"));
4528 // final JMenu analymenu = new
4529 // JMenu(MessageManager.getString("label.analysis"));
4530 // final JMenu dismenu = new
4531 // JMenu(MessageManager.getString("label.protein_disorder"));
4532 // JAL-940 - only show secondary structure prediction services from
4533 // the legacy server
4534 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4536 Discoverer.services != null && (Discoverer.services.size() > 0))
4538 // TODO: refactor to allow list of AbstractName/Handler bindings to
4540 // stored or retrieved from elsewhere
4541 // No MSAWS used any more:
4542 // Vector msaws = null; // (Vector)
4543 // Discoverer.services.get("MsaWS");
4544 Vector secstrpr = (Vector) Discoverer.services
4546 if (secstrpr != null)
4548 // Add any secondary structure prediction services
4549 for (int i = 0, j = secstrpr.size(); i < j; i++)
4551 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4553 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4554 .getServiceClient(sh);
4555 int p = secstrmenu.getItemCount();
4556 impl.attachWSMenuEntry(secstrmenu, me);
4557 int q = secstrmenu.getItemCount();
4558 for (int litm = p; litm < q; litm++)
4560 legacyItems.add(secstrmenu.getItem(litm));
4566 // Add all submenus in the order they should appear on the web
4568 wsmenu.add(msawsmenu);
4569 wsmenu.add(secstrmenu);
4570 wsmenu.add(dismenu);
4571 wsmenu.add(analymenu);
4572 // No search services yet
4573 // wsmenu.add(seqsrchmenu);
4575 javax.swing.SwingUtilities.invokeLater(new Runnable()
4582 webService.removeAll();
4583 // first, add discovered services onto the webservices menu
4584 if (wsmenu.size() > 0)
4586 for (int i = 0, j = wsmenu.size(); i < j; i++)
4588 webService.add(wsmenu.get(i));
4593 webService.add(me.webServiceNoServices);
4595 // TODO: move into separate menu builder class.
4596 boolean new_sspred = false;
4597 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4599 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4600 if (jws2servs != null)
4602 if (jws2servs.hasServices())
4604 jws2servs.attachWSMenuEntry(webService, me);
4605 for (Jws2Instance sv : jws2servs.getServices())
4607 if (sv.description.toLowerCase().contains("jpred"))
4609 for (JMenuItem jmi : legacyItems)
4611 jmi.setVisible(false);
4617 if (jws2servs.isRunning())
4619 JMenuItem tm = new JMenuItem(
4620 "Still discovering JABA Services");
4621 tm.setEnabled(false);
4626 build_urlServiceMenu(me.webService);
4627 build_fetchdbmenu(webService);
4628 for (JMenu item : wsmenu)
4630 if (item.getItemCount() == 0)
4632 item.setEnabled(false);
4636 item.setEnabled(true);
4639 } catch (Exception e)
4642 .debug("Exception during web service menu building process.",
4648 } catch (Exception e)
4653 buildingMenu = false;
4660 * construct any groupURL type service menu entries.
4664 private void build_urlServiceMenu(JMenu webService)
4666 // TODO: remove this code when 2.7 is released
4667 // DEBUG - alignmentView
4669 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4670 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4672 * @Override public void actionPerformed(ActionEvent e) {
4673 * jalview.datamodel.AlignmentView
4674 * .testSelectionViews(af.viewport.getAlignment(),
4675 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4677 * }); webService.add(testAlView);
4679 // TODO: refactor to RestClient discoverer and merge menu entries for
4680 // rest-style services with other types of analysis/calculation service
4681 // SHmmr test client - still being implemented.
4682 // DEBUG - alignmentView
4684 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4687 client.attachWSMenuEntry(
4688 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4694 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4695 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4696 * getProperty("LAST_DIRECTORY"));
4698 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4699 * to Vamsas file"); chooser.setToolTipText("Export");
4701 * int value = chooser.showSaveDialog(this);
4703 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4704 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4705 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4706 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4709 * prototype of an automatically enabled/disabled analysis function
4712 protected void setShowProductsEnabled()
4714 SequenceI[] selection = viewport.getSequenceSelection();
4715 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4716 viewport.getAlignment().getDataset()))
4718 showProducts.setEnabled(true);
4723 showProducts.setEnabled(false);
4728 * search selection for sequence xRef products and build the show products
4733 * @return true if showProducts menu should be enabled.
4735 public boolean canShowProducts(SequenceI[] selection,
4736 boolean isRegionSelection, Alignment dataset)
4738 boolean showp = false;
4741 showProducts.removeAll();
4742 final boolean dna = viewport.getAlignment().isNucleotide();
4743 final Alignment ds = dataset;
4744 String[] ptypes = (selection == null || selection.length == 0) ? null
4745 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4747 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4748 // selection, dataset, true);
4749 final SequenceI[] sel = selection;
4750 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4753 final boolean isRegSel = isRegionSelection;
4754 final AlignFrame af = this;
4755 final String source = ptypes[t];
4756 JMenuItem xtype = new JMenuItem(ptypes[t]);
4757 xtype.addActionListener(new ActionListener()
4761 public void actionPerformed(ActionEvent e)
4763 // TODO: new thread for this call with vis-delay
4764 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4765 isRegSel, dna, source);
4769 showProducts.add(xtype);
4771 showProducts.setVisible(showp);
4772 showProducts.setEnabled(showp);
4773 } catch (Exception e)
4775 jalview.bin.Cache.log
4776 .warn("canTranslate threw an exception - please report to help@jalview.org",
4783 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4784 boolean isRegSel, boolean dna, String source)
4786 final boolean fisRegSel = isRegSel;
4787 final boolean fdna = dna;
4788 final String fsrc = source;
4789 final AlignFrame ths = this;
4790 final SequenceI[] fsel = sel;
4791 Runnable foo = new Runnable()
4797 final long sttime = System.currentTimeMillis();
4798 ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{fsrc}), sttime);
4801 Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4805 Alignment prods = CrossRef
4806 .findXrefSequences(fsel, fdna, fsrc, ds);
4809 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4810 for (int s = 0; s < sprods.length; s++)
4812 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4813 if (ds.getSequences() == null
4814 || !ds.getSequences().contains(
4815 sprods[s].getDatasetSequence()))
4817 ds.addSequence(sprods[s].getDatasetSequence());
4819 sprods[s].updatePDBIds();
4821 Alignment al = new Alignment(sprods);
4822 AlignedCodonFrame[] cf = prods.getCodonFrames();
4824 for (int s = 0; cf != null && s < cf.length; s++)
4826 al.addCodonFrame(cf[s]);
4829 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4831 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4832 + " for " + ((fisRegSel) ? "selected region of " : "")
4834 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4839 System.err.println("No Sequences generated for xRef type "
4842 } catch (Exception e)
4844 jalview.bin.Cache.log.error(
4845 "Exception when finding crossreferences", e);
4846 } catch (OutOfMemoryError e)
4848 new OOMWarning("whilst fetching crossreferences", e);
4851 jalview.bin.Cache.log.error("Error when finding crossreferences",
4854 ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{fsrc}),
4859 Thread frunner = new Thread(foo);
4863 public boolean canShowTranslationProducts(SequenceI[] selection,
4864 AlignmentI alignment)
4869 return (jalview.analysis.Dna.canTranslate(selection,
4870 viewport.getViewAsVisibleContigs(true)));
4871 } catch (Exception e)
4873 jalview.bin.Cache.log
4874 .warn("canTranslate threw an exception - please report to help@jalview.org",
4881 * Construct and display a new frame containing the translation of this
4882 * frame's cDNA sequences to their aligned protein (amino acid) equivalents.
4885 public void showTranslation_actionPerformed(ActionEvent e)
4887 AlignmentI al = null;
4890 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4892 al = dna.translateCdna();
4893 } catch (Exception ex)
4895 jalview.bin.Cache.log.error(
4896 "Exception during translation. Please report this !", ex);
4897 final String msg = MessageManager
4898 .getString("label.error_when_translating_sequences_submit_bug_report");
4899 final String title = MessageManager
4900 .getString("label.implementation_error")
4901 + MessageManager.getString("translation_failed");
4902 JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
4903 JOptionPane.ERROR_MESSAGE);
4906 if (al == null || al.getHeight() == 0)
4908 final String msg = MessageManager
4909 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4910 final String title = MessageManager
4911 .getString("label.translation_failed");
4912 JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
4913 JOptionPane.WARNING_MESSAGE);
4917 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4918 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4919 "label.translation_of_params", new String[]
4920 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4921 // enable next line for linked editing
4922 // viewport.getStructureSelectionManager().addCommandListener(viewport);
4927 * Try to load a features file onto the alignment.
4930 * contents or path to retrieve file
4932 * access mode of file (see jalview.io.AlignFile)
4933 * @return true if features file was parsed corectly.
4935 public boolean parseFeaturesFile(String file, String type)
4937 boolean featuresFile = false;
4940 featuresFile = new FeaturesFile(file, type).parse(viewport
4941 .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4942 .getFeatureRenderer().featureColours, false,
4943 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4944 } catch (Exception ex)
4946 ex.printStackTrace();
4951 viewport.showSequenceFeatures = true;
4952 showSeqFeatures.setSelected(true);
4953 if (alignPanel.seqPanel.seqCanvas.fr != null)
4955 // update the min/max ranges where necessary
4956 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4958 if (featureSettings != null)
4960 featureSettings.setTableData();
4962 alignPanel.paintAlignment(true);
4965 return featuresFile;
4969 public void dragEnter(DropTargetDragEvent evt)
4974 public void dragExit(DropTargetEvent evt)
4979 public void dragOver(DropTargetDragEvent evt)
4984 public void dropActionChanged(DropTargetDragEvent evt)
4989 public void drop(DropTargetDropEvent evt)
4991 Transferable t = evt.getTransferable();
4992 java.util.List files = null;
4996 DataFlavor uriListFlavor = new DataFlavor(
4997 "text/uri-list;class=java.lang.String");
4998 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
5000 // Works on Windows and MacOSX
5001 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5002 files = (java.util.List) t
5003 .getTransferData(DataFlavor.javaFileListFlavor);
5005 else if (t.isDataFlavorSupported(uriListFlavor))
5007 // This is used by Unix drag system
5008 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
5009 String data = (String) t.getTransferData(uriListFlavor);
5010 files = new java.util.ArrayList(1);
5011 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
5012 data, "\r\n"); st.hasMoreTokens();)
5014 String s = st.nextToken();
5015 if (s.startsWith("#"))
5017 // the line is a comment (as per the RFC 2483)
5021 java.net.URI uri = new java.net.URI(s);
5022 // check to see if we can handle this kind of URI
5023 if (uri.getScheme().toLowerCase().startsWith("http"))
5025 files.add(uri.toString());
5029 // otherwise preserve old behaviour: catch all for file objects
5030 java.io.File file = new java.io.File(uri);
5031 files.add(file.toString());
5035 } catch (Exception e)
5037 e.printStackTrace();
5043 // check to see if any of these files have names matching sequences in
5045 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5046 .getAlignment().getSequencesArray());
5048 * Object[] { String,SequenceI}
5050 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
5051 ArrayList<String> filesnotmatched = new ArrayList<String>();
5052 for (int i = 0; i < files.size(); i++)
5054 String file = files.get(i).toString();
5056 String protocol = FormatAdapter.checkProtocol(file);
5057 if (protocol == jalview.io.FormatAdapter.FILE)
5059 File fl = new File(file);
5060 pdbfn = fl.getName();
5062 else if (protocol == jalview.io.FormatAdapter.URL)
5064 URL url = new URL(file);
5065 pdbfn = url.getFile();
5067 if (pdbfn.length() > 0)
5069 // attempt to find a match in the alignment
5070 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5071 int l = 0, c = pdbfn.indexOf(".");
5072 while (mtch == null && c != -1)
5077 } while ((c = pdbfn.indexOf(".", l)) > l);
5080 pdbfn = pdbfn.substring(0, l);
5082 mtch = idm.findAllIdMatches(pdbfn);
5089 type = new IdentifyFile().Identify(file, protocol);
5090 } catch (Exception ex)
5096 if (type.equalsIgnoreCase("PDB"))
5098 filesmatched.add(new Object[]
5099 { file, protocol, mtch });
5104 // File wasn't named like one of the sequences or wasn't a PDB file.
5105 filesnotmatched.add(file);
5109 if (filesmatched.size() > 0)
5111 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5117 "label.automatically_associate_pdb_files_with_sequences_same_name",
5124 .getString("label.automatically_associate_pdb_files_by_name"),
5125 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5128 for (Object[] fm : filesmatched)
5130 // try and associate
5131 // TODO: may want to set a standard ID naming formalism for
5132 // associating PDB files which have no IDs.
5133 for (SequenceI toassoc : (SequenceI[]) fm[2])
5135 PDBEntry pe = new AssociatePdbFileWithSeq()
5136 .associatePdbWithSeq((String) fm[0],
5137 (String) fm[1], toassoc, false,
5141 System.err.println("Associated file : "
5142 + ((String) fm[0]) + " with "
5143 + toassoc.getDisplayId(true));
5147 alignPanel.paintAlignment(true);
5151 if (filesnotmatched.size() > 0)
5154 && (Cache.getDefault(
5155 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5158 "<html>"+MessageManager
5160 "label.ignore_unmatched_dropped_files_info",
5165 .toString() })+"</html>",
5167 .getString("label.ignore_unmatched_dropped_files"),
5168 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5172 for (String fn : filesnotmatched)
5174 loadJalviewDataFile(fn, null, null, null);
5178 } catch (Exception ex)
5180 ex.printStackTrace();
5186 * Attempt to load a "dropped" file or URL string: First by testing whether
5187 * it's and Annotation file, then a JNet file, and finally a features file. If
5188 * all are false then the user may have dropped an alignment file onto this
5192 * either a filename or a URL string.
5194 public void loadJalviewDataFile(String file, String protocol,
5195 String format, SequenceI assocSeq)
5199 if (protocol == null)
5201 protocol = jalview.io.FormatAdapter.checkProtocol(file);
5203 // if the file isn't identified, or not positively identified as some
5204 // other filetype (PFAM is default unidentified alignment file type) then
5205 // try to parse as annotation.
5206 boolean isAnnotation = (format == null || format
5207 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5208 .readAnnotationFile(viewport.getAlignment(), file, protocol)
5213 // first see if its a T-COFFEE score file
5214 TCoffeeScoreFile tcf = null;
5217 tcf = new TCoffeeScoreFile(file, protocol);
5220 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5222 tcoffeeColour.setEnabled(true);
5223 tcoffeeColour.setSelected(true);
5224 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5225 isAnnotation = true;
5227 .setText(MessageManager
5228 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5232 // some problem - if no warning its probable that the ID matching
5233 // process didn't work
5237 tcf.getWarningMessage() == null ? MessageManager
5238 .getString("label.check_file_matches_sequence_ids_alignment")
5239 : tcf.getWarningMessage(),
5241 .getString("label.problem_reading_tcoffee_score_file"),
5242 JOptionPane.WARNING_MESSAGE);
5249 } catch (Exception x)
5252 .debug("Exception when processing data source as T-COFFEE score file",
5258 // try to see if its a JNet 'concise' style annotation file *before*
5260 // try to parse it as a features file
5263 format = new IdentifyFile().Identify(file, protocol);
5265 if (format.equalsIgnoreCase("JnetFile"))
5267 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5269 new JnetAnnotationMaker().add_annotation(predictions,
5270 viewport.getAlignment(), 0, false);
5271 isAnnotation = true;
5276 * if (format.equalsIgnoreCase("PDB")) {
5278 * String pdbfn = ""; // try to match up filename with sequence id
5279 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5280 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5281 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5282 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5283 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5284 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5285 * // attempt to find a match in the alignment SequenceI mtch =
5286 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5287 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5288 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5289 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5290 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5291 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5292 * { System.err.println("Associated file : " + file + " with " +
5293 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5294 * TODO: maybe need to load as normal otherwise return; } }
5296 // try to parse it as a features file
5297 boolean isGroupsFile = parseFeaturesFile(file, protocol);
5298 // if it wasn't a features file then we just treat it as a general
5299 // alignment file to load into the current view.
5302 new FileLoader().LoadFile(viewport, file, protocol, format);
5306 alignPanel.paintAlignment(true);
5314 alignPanel.adjustAnnotationHeight();
5315 viewport.updateSequenceIdColours();
5316 buildSortByAnnotationScoresMenu();
5317 alignPanel.paintAlignment(true);
5319 } catch (Exception ex)
5321 ex.printStackTrace();
5322 } catch (OutOfMemoryError oom)
5327 } catch (Exception x)
5333 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5334 : "using " + protocol + " from " + file)
5336 + (format != null ? "(parsing as '" + format
5337 + "' file)" : ""), oom, Desktop.desktop);
5342 public void tabSelectionChanged(int index)
5346 alignPanel = alignPanels.get(index);
5347 viewport = alignPanel.av;
5348 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5349 setMenusFromViewport(viewport);
5354 public void tabbedPane_mousePressed(MouseEvent e)
5356 if (SwingUtilities.isRightMouseButton(e))
5358 String reply = JOptionPane.showInternalInputDialog(this,
5359 MessageManager.getString("label.enter_view_name"),
5360 MessageManager.getString("label.enter_view_name"),
5361 JOptionPane.QUESTION_MESSAGE);
5365 viewport.viewName = reply;
5366 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5371 public AlignViewport getCurrentView()
5377 * Open the dialog for regex description parsing.
5380 protected void extractScores_actionPerformed(ActionEvent e)
5382 ParseProperties pp = new jalview.analysis.ParseProperties(
5383 viewport.getAlignment());
5384 // TODO: verify regex and introduce GUI dialog for version 2.5
5385 // if (pp.getScoresFromDescription("col", "score column ",
5386 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5388 if (pp.getScoresFromDescription("description column",
5389 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5391 buildSortByAnnotationScoresMenu();
5399 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5403 protected void showDbRefs_actionPerformed(ActionEvent e)
5405 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
5411 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5415 protected void showNpFeats_actionPerformed(ActionEvent e)
5417 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
5421 * find the viewport amongst the tabs in this alignment frame and close that
5426 public boolean closeView(AlignViewport av)
5430 this.closeMenuItem_actionPerformed(false);
5433 Component[] comp = tabbedPane.getComponents();
5434 for (int i = 0; comp != null && i < comp.length; i++)
5436 if (comp[i] instanceof AlignmentPanel)
5438 if (((AlignmentPanel) comp[i]).av == av)
5441 closeView((AlignmentPanel) comp[i]);
5449 protected void build_fetchdbmenu(JMenu webService)
5451 // Temporary hack - DBRef Fetcher always top level ws entry.
5452 // TODO We probably want to store a sequence database checklist in
5453 // preferences and have checkboxes.. rather than individual sources selected
5455 final JMenu rfetch = new JMenu(
5456 MessageManager.getString("action.fetch_db_references"));
5457 rfetch.setToolTipText(MessageManager
5458 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5459 webService.add(rfetch);
5461 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5462 MessageManager.getString("option.trim_retrieved_seqs"));
5463 trimrs.setToolTipText(MessageManager
5464 .getString("label.trim_retrieved_sequences"));
5465 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5466 trimrs.addActionListener(new ActionListener()
5469 public void actionPerformed(ActionEvent e)
5471 trimrs.setSelected(trimrs.isSelected());
5472 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5473 Boolean.valueOf(trimrs.isSelected()).toString());
5477 JMenuItem fetchr = new JMenuItem(
5478 MessageManager.getString("label.standard_databases"));
5479 fetchr.setToolTipText(MessageManager
5480 .getString("label.fetch_embl_uniprot"));
5481 fetchr.addActionListener(new ActionListener()
5485 public void actionPerformed(ActionEvent e)
5487 new Thread(new Runnable()
5493 new jalview.ws.DBRefFetcher(alignPanel.av
5494 .getSequenceSelection(), alignPanel.alignFrame)
5495 .fetchDBRefs(false);
5503 final AlignFrame me = this;
5504 new Thread(new Runnable()
5509 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5510 .getSequenceFetcherSingleton(me);
5511 javax.swing.SwingUtilities.invokeLater(new Runnable()
5516 String[] dbclasses = sf.getOrderedSupportedSources();
5517 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5518 // jalview.util.QuickSort.sort(otherdb, otherdb);
5519 List<DbSourceProxy> otherdb;
5520 JMenu dfetch = new JMenu();
5521 JMenu ifetch = new JMenu();
5522 JMenuItem fetchr = null;
5523 int comp = 0, icomp = 0, mcomp = 15;
5524 String mname = null;
5526 for (String dbclass : dbclasses)
5528 otherdb = sf.getSourceProxy(dbclass);
5529 // add a single entry for this class, or submenu allowing 'fetch
5531 if (otherdb == null || otherdb.size() < 1)
5535 // List<DbSourceProxy> dbs=otherdb;
5536 // otherdb=new ArrayList<DbSourceProxy>();
5537 // for (DbSourceProxy db:dbs)
5539 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5543 mname = "From " + dbclass;
5545 if (otherdb.size() == 1)
5547 final DbSourceProxy[] dassource = otherdb
5548 .toArray(new DbSourceProxy[0]);
5549 DbSourceProxy src = otherdb.get(0);
5550 fetchr = new JMenuItem(src.getDbSource());
5551 fetchr.addActionListener(new ActionListener()
5555 public void actionPerformed(ActionEvent e)
5557 new Thread(new Runnable()
5563 new jalview.ws.DBRefFetcher(alignPanel.av
5564 .getSequenceSelection(),
5565 alignPanel.alignFrame, dassource)
5566 .fetchDBRefs(false);
5572 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{src.getDbName()})));
5578 final DbSourceProxy[] dassource = otherdb
5579 .toArray(new DbSourceProxy[0]);
5581 DbSourceProxy src = otherdb.get(0);
5582 fetchr = new JMenuItem(MessageManager.formatMessage(
5583 "label.fetch_all_param", new String[]
5584 { src.getDbSource() }));
5585 fetchr.addActionListener(new ActionListener()
5588 public void actionPerformed(ActionEvent e)
5590 new Thread(new Runnable()
5596 new jalview.ws.DBRefFetcher(alignPanel.av
5597 .getSequenceSelection(),
5598 alignPanel.alignFrame, dassource)
5599 .fetchDBRefs(false);
5605 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new String[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
5608 // and then build the rest of the individual menus
5609 ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new String[]{src.getDbSource()}));
5611 String imname = null;
5613 for (DbSourceProxy sproxy : otherdb)
5615 String dbname = sproxy.getDbName();
5616 String sname = dbname.length() > 5 ? dbname.substring(0,
5617 5) + "..." : dbname;
5618 String msname = dbname.length() > 10 ? dbname.substring(
5619 0, 10) + "..." : dbname;
5622 imname = MessageManager.formatMessage("label.from_msname", new String[]{sname});
5624 fetchr = new JMenuItem(msname);
5625 final DbSourceProxy[] dassrc =
5627 fetchr.addActionListener(new ActionListener()
5631 public void actionPerformed(ActionEvent e)
5633 new Thread(new Runnable()
5639 new jalview.ws.DBRefFetcher(alignPanel.av
5640 .getSequenceSelection(),
5641 alignPanel.alignFrame, dassrc)
5642 .fetchDBRefs(false);
5648 fetchr.setToolTipText("<html>"
5649 + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname}));
5652 if (++icomp >= mcomp || i == (otherdb.size()))
5654 ifetch.setText(MessageManager.formatMessage(
5655 "label.source_to_target", imname, sname));
5657 ifetch = new JMenu();
5665 if (comp >= mcomp || dbi >= (dbclasses.length))
5667 dfetch.setText(MessageManager.formatMessage(
5668 "label.source_to_target", mname, dbclass));
5670 dfetch = new JMenu();
5683 * Left justify the whole alignment.
5686 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5688 AlignmentI al = viewport.getAlignment();
5690 viewport.firePropertyChange("alignment", null, al);
5694 * Right justify the whole alignment.
5697 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5699 AlignmentI al = viewport.getAlignment();
5701 viewport.firePropertyChange("alignment", null, al);
5704 public void setShowSeqFeatures(boolean b)
5706 showSeqFeatures.setSelected(true);
5707 viewport.setShowSequenceFeatures(true);
5714 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5715 * awt.event.ActionEvent)
5718 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5720 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5721 alignPanel.paintAlignment(true);
5728 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5732 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5734 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5735 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5743 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5744 * .event.ActionEvent)
5747 protected void showGroupConservation_actionPerformed(ActionEvent e)
5749 viewport.setShowGroupConservation(showGroupConservation.getState());
5750 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5757 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5758 * .event.ActionEvent)
5761 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5763 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5764 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5771 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5772 * .event.ActionEvent)
5775 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5777 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5778 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5782 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5784 showSequenceLogo.setState(true);
5785 viewport.setShowSequenceLogo(true);
5786 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5787 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5791 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5793 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5800 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5801 * .event.ActionEvent)
5804 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5806 if (avc.makeGroupsFromSelection())
5808 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5809 alignPanel.updateAnnotation();
5810 alignPanel.paintAlignment(true);
5815 protected void createGroup_actionPerformed(ActionEvent e)
5817 if (avc.createGroup())
5819 alignPanel.alignmentChanged();
5824 protected void unGroup_actionPerformed(ActionEvent e)
5828 alignPanel.alignmentChanged();
5833 * make the given alignmentPanel the currently selected tab
5835 * @param alignmentPanel
5837 public void setDisplayedView(AlignmentPanel alignmentPanel)
5839 if (!viewport.getSequenceSetId().equals(
5840 alignmentPanel.av.getSequenceSetId()))
5842 throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
5844 if (tabbedPane != null
5845 & alignPanels.indexOf(alignmentPanel) != tabbedPane
5846 .getSelectedIndex())
5848 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5853 * Action on selection of menu options to Show or Hide annotations.
5856 * @param forSequences
5857 * update sequence-related annotations
5858 * @param forAlignment
5859 * update non-sequence-related annotations
5862 protected void setAnnotationsVisibility(boolean visible,
5863 boolean forSequences, boolean forAlignment)
5865 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5866 .getAlignmentAnnotation())
5868 boolean apply = (aa.sequenceRef == null && forAlignment)
5869 || (aa.sequenceRef != null && forSequences);
5872 aa.visible = visible;
5875 alignPanel.validateAnnotationDimensions(false);
5876 alignPanel.alignmentChanged();
5880 * Store selected annotation sort order for the view and repaint.
5883 protected void sortAnnotations_actionPerformed()
5885 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5887 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5888 alignPanel.paintAlignment(true);
5893 * @return alignment panels in this alignment frame
5895 public List<? extends AlignmentViewPanel> getAlignPanels()
5897 return alignPanels == null ? Arrays.asList(alignPanel)
5902 * Open a new alignment window, with the cDNA associated with this (protein)
5903 * alignment, aligned as is the protein.
5906 protected void viewAsCdna_actionPerformed()
5908 final AlignmentI alignment = getViewport().getAlignment();
5909 AlignedCodonFrame[] mappings = alignment.getCodonFrames();
5910 if (mappings == null)
5914 List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5915 for (SequenceI aaSeq : alignment.getSequences()) {
5916 for (AlignedCodonFrame acf : mappings) {
5917 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5921 * There is a cDNA mapping for this protein sequence - add to new
5922 * alignment. It will share the same dataset sequence as other mapped
5923 * cDNA (no new mappings need to be created).
5925 final Sequence newSeq = new Sequence(dnaSeq);
5926 newSeq.setDatasetSequence(dnaSeq);
5927 cdnaSeqs.add(newSeq);
5931 if (cdnaSeqs.size() == 0)
5933 // show a warning dialog no mapped cDNA
5936 AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5938 AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5939 AlignFrame.DEFAULT_HEIGHT);
5940 cdna.alignAs(alignment);
5941 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5943 Desktop.addInternalFrame(alignFrame, newtitle,
5944 AlignFrame.DEFAULT_WIDTH,
5945 AlignFrame.DEFAULT_HEIGHT);
5950 class PrintThread extends Thread
5954 public PrintThread(AlignmentPanel ap)
5959 static PageFormat pf;
5964 PrinterJob printJob = PrinterJob.getPrinterJob();
5968 printJob.setPrintable(ap, pf);
5972 printJob.setPrintable(ap);
5975 if (printJob.printDialog())
5980 } catch (Exception PrintException)
5982 PrintException.printStackTrace();