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.Conservation;
27 import jalview.analysis.CrossRef;
28 import jalview.analysis.NJTree;
29 import jalview.analysis.ParseProperties;
30 import jalview.analysis.SequenceIdMatcher;
31 import jalview.api.AlignViewControllerGuiI;
32 import jalview.api.AlignViewControllerI;
33 import jalview.api.analysis.ScoreModelI;
34 import jalview.bin.Cache;
35 import jalview.commands.CommandI;
36 import jalview.commands.EditCommand;
37 import jalview.commands.OrderCommand;
38 import jalview.commands.RemoveGapColCommand;
39 import jalview.commands.RemoveGapsCommand;
40 import jalview.commands.SlideSequencesCommand;
41 import jalview.commands.TrimRegionCommand;
42 import jalview.datamodel.AlignedCodonFrame;
43 import jalview.datamodel.Alignment;
44 import jalview.datamodel.AlignmentAnnotation;
45 import jalview.datamodel.AlignmentI;
46 import jalview.datamodel.AlignmentOrder;
47 import jalview.datamodel.AlignmentView;
48 import jalview.datamodel.ColumnSelection;
49 import jalview.datamodel.PDBEntry;
50 import jalview.datamodel.SeqCigar;
51 import jalview.datamodel.Sequence;
52 import jalview.datamodel.SequenceGroup;
53 import jalview.datamodel.SequenceI;
54 import jalview.io.AlignmentProperties;
55 import jalview.io.AnnotationFile;
56 import jalview.io.BioJsHTMLOutput;
57 import jalview.io.FeaturesFile;
58 import jalview.io.FileLoader;
59 import jalview.io.FormatAdapter;
60 import jalview.io.HTMLOutput;
61 import jalview.io.IdentifyFile;
62 import jalview.io.JalviewFileChooser;
63 import jalview.io.JalviewFileView;
64 import jalview.io.JnetAnnotationMaker;
65 import jalview.io.NewickFile;
66 import jalview.io.TCoffeeScoreFile;
67 import jalview.jbgui.GAlignFrame;
68 import jalview.schemes.Blosum62ColourScheme;
69 import jalview.schemes.BuriedColourScheme;
70 import jalview.schemes.ClustalxColourScheme;
71 import jalview.schemes.ColourSchemeI;
72 import jalview.schemes.ColourSchemeProperty;
73 import jalview.schemes.HelixColourScheme;
74 import jalview.schemes.HydrophobicColourScheme;
75 import jalview.schemes.NucleotideColourScheme;
76 import jalview.schemes.PIDColourScheme;
77 import jalview.schemes.PurinePyrimidineColourScheme;
78 import jalview.schemes.RNAHelicesColourChooser;
79 import jalview.schemes.ResidueProperties;
80 import jalview.schemes.StrandColourScheme;
81 import jalview.schemes.TCoffeeColourScheme;
82 import jalview.schemes.TaylorColourScheme;
83 import jalview.schemes.TurnColourScheme;
84 import jalview.schemes.UserColourScheme;
85 import jalview.schemes.ZappoColourScheme;
86 import jalview.util.MessageManager;
87 import jalview.ws.jws1.Discoverer;
88 import jalview.ws.jws2.Jws2Discoverer;
89 import jalview.ws.jws2.jabaws2.Jws2Instance;
90 import jalview.ws.seqfetcher.DbSourceProxy;
92 import java.awt.BorderLayout;
93 import java.awt.Component;
94 import java.awt.GridLayout;
95 import java.awt.Rectangle;
96 import java.awt.Toolkit;
97 import java.awt.datatransfer.Clipboard;
98 import java.awt.datatransfer.DataFlavor;
99 import java.awt.datatransfer.StringSelection;
100 import java.awt.datatransfer.Transferable;
101 import java.awt.dnd.DnDConstants;
102 import java.awt.dnd.DropTargetDragEvent;
103 import java.awt.dnd.DropTargetDropEvent;
104 import java.awt.dnd.DropTargetEvent;
105 import java.awt.dnd.DropTargetListener;
106 import java.awt.event.ActionEvent;
107 import java.awt.event.ActionListener;
108 import java.awt.event.KeyAdapter;
109 import java.awt.event.KeyEvent;
110 import java.awt.event.MouseAdapter;
111 import java.awt.event.MouseEvent;
112 import java.awt.print.PageFormat;
113 import java.awt.print.PrinterJob;
114 import java.beans.PropertyChangeEvent;
117 import java.util.ArrayList;
118 import java.util.Enumeration;
119 import java.util.Hashtable;
120 import java.util.List;
121 import java.util.Vector;
123 import javax.swing.JButton;
124 import javax.swing.JCheckBoxMenuItem;
125 import javax.swing.JEditorPane;
126 import javax.swing.JInternalFrame;
127 import javax.swing.JLabel;
128 import javax.swing.JLayeredPane;
129 import javax.swing.JMenu;
130 import javax.swing.JMenuItem;
131 import javax.swing.JOptionPane;
132 import javax.swing.JPanel;
133 import javax.swing.JProgressBar;
134 import javax.swing.JRadioButtonMenuItem;
135 import javax.swing.JScrollPane;
136 import javax.swing.SwingUtilities;
142 * @version $Revision$
144 public class AlignFrame extends GAlignFrame implements DropTargetListener,
145 IProgressIndicator, AlignViewControllerGuiI
149 public static final int DEFAULT_WIDTH = 700;
152 public static final int DEFAULT_HEIGHT = 500;
154 public AlignmentPanel alignPanel;
156 AlignViewport viewport;
158 public AlignViewControllerI avc;
160 Vector alignPanels = new Vector();
163 * Last format used to load or save alignments in this window
165 String currentFileFormat = null;
168 * Current filename for this alignment
170 String fileName = null;
173 * Creates a new AlignFrame object with specific width and height.
179 public AlignFrame(AlignmentI al, int width, int height)
181 this(al, null, width, height);
185 * Creates a new AlignFrame object with specific width, height and
191 * @param sequenceSetId
193 public AlignFrame(AlignmentI al, int width, int height,
194 String sequenceSetId)
196 this(al, null, width, height, sequenceSetId);
200 * Creates a new AlignFrame object with specific width, height and
206 * @param sequenceSetId
209 public AlignFrame(AlignmentI al, int width, int height,
210 String sequenceSetId, String viewId)
212 this(al, null, width, height, sequenceSetId, viewId);
216 * new alignment window with hidden columns
220 * @param hiddenColumns
221 * ColumnSelection or null
223 * Width of alignment frame
227 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
228 int width, int height)
230 this(al, hiddenColumns, width, height, null);
234 * Create alignment frame for al with hiddenColumns, a specific width and
235 * height, and specific sequenceId
238 * @param hiddenColumns
241 * @param sequenceSetId
244 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
245 int width, int height, String sequenceSetId)
247 this(al, hiddenColumns, width, height, sequenceSetId, null);
251 * Create alignment frame for al with hiddenColumns, a specific width and
252 * height, and specific sequenceId
255 * @param hiddenColumns
258 * @param sequenceSetId
263 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
264 int width, int height, String sequenceSetId, String viewId)
266 setSize(width, height);
268 if (al.getDataset() == null)
273 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
275 alignPanel = new AlignmentPanel(this, viewport);
278 addAlignmentPanel(alignPanel, true);
283 * Make a new AlignFrame from existing alignmentPanels
290 public AlignFrame(AlignmentPanel ap)
294 addAlignmentPanel(ap, false);
299 * initalise the alignframe from the underlying viewport data and the
304 avc = new jalview.controller.AlignViewController(this, viewport,
306 if (viewport.getAlignmentConservationAnnotation() == null)
308 BLOSUM62Colour.setEnabled(false);
309 conservationMenuItem.setEnabled(false);
310 modifyConservation.setEnabled(false);
311 // PIDColour.setEnabled(false);
312 // abovePIDThreshold.setEnabled(false);
313 // modifyPID.setEnabled(false);
316 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
319 if (sortby.equals("Id"))
321 sortIDMenuItem_actionPerformed(null);
323 else if (sortby.equals("Pairwise Identity"))
325 sortPairwiseMenuItem_actionPerformed(null);
328 if (Desktop.desktop != null)
330 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
331 addServiceListeners();
332 setGUINucleotide(viewport.getAlignment().isNucleotide());
335 setMenusFromViewport(viewport);
336 buildSortByAnnotationScoresMenu();
339 if (viewport.wrapAlignment)
341 wrapMenuItem_actionPerformed(null);
344 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
346 this.overviewMenuItem_actionPerformed(null);
354 * Change the filename and format for the alignment, and enable the 'reload'
355 * button functionality.
362 public void setFileName(String file, String format)
365 currentFileFormat = format;
366 reload.setEnabled(true);
369 void addKeyListener()
371 addKeyListener(new KeyAdapter()
374 public void keyPressed(KeyEvent evt)
376 if (viewport.cursorMode
377 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
378 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
379 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
380 && Character.isDigit(evt.getKeyChar()))
382 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
385 switch (evt.getKeyCode())
388 case 27: // escape key
389 deselectAllSequenceMenuItem_actionPerformed(null);
393 case KeyEvent.VK_DOWN:
394 if (evt.isAltDown() || !viewport.cursorMode)
396 moveSelectedSequences(false);
398 if (viewport.cursorMode)
400 alignPanel.seqPanel.moveCursor(0, 1);
405 if (evt.isAltDown() || !viewport.cursorMode)
407 moveSelectedSequences(true);
409 if (viewport.cursorMode)
411 alignPanel.seqPanel.moveCursor(0, -1);
416 case KeyEvent.VK_LEFT:
417 if (evt.isAltDown() || !viewport.cursorMode)
419 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
423 alignPanel.seqPanel.moveCursor(-1, 0);
428 case KeyEvent.VK_RIGHT:
429 if (evt.isAltDown() || !viewport.cursorMode)
431 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
435 alignPanel.seqPanel.moveCursor(1, 0);
439 case KeyEvent.VK_SPACE:
440 if (viewport.cursorMode)
442 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
443 || evt.isShiftDown() || evt.isAltDown());
447 // case KeyEvent.VK_A:
448 // if (viewport.cursorMode)
450 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
451 // //System.out.println("A");
455 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
456 * System.out.println("closing bracket"); } break;
458 case KeyEvent.VK_DELETE:
459 case KeyEvent.VK_BACK_SPACE:
460 if (!viewport.cursorMode)
462 cut_actionPerformed(null);
466 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
467 || evt.isShiftDown() || evt.isAltDown());
473 if (viewport.cursorMode)
475 alignPanel.seqPanel.setCursorRow();
479 if (viewport.cursorMode && !evt.isControlDown())
481 alignPanel.seqPanel.setCursorColumn();
485 if (viewport.cursorMode)
487 alignPanel.seqPanel.setCursorPosition();
491 case KeyEvent.VK_ENTER:
492 case KeyEvent.VK_COMMA:
493 if (viewport.cursorMode)
495 alignPanel.seqPanel.setCursorRowAndColumn();
500 if (viewport.cursorMode)
502 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
506 if (viewport.cursorMode)
508 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
513 viewport.cursorMode = !viewport.cursorMode;
514 statusBar.setText(MessageManager.formatMessage(
515 "label.keyboard_editing_mode", new String[]
516 { (viewport.cursorMode ? "on" : "off") }));
517 if (viewport.cursorMode)
519 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
520 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
522 alignPanel.seqPanel.seqCanvas.repaint();
528 Help.showHelpWindow();
529 } catch (Exception ex)
531 ex.printStackTrace();
536 boolean toggleSeqs = !evt.isControlDown();
537 boolean toggleCols = !evt.isShiftDown();
538 toggleHiddenRegions(toggleSeqs, toggleCols);
541 case KeyEvent.VK_PAGE_UP:
542 if (viewport.wrapAlignment)
544 alignPanel.scrollUp(true);
548 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
549 - viewport.endSeq + viewport.startSeq);
552 case KeyEvent.VK_PAGE_DOWN:
553 if (viewport.wrapAlignment)
555 alignPanel.scrollUp(false);
559 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
560 + viewport.endSeq - viewport.startSeq);
567 public void keyReleased(KeyEvent evt)
569 switch (evt.getKeyCode())
571 case KeyEvent.VK_LEFT:
572 if (evt.isAltDown() || !viewport.cursorMode)
574 viewport.firePropertyChange("alignment", null, viewport
575 .getAlignment().getSequences());
579 case KeyEvent.VK_RIGHT:
580 if (evt.isAltDown() || !viewport.cursorMode)
582 viewport.firePropertyChange("alignment", null, viewport
583 .getAlignment().getSequences());
591 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
593 ap.alignFrame = this;
594 avc = new jalview.controller.AlignViewController(this, viewport,
597 alignPanels.addElement(ap);
599 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
601 int aSize = alignPanels.size();
603 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
605 if (aSize == 1 && ap.av.viewName == null)
607 this.getContentPane().add(ap, BorderLayout.CENTER);
613 setInitialTabVisible();
616 expandViews.setEnabled(true);
617 gatherViews.setEnabled(true);
618 tabbedPane.addTab(ap.av.viewName, ap);
620 ap.setVisible(false);
625 if (ap.av.isPadGaps())
627 ap.av.getAlignment().padGaps();
629 ap.av.updateConservation(ap);
630 ap.av.updateConsensus(ap);
631 ap.av.updateStrucConsensus(ap);
635 public void setInitialTabVisible()
637 expandViews.setEnabled(true);
638 gatherViews.setEnabled(true);
639 tabbedPane.setVisible(true);
640 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
641 tabbedPane.addTab(first.av.viewName, first);
642 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
645 public AlignViewport getViewport()
650 /* Set up intrinsic listeners for dynamically generated GUI bits. */
651 private void addServiceListeners()
653 final java.beans.PropertyChangeListener thisListener;
654 Desktop.instance.addJalviewPropertyChangeListener("services",
655 thisListener = new java.beans.PropertyChangeListener()
658 public void propertyChange(PropertyChangeEvent evt)
660 // // System.out.println("Discoverer property change.");
661 // if (evt.getPropertyName().equals("services"))
663 SwingUtilities.invokeLater(new Runnable()
670 .println("Rebuild WS Menu for service change");
671 BuildWebServiceMenu();
678 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
681 public void internalFrameClosed(
682 javax.swing.event.InternalFrameEvent evt)
684 System.out.println("deregistering discoverer listener");
685 Desktop.instance.removeJalviewPropertyChangeListener("services",
687 closeMenuItem_actionPerformed(true);
690 // Finally, build the menu once to get current service state
691 new Thread(new Runnable()
696 BuildWebServiceMenu();
701 public void setGUINucleotide(boolean nucleotide)
703 showTranslation.setVisible(nucleotide);
704 conservationMenuItem.setEnabled(!nucleotide);
705 modifyConservation.setEnabled(!nucleotide);
706 showGroupConservation.setEnabled(!nucleotide);
707 rnahelicesColour.setEnabled(nucleotide);
708 purinePyrimidineColour.setEnabled(nucleotide);
709 // Remember AlignFrame always starts as protein
713 // calculateMenu.remove(calculateMenu.getItemCount() - 2);
718 * set up menus for the currently viewport. This may be called after any
719 * operation that affects the data in the current view (selection changed,
720 * etc) to update the menus to reflect the new state.
722 public void setMenusForViewport()
724 setMenusFromViewport(viewport);
728 * Need to call this method when tabs are selected for multiple views, or when
729 * loading from Jalview2XML.java
734 void setMenusFromViewport(AlignViewport av)
736 padGapsMenuitem.setSelected(av.isPadGaps());
737 colourTextMenuItem.setSelected(av.showColourText);
738 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
739 conservationMenuItem.setSelected(av.getConservationSelected());
740 seqLimits.setSelected(av.getShowJVSuffix());
741 idRightAlign.setSelected(av.rightAlignIds);
742 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
743 renderGapsMenuItem.setSelected(av.renderGaps);
744 wrapMenuItem.setSelected(av.wrapAlignment);
745 scaleAbove.setVisible(av.wrapAlignment);
746 scaleLeft.setVisible(av.wrapAlignment);
747 scaleRight.setVisible(av.wrapAlignment);
748 annotationPanelMenuItem.setState(av.showAnnotation);
750 * Show/hide annotations only enabled if annotation panel is shown
752 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
753 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
754 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
755 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
756 viewBoxesMenuItem.setSelected(av.showBoxes);
757 viewTextMenuItem.setSelected(av.showText);
758 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
759 showGroupConsensus.setSelected(av.isShowGroupConsensus());
760 showGroupConservation.setSelected(av.isShowGroupConservation());
761 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
762 showSequenceLogo.setSelected(av.isShowSequenceLogo());
763 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
765 setColourSelected(ColourSchemeProperty.getColourName(av
766 .getGlobalColourScheme()));
768 showSeqFeatures.setSelected(av.showSequenceFeatures);
769 hiddenMarkers.setState(av.showHiddenMarkers);
770 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
771 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
772 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
773 autoCalculate.setSelected(av.autoCalculateConsensus);
774 sortByTree.setSelected(av.sortByTree);
775 listenToViewSelections.setSelected(av.followSelection);
776 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
778 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
779 setShowProductsEnabled();
783 // methods for implementing IProgressIndicator
784 // need to refactor to a reusable stub class
785 Hashtable progressBars, progressBarHandlers;
790 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
793 public void setProgressBar(String message, long id)
795 if (progressBars == null)
797 progressBars = new Hashtable();
798 progressBarHandlers = new Hashtable();
801 JPanel progressPanel;
802 Long lId = new Long(id);
803 GridLayout layout = (GridLayout) statusPanel.getLayout();
804 if (progressBars.get(lId) != null)
806 progressPanel = (JPanel) progressBars.get(new Long(id));
807 statusPanel.remove(progressPanel);
808 progressBars.remove(lId);
809 progressPanel = null;
812 statusBar.setText(message);
814 if (progressBarHandlers.contains(lId))
816 progressBarHandlers.remove(lId);
818 layout.setRows(layout.getRows() - 1);
822 progressPanel = new JPanel(new BorderLayout(10, 5));
824 JProgressBar progressBar = new JProgressBar();
825 progressBar.setIndeterminate(true);
827 progressPanel.add(new JLabel(message), BorderLayout.WEST);
828 progressPanel.add(progressBar, BorderLayout.CENTER);
830 layout.setRows(layout.getRows() + 1);
831 statusPanel.add(progressPanel);
833 progressBars.put(lId, progressPanel);
836 // setMenusForViewport();
841 public void registerHandler(final long id,
842 final IProgressIndicatorHandler handler)
844 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
846 throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
848 progressBarHandlers.put(new Long(id), handler);
849 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
850 if (handler.canCancel())
852 JButton cancel = new JButton(
853 MessageManager.getString("action.cancel"));
854 final IProgressIndicator us = this;
855 cancel.addActionListener(new ActionListener()
859 public void actionPerformed(ActionEvent e)
861 handler.cancelActivity(id);
862 us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
865 progressPanel.add(cancel, BorderLayout.EAST);
871 * @return true if any progress bars are still active
874 public boolean operationInProgress()
876 if (progressBars != null && progressBars.size() > 0)
884 public void setStatus(String text)
886 statusBar.setText(text);
890 * Added so Castor Mapping file can obtain Jalview Version
892 public String getVersion()
894 return jalview.bin.Cache.getProperty("VERSION");
897 public FeatureRenderer getFeatureRenderer()
899 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
903 public void fetchSequence_actionPerformed(ActionEvent e)
905 new SequenceFetcher(this);
909 public void addFromFile_actionPerformed(ActionEvent e)
911 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
915 public void reload_actionPerformed(ActionEvent e)
917 if (fileName != null)
919 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
920 // originating file's format
921 // TODO: work out how to recover feature settings for correct view(s) when
923 if (currentFileFormat.equals("Jalview"))
925 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
926 for (int i = 0; i < frames.length; i++)
928 if (frames[i] instanceof AlignFrame && frames[i] != this
929 && ((AlignFrame) frames[i]).fileName != null
930 && ((AlignFrame) frames[i]).fileName.equals(fileName))
934 frames[i].setSelected(true);
935 Desktop.instance.closeAssociatedWindows();
936 } catch (java.beans.PropertyVetoException ex)
942 Desktop.instance.closeAssociatedWindows();
944 FileLoader loader = new FileLoader();
945 String protocol = fileName.startsWith("http:") ? "URL" : "File";
946 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
950 Rectangle bounds = this.getBounds();
952 FileLoader loader = new FileLoader();
953 String protocol = fileName.startsWith("http:") ? "URL" : "File";
954 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
955 protocol, currentFileFormat);
957 newframe.setBounds(bounds);
958 if (featureSettings != null && featureSettings.isShowing())
960 final Rectangle fspos = featureSettings.frame.getBounds();
961 // TODO: need a 'show feature settings' function that takes bounds -
962 // need to refactor Desktop.addFrame
963 newframe.featureSettings_actionPerformed(null);
964 final FeatureSettings nfs = newframe.featureSettings;
965 SwingUtilities.invokeLater(new Runnable()
970 nfs.frame.setBounds(fspos);
973 this.featureSettings.close();
974 this.featureSettings = null;
976 this.closeMenuItem_actionPerformed(true);
982 public void addFromText_actionPerformed(ActionEvent e)
984 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
988 public void addFromURL_actionPerformed(ActionEvent e)
990 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
994 public void save_actionPerformed(ActionEvent e)
997 || (currentFileFormat == null || !jalview.io.FormatAdapter
998 .isValidIOFormat(currentFileFormat, true))
999 || fileName.startsWith("http"))
1001 saveAs_actionPerformed(null);
1005 saveAlignment(fileName, currentFileFormat);
1016 public void saveAs_actionPerformed(ActionEvent e)
1018 JalviewFileChooser chooser = new JalviewFileChooser(
1019 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
1020 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1021 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1022 currentFileFormat, false);
1024 chooser.setFileView(new JalviewFileView());
1025 chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
1026 chooser.setToolTipText(MessageManager.getString("action.save"));
1028 int value = chooser.showSaveDialog(this);
1030 if (value == JalviewFileChooser.APPROVE_OPTION)
1032 currentFileFormat = chooser.getSelectedFormat();
1033 if (currentFileFormat == null)
1036 .showInternalMessageDialog(
1039 .getString("label.select_file_format_before_saving"),
1041 .getString("label.file_format_not_specified"),
1042 JOptionPane.WARNING_MESSAGE);
1043 value = chooser.showSaveDialog(this);
1047 fileName = chooser.getSelectedFile().getPath();
1049 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1052 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1053 if (currentFileFormat.indexOf(" ") > -1)
1055 currentFileFormat = currentFileFormat.substring(0,
1056 currentFileFormat.indexOf(" "));
1058 saveAlignment(fileName, currentFileFormat);
1062 public boolean saveAlignment(String file, String format)
1064 boolean success = true;
1066 if (format.equalsIgnoreCase("Jalview"))
1068 String shortName = title;
1070 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1072 shortName = shortName.substring(shortName
1073 .lastIndexOf(java.io.File.separatorChar) + 1);
1076 success = new Jalview2XML().SaveAlignment(this, file, shortName);
1078 statusBar.setText(MessageManager.formatMessage(
1079 "label.successfully_saved_to_file_in_format", new String[]
1080 { fileName, format }));
1085 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1087 warningMessage("Cannot save file " + fileName + " using format "
1088 + format, "Alignment output format not supported");
1089 saveAs_actionPerformed(null);
1090 // JBPNote need to have a raise_gui flag here
1094 String[] omitHidden = null;
1096 if (viewport.hasHiddenColumns())
1098 int reply = JOptionPane
1099 .showInternalConfirmDialog(
1102 .getString("label.alignment_contains_hidden_columns"),
1104 .getString("action.save_omit_hidden_columns"),
1105 JOptionPane.YES_NO_OPTION,
1106 JOptionPane.QUESTION_MESSAGE);
1108 if (reply == JOptionPane.YES_OPTION)
1110 omitHidden = viewport.getViewAsString(false);
1113 FormatAdapter f = new FormatAdapter();
1114 String output = f.formatSequences(format,
1115 viewport.getAlignment(), // class cast exceptions will
1116 // occur in the distant future
1117 omitHidden, f.getCacheSuffixDefault(format),
1118 viewport.getColumnSelection());
1128 java.io.PrintWriter out = new java.io.PrintWriter(
1129 new java.io.FileWriter(file));
1133 this.setTitle(file);
1134 statusBar.setText(MessageManager.formatMessage(
1135 "label.successfully_saved_to_file_in_format",
1137 { fileName, format }));
1138 } catch (Exception ex)
1141 ex.printStackTrace();
1148 JOptionPane.showInternalMessageDialog(this, MessageManager
1149 .formatMessage("label.couldnt_save_file", new String[]
1150 { fileName }), MessageManager
1151 .getString("label.error_saving_file"),
1152 JOptionPane.WARNING_MESSAGE);
1158 private void warningMessage(String warning, String title)
1160 if (new jalview.util.Platform().isHeadless())
1162 System.err.println("Warning: " + title + "\nWarning: " + warning);
1167 JOptionPane.showInternalMessageDialog(this, warning, title,
1168 JOptionPane.WARNING_MESSAGE);
1180 protected void outputText_actionPerformed(ActionEvent e)
1182 String[] omitHidden = null;
1184 if (viewport.hasHiddenColumns())
1186 int reply = JOptionPane
1187 .showInternalConfirmDialog(
1190 .getString("label.alignment_contains_hidden_columns"),
1192 .getString("action.save_omit_hidden_columns"),
1193 JOptionPane.YES_NO_OPTION,
1194 JOptionPane.QUESTION_MESSAGE);
1196 if (reply == JOptionPane.YES_OPTION)
1198 omitHidden = viewport.getViewAsString(false);
1202 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1203 cap.setForInput(null);
1207 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1208 viewport.getAlignment(), omitHidden,
1209 viewport.getColumnSelection()));
1210 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1211 "label.alignment_output_command", new String[]
1212 { e.getActionCommand() }), 600, 500);
1213 } catch (OutOfMemoryError oom)
1215 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1228 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1230 new HTMLOutput(alignPanel,
1231 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1232 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1236 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1238 new BioJsHTMLOutput(alignPanel,
1239 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1241 public void createImageMap(File file, String image)
1243 alignPanel.makePNGImageMap(file, image);
1253 public void createPNG(File f)
1255 alignPanel.makePNG(f);
1265 public void createEPS(File f)
1267 alignPanel.makeEPS(f);
1270 public void createSVG(File f)
1272 alignPanel.makeSVG(f);
1275 public void pageSetup_actionPerformed(ActionEvent e)
1277 PrinterJob printJob = PrinterJob.getPrinterJob();
1278 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1288 public void printMenuItem_actionPerformed(ActionEvent e)
1290 // Putting in a thread avoids Swing painting problems
1291 PrintThread thread = new PrintThread(alignPanel);
1296 public void exportFeatures_actionPerformed(ActionEvent e)
1298 new AnnotationExporter().exportFeatures(alignPanel);
1302 public void exportAnnotations_actionPerformed(ActionEvent e)
1304 new AnnotationExporter().exportAnnotations(alignPanel,
1305 viewport.showAnnotation ? viewport.getAlignment()
1306 .getAlignmentAnnotation() : null, viewport
1307 .getAlignment().getGroups(), ((Alignment) viewport
1308 .getAlignment()).alignmentProperties);
1312 public void associatedData_actionPerformed(ActionEvent e)
1314 // Pick the tree file
1315 JalviewFileChooser chooser = new JalviewFileChooser(
1316 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1317 chooser.setFileView(new JalviewFileView());
1318 chooser.setDialogTitle(MessageManager
1319 .getString("label.load_jalview_annotations"));
1320 chooser.setToolTipText(MessageManager
1321 .getString("label.load_jalview_annotations"));
1323 int value = chooser.showOpenDialog(null);
1325 if (value == JalviewFileChooser.APPROVE_OPTION)
1327 String choice = chooser.getSelectedFile().getPath();
1328 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1329 loadJalviewDataFile(choice, null, null, null);
1335 * Close the current view or all views in the alignment frame. If the frame
1336 * only contains one view then the alignment will be removed from memory.
1338 * @param closeAllTabs
1341 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1343 if (alignPanels != null && alignPanels.size() < 2)
1345 closeAllTabs = true;
1350 if (alignPanels != null)
1354 if (this.isClosed())
1356 // really close all the windows - otherwise wait till
1357 // setClosed(true) is called
1358 for (int i = 0; i < alignPanels.size(); i++)
1360 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1367 closeView(alignPanel);
1373 this.setClosed(true);
1375 } catch (Exception ex)
1377 ex.printStackTrace();
1382 * close alignPanel2 and shuffle tabs appropriately.
1384 * @param alignPanel2
1386 public void closeView(AlignmentPanel alignPanel2)
1388 int index = tabbedPane.getSelectedIndex();
1389 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1390 alignPanels.removeElement(alignPanel2);
1392 // if (viewport == alignPanel2.av)
1396 alignPanel2.closePanel();
1399 tabbedPane.removeTabAt(closedindex);
1400 tabbedPane.validate();
1402 if (index > closedindex || index == tabbedPane.getTabCount())
1404 // modify currently selected tab index if necessary.
1408 this.tabSelectionChanged(index);
1414 void updateEditMenuBar()
1417 if (viewport.historyList.size() > 0)
1419 undoMenuItem.setEnabled(true);
1420 CommandI command = (CommandI) viewport.historyList.peek();
1421 undoMenuItem.setText(MessageManager.formatMessage(
1422 "label.undo_command", new String[]
1423 { command.getDescription() }));
1427 undoMenuItem.setEnabled(false);
1428 undoMenuItem.setText(MessageManager.getString("action.undo"));
1431 if (viewport.redoList.size() > 0)
1433 redoMenuItem.setEnabled(true);
1435 CommandI command = (CommandI) viewport.redoList.peek();
1436 redoMenuItem.setText(MessageManager.formatMessage(
1437 "label.redo_command", new String[]
1438 { command.getDescription() }));
1442 redoMenuItem.setEnabled(false);
1443 redoMenuItem.setText(MessageManager.getString("action.redo"));
1447 public void addHistoryItem(CommandI command)
1449 if (command.getSize() > 0)
1451 viewport.historyList.push(command);
1452 viewport.redoList.clear();
1453 updateEditMenuBar();
1454 viewport.updateHiddenColumns();
1455 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1456 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1457 // viewport.getColumnSelection()
1458 // .getHiddenColumns().size() > 0);
1464 * @return alignment objects for all views
1466 AlignmentI[] getViewAlignments()
1468 if (alignPanels != null)
1470 Enumeration e = alignPanels.elements();
1471 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1472 for (int i = 0; e.hasMoreElements(); i++)
1474 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1478 if (viewport != null)
1480 return new AlignmentI[]
1481 { viewport.getAlignment() };
1493 protected void undoMenuItem_actionPerformed(ActionEvent e)
1495 if (viewport.historyList.empty())
1499 CommandI command = (CommandI) viewport.historyList.pop();
1500 viewport.redoList.push(command);
1501 command.undoCommand(getViewAlignments());
1503 AlignViewport originalSource = getOriginatingSource(command);
1504 updateEditMenuBar();
1506 if (originalSource != null)
1508 if (originalSource != viewport)
1511 .warn("Implementation worry: mismatch of viewport origin for undo");
1513 originalSource.updateHiddenColumns();
1514 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1516 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1517 // viewport.getColumnSelection()
1518 // .getHiddenColumns().size() > 0);
1519 originalSource.firePropertyChange("alignment", null, originalSource
1520 .getAlignment().getSequences());
1531 protected void redoMenuItem_actionPerformed(ActionEvent e)
1533 if (viewport.redoList.size() < 1)
1538 CommandI command = (CommandI) viewport.redoList.pop();
1539 viewport.historyList.push(command);
1540 command.doCommand(getViewAlignments());
1542 AlignViewport originalSource = getOriginatingSource(command);
1543 updateEditMenuBar();
1545 if (originalSource != null)
1548 if (originalSource != viewport)
1551 .warn("Implementation worry: mismatch of viewport origin for redo");
1553 originalSource.updateHiddenColumns();
1554 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1556 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1557 // viewport.getColumnSelection()
1558 // .getHiddenColumns().size() > 0);
1559 originalSource.firePropertyChange("alignment", null, originalSource
1560 .getAlignment().getSequences());
1564 AlignViewport getOriginatingSource(CommandI command)
1566 AlignViewport originalSource = null;
1567 // For sequence removal and addition, we need to fire
1568 // the property change event FROM the viewport where the
1569 // original alignment was altered
1570 AlignmentI al = null;
1571 if (command instanceof EditCommand)
1573 EditCommand editCommand = (EditCommand) command;
1574 al = editCommand.getAlignment();
1575 Vector comps = (Vector) PaintRefresher.components.get(viewport
1576 .getSequenceSetId());
1578 for (int i = 0; i < comps.size(); i++)
1580 if (comps.elementAt(i) instanceof AlignmentPanel)
1582 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1584 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1591 if (originalSource == null)
1593 // The original view is closed, we must validate
1594 // the current view against the closed view first
1597 PaintRefresher.validateSequences(al, viewport.getAlignment());
1600 originalSource = viewport;
1603 return originalSource;
1612 public void moveSelectedSequences(boolean up)
1614 SequenceGroup sg = viewport.getSelectionGroup();
1620 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1621 viewport.getHiddenRepSequences(), up);
1622 alignPanel.paintAlignment(true);
1625 synchronized void slideSequences(boolean right, int size)
1627 List<SequenceI> sg = new Vector();
1628 if (viewport.cursorMode)
1630 sg.add(viewport.getAlignment().getSequenceAt(
1631 alignPanel.seqPanel.seqCanvas.cursorY));
1633 else if (viewport.getSelectionGroup() != null
1634 && viewport.getSelectionGroup().getSize() != viewport
1635 .getAlignment().getHeight())
1637 sg = viewport.getSelectionGroup().getSequences(
1638 viewport.getHiddenRepSequences());
1646 Vector invertGroup = new Vector();
1648 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1650 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1652 invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1656 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1658 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1659 for (int i = 0; i < invertGroup.size(); i++)
1661 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1664 SlideSequencesCommand ssc;
1667 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1668 size, viewport.getGapCharacter());
1672 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1673 size, viewport.getGapCharacter());
1676 int groupAdjustment = 0;
1677 if (ssc.getGapsInsertedBegin() && right)
1679 if (viewport.cursorMode)
1681 alignPanel.seqPanel.moveCursor(size, 0);
1685 groupAdjustment = size;
1688 else if (!ssc.getGapsInsertedBegin() && !right)
1690 if (viewport.cursorMode)
1692 alignPanel.seqPanel.moveCursor(-size, 0);
1696 groupAdjustment = -size;
1700 if (groupAdjustment != 0)
1702 viewport.getSelectionGroup().setStartRes(
1703 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1704 viewport.getSelectionGroup().setEndRes(
1705 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1708 boolean appendHistoryItem = false;
1709 if (viewport.historyList != null && viewport.historyList.size() > 0
1710 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1712 appendHistoryItem = ssc
1713 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1717 if (!appendHistoryItem)
1719 addHistoryItem(ssc);
1732 protected void copy_actionPerformed(ActionEvent e)
1735 if (viewport.getSelectionGroup() == null)
1739 // TODO: preserve the ordering of displayed alignment annotation in any
1740 // internal paste (particularly sequence associated annotation)
1741 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1742 String[] omitHidden = null;
1744 if (viewport.hasHiddenColumns())
1746 omitHidden = viewport.getViewAsString(true);
1749 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1752 StringSelection ss = new StringSelection(output);
1756 jalview.gui.Desktop.internalCopy = true;
1757 // Its really worth setting the clipboard contents
1758 // to empty before setting the large StringSelection!!
1759 Toolkit.getDefaultToolkit().getSystemClipboard()
1760 .setContents(new StringSelection(""), null);
1762 Toolkit.getDefaultToolkit().getSystemClipboard()
1763 .setContents(ss, Desktop.instance);
1764 } catch (OutOfMemoryError er)
1766 new OOMWarning("copying region", er);
1770 Vector hiddenColumns = null;
1771 if (viewport.hasHiddenColumns())
1773 hiddenColumns = new Vector();
1774 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1775 .getSelectionGroup().getEndRes();
1776 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1779 int[] region = (int[]) viewport.getColumnSelection()
1780 .getHiddenColumns().elementAt(i);
1781 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1783 hiddenColumns.addElement(new int[]
1784 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1789 Desktop.jalviewClipboard = new Object[]
1790 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1791 statusBar.setText(MessageManager.formatMessage(
1792 "label.copied_sequences_to_clipboard", new String[]
1793 { Integer.valueOf(seqs.length).toString() }));
1803 protected void pasteNew_actionPerformed(ActionEvent e)
1815 protected void pasteThis_actionPerformed(ActionEvent e)
1821 * Paste contents of Jalview clipboard
1823 * @param newAlignment
1824 * true to paste to a new alignment, otherwise add to this.
1826 void paste(boolean newAlignment)
1828 boolean externalPaste = true;
1831 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1832 Transferable contents = c.getContents(this);
1834 if (contents == null)
1842 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1843 if (str.length() < 1)
1848 format = new IdentifyFile().Identify(str, "Paste");
1850 } catch (OutOfMemoryError er)
1852 new OOMWarning("Out of memory pasting sequences!!", er);
1856 SequenceI[] sequences;
1857 boolean annotationAdded = false;
1858 AlignmentI alignment = null;
1860 if (Desktop.jalviewClipboard != null)
1862 // The clipboard was filled from within Jalview, we must use the
1864 // And dataset from the copied alignment
1865 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1866 // be doubly sure that we create *new* sequence objects.
1867 sequences = new SequenceI[newseq.length];
1868 for (int i = 0; i < newseq.length; i++)
1870 sequences[i] = new Sequence(newseq[i]);
1872 alignment = new Alignment(sequences);
1873 externalPaste = false;
1877 // parse the clipboard as an alignment.
1878 alignment = new FormatAdapter().readFile(str, "Paste", format);
1879 sequences = alignment.getSequencesArray();
1883 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1889 if (Desktop.jalviewClipboard != null)
1891 // dataset is inherited
1892 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1896 // new dataset is constructed
1897 alignment.setDataset(null);
1899 alwidth = alignment.getWidth() + 1;
1903 AlignmentI pastedal = alignment; // preserve pasted alignment object
1904 // Add pasted sequences and dataset into existing alignment.
1905 alignment = viewport.getAlignment();
1906 alwidth = alignment.getWidth() + 1;
1907 // decide if we need to import sequences from an existing dataset
1908 boolean importDs = Desktop.jalviewClipboard != null
1909 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1910 // importDs==true instructs us to copy over new dataset sequences from
1911 // an existing alignment
1912 Vector newDs = (importDs) ? new Vector() : null; // used to create
1913 // minimum dataset set
1915 for (int i = 0; i < sequences.length; i++)
1919 newDs.addElement(null);
1921 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1923 if (importDs && ds != null)
1925 if (!newDs.contains(ds))
1927 newDs.setElementAt(ds, i);
1928 ds = new Sequence(ds);
1929 // update with new dataset sequence
1930 sequences[i].setDatasetSequence(ds);
1934 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1939 // copy and derive new dataset sequence
1940 sequences[i] = sequences[i].deriveSequence();
1941 alignment.getDataset().addSequence(
1942 sequences[i].getDatasetSequence());
1943 // TODO: avoid creation of duplicate dataset sequences with a
1944 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1946 alignment.addSequence(sequences[i]); // merges dataset
1950 newDs.clear(); // tidy up
1952 if (alignment.getAlignmentAnnotation() != null)
1954 for (AlignmentAnnotation alan : alignment
1955 .getAlignmentAnnotation())
1957 if (alan.graphGroup > fgroup)
1959 fgroup = alan.graphGroup;
1963 if (pastedal.getAlignmentAnnotation() != null)
1965 // Add any annotation attached to alignment.
1966 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1967 for (int i = 0; i < alann.length; i++)
1969 annotationAdded = true;
1970 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1972 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1973 if (newann.graphGroup > -1)
1975 if (newGraphGroups.size() <= newann.graphGroup
1976 || newGraphGroups.get(newann.graphGroup) == null)
1978 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1980 newGraphGroups.add(q, null);
1982 newGraphGroups.set(newann.graphGroup, new Integer(
1985 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1989 newann.padAnnotation(alwidth);
1990 alignment.addAnnotation(newann);
2000 addHistoryItem(new EditCommand(MessageManager.getString("label.add_sequences"), EditCommand.PASTE,
2001 sequences, 0, alignment.getWidth(), alignment));
2003 // Add any annotations attached to sequences
2004 for (int i = 0; i < sequences.length; i++)
2006 if (sequences[i].getAnnotation() != null)
2008 AlignmentAnnotation newann;
2009 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2011 annotationAdded = true;
2012 newann = sequences[i].getAnnotation()[a];
2013 newann.adjustForAlignment();
2014 newann.padAnnotation(alwidth);
2015 if (newann.graphGroup > -1)
2017 if (newann.graphGroup > -1)
2019 if (newGraphGroups.size() <= newann.graphGroup
2020 || newGraphGroups.get(newann.graphGroup) == null)
2022 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2024 newGraphGroups.add(q, null);
2026 newGraphGroups.set(newann.graphGroup, new Integer(
2029 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2033 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2038 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2045 // propagate alignment changed.
2046 viewport.setEndSeq(alignment.getHeight());
2047 if (annotationAdded)
2049 // Duplicate sequence annotation in all views.
2050 AlignmentI[] alview = this.getViewAlignments();
2051 for (int i = 0; i < sequences.length; i++)
2053 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2058 for (int avnum = 0; avnum < alview.length; avnum++)
2060 if (alview[avnum] != alignment)
2062 // duplicate in a view other than the one with input focus
2063 int avwidth = alview[avnum].getWidth() + 1;
2064 // this relies on sann being preserved after we
2065 // modify the sequence's annotation array for each duplication
2066 for (int a = 0; a < sann.length; a++)
2068 AlignmentAnnotation newann = new AlignmentAnnotation(
2070 sequences[i].addAlignmentAnnotation(newann);
2071 newann.padAnnotation(avwidth);
2072 alview[avnum].addAnnotation(newann); // annotation was
2073 // duplicated earlier
2074 // TODO JAL-1145 graphGroups are not updated for sequence
2075 // annotation added to several views. This may cause
2077 alview[avnum].setAnnotationIndex(newann, a);
2082 buildSortByAnnotationScoresMenu();
2084 viewport.firePropertyChange("alignment", null,
2085 alignment.getSequences());
2086 if (alignPanels != null)
2088 for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
2090 ap.validateAnnotationDimensions(false);
2095 alignPanel.validateAnnotationDimensions(false);
2101 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2103 String newtitle = new String("Copied sequences");
2105 if (Desktop.jalviewClipboard != null
2106 && Desktop.jalviewClipboard[2] != null)
2108 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2109 for (int i = 0; i < hc.size(); i++)
2111 int[] region = (int[]) hc.elementAt(i);
2112 af.viewport.hideColumns(region[0], region[1]);
2116 // >>>This is a fix for the moment, until a better solution is
2118 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2120 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2122 // TODO: maintain provenance of an alignment, rather than just make the
2123 // title a concatenation of operations.
2126 if (title.startsWith("Copied sequences"))
2132 newtitle = newtitle.concat("- from " + title);
2137 newtitle = new String("Pasted sequences");
2140 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2145 } catch (Exception ex)
2147 ex.printStackTrace();
2148 System.out.println("Exception whilst pasting: " + ex);
2149 // could be anything being pasted in here
2155 protected void expand_newalign(ActionEvent e)
2159 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2160 .getAlignment(), -1);
2161 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2163 String newtitle = new String("Flanking alignment");
2165 if (Desktop.jalviewClipboard != null
2166 && Desktop.jalviewClipboard[2] != null)
2168 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2169 for (int i = 0; i < hc.size(); i++)
2171 int[] region = (int[]) hc.elementAt(i);
2172 af.viewport.hideColumns(region[0], region[1]);
2176 // >>>This is a fix for the moment, until a better solution is
2178 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2180 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2182 // TODO: maintain provenance of an alignment, rather than just make the
2183 // title a concatenation of operations.
2185 if (title.startsWith("Copied sequences"))
2191 newtitle = newtitle.concat("- from " + title);
2195 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2197 } catch (Exception ex)
2199 ex.printStackTrace();
2200 System.out.println("Exception whilst pasting: " + ex);
2201 // could be anything being pasted in here
2202 } catch (OutOfMemoryError oom)
2204 new OOMWarning("Viewing flanking region of alignment", oom);
2215 protected void cut_actionPerformed(ActionEvent e)
2217 copy_actionPerformed(null);
2218 delete_actionPerformed(null);
2228 protected void delete_actionPerformed(ActionEvent evt)
2231 SequenceGroup sg = viewport.getSelectionGroup();
2237 List<SequenceI> seqs = new ArrayList<SequenceI>(sg.getSize());
2239 for (int i = 0; i < sg.getSize(); i++)
2241 seq = sg.getSequenceAt(i);
2245 // If the cut affects all sequences, warn, remove highlighted columns
2246 if (sg.getSize() == viewport.getAlignment().getHeight())
2248 int confirm = JOptionPane.showConfirmDialog(this,
2249 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2250 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2251 JOptionPane.OK_CANCEL_OPTION);
2253 if (confirm == JOptionPane.CANCEL_OPTION
2254 || confirm == JOptionPane.CLOSED_OPTION)
2258 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2259 sg.getEndRes() + 1);
2262 SequenceI[] cut = new SequenceI[seqs.size()];
2263 for (int i = 0; i < seqs.size(); i++)
2265 cut[i] = seqs.get(i);
2269 * //ADD HISTORY ITEM
2271 addHistoryItem(new EditCommand(MessageManager.getString("label.cut_sequences"), EditCommand.CUT, cut,
2272 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2273 viewport.getAlignment()));
2275 viewport.setSelectionGroup(null);
2276 viewport.sendSelection();
2277 viewport.getAlignment().deleteGroup(sg);
2279 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2281 if (viewport.getAlignment().getHeight() < 1)
2285 this.setClosed(true);
2286 } catch (Exception ex)
2299 protected void deleteGroups_actionPerformed(ActionEvent e)
2301 if (avc.deleteGroups())
2303 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2304 alignPanel.updateAnnotation();
2305 alignPanel.paintAlignment(true);
2316 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2318 SequenceGroup sg = new SequenceGroup();
2320 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2322 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2325 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2326 viewport.setSelectionGroup(sg);
2327 viewport.sendSelection();
2328 alignPanel.paintAlignment(true);
2329 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2339 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2341 if (viewport.cursorMode)
2343 alignPanel.seqPanel.keyboardNo1 = null;
2344 alignPanel.seqPanel.keyboardNo2 = null;
2346 viewport.setSelectionGroup(null);
2347 viewport.getColumnSelection().clear();
2348 viewport.setSelectionGroup(null);
2349 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2350 alignPanel.idPanel.idCanvas.searchResults = null;
2351 alignPanel.paintAlignment(true);
2352 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2353 viewport.sendSelection();
2363 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2365 SequenceGroup sg = viewport.getSelectionGroup();
2369 selectAllSequenceMenuItem_actionPerformed(null);
2374 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2376 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2379 alignPanel.paintAlignment(true);
2380 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2381 viewport.sendSelection();
2385 public void invertColSel_actionPerformed(ActionEvent e)
2387 viewport.invertColumnSelection();
2388 alignPanel.paintAlignment(true);
2389 viewport.sendSelection();
2399 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2401 trimAlignment(true);
2411 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2413 trimAlignment(false);
2416 void trimAlignment(boolean trimLeft)
2418 ColumnSelection colSel = viewport.getColumnSelection();
2421 if (colSel.size() > 0)
2425 column = colSel.getMin();
2429 column = colSel.getMax();
2433 if (viewport.getSelectionGroup() != null)
2435 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2436 viewport.getHiddenRepSequences());
2440 seqs = viewport.getAlignment().getSequencesArray();
2443 TrimRegionCommand trimRegion;
2446 trimRegion = new TrimRegionCommand("Remove Left",
2447 TrimRegionCommand.TRIM_LEFT, seqs, column,
2448 viewport.getAlignment(), viewport.getColumnSelection(),
2449 viewport.getSelectionGroup());
2450 viewport.setStartRes(0);
2454 trimRegion = new TrimRegionCommand("Remove Right",
2455 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2456 viewport.getAlignment(), viewport.getColumnSelection(),
2457 viewport.getSelectionGroup());
2460 statusBar.setText(MessageManager.formatMessage(
2461 "label.removed_columns", new String[]
2462 { Integer.valueOf(trimRegion.getSize()).toString() }));
2464 addHistoryItem(trimRegion);
2466 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2468 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2469 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2471 viewport.getAlignment().deleteGroup(sg);
2475 viewport.firePropertyChange("alignment", null, viewport
2476 .getAlignment().getSequences());
2487 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2489 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2492 if (viewport.getSelectionGroup() != null)
2494 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2495 viewport.getHiddenRepSequences());
2496 start = viewport.getSelectionGroup().getStartRes();
2497 end = viewport.getSelectionGroup().getEndRes();
2501 seqs = viewport.getAlignment().getSequencesArray();
2504 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2505 "Remove Gapped Columns", seqs, start, end,
2506 viewport.getAlignment());
2508 addHistoryItem(removeGapCols);
2510 statusBar.setText(MessageManager.formatMessage(
2511 "label.removed_empty_columns", new String[]
2512 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2514 // This is to maintain viewport position on first residue
2515 // of first sequence
2516 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2517 int startRes = seq.findPosition(viewport.startRes);
2518 // ShiftList shifts;
2519 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2520 // edit.alColumnChanges=shifts.getInverse();
2521 // if (viewport.hasHiddenColumns)
2522 // viewport.getColumnSelection().compensateForEdits(shifts);
2523 viewport.setStartRes(seq.findIndex(startRes) - 1);
2524 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2536 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2538 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2541 if (viewport.getSelectionGroup() != null)
2543 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2544 viewport.getHiddenRepSequences());
2545 start = viewport.getSelectionGroup().getStartRes();
2546 end = viewport.getSelectionGroup().getEndRes();
2550 seqs = viewport.getAlignment().getSequencesArray();
2553 // This is to maintain viewport position on first residue
2554 // of first sequence
2555 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2556 int startRes = seq.findPosition(viewport.startRes);
2558 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2559 viewport.getAlignment()));
2561 viewport.setStartRes(seq.findIndex(startRes) - 1);
2563 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2575 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2577 viewport.setPadGaps(padGapsMenuitem.isSelected());
2578 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2584 // if (justifySeqs>0)
2586 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2599 public void findMenuItem_actionPerformed(ActionEvent e)
2605 public void newView_actionPerformed(ActionEvent e)
2612 * @param copyAnnotation
2613 * if true then duplicate all annnotation, groups and settings
2614 * @return new alignment panel, already displayed.
2616 public AlignmentPanel newView(boolean copyAnnotation)
2618 return newView(null, copyAnnotation);
2624 * title of newly created view
2625 * @return new alignment panel, already displayed.
2627 public AlignmentPanel newView(String viewTitle)
2629 return newView(viewTitle, true);
2635 * title of newly created view
2636 * @param copyAnnotation
2637 * if true then duplicate all annnotation, groups and settings
2638 * @return new alignment panel, already displayed.
2640 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2642 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2644 if (!copyAnnotation)
2646 // just remove all the current annotation except for the automatic stuff
2647 newap.av.getAlignment().deleteAllGroups();
2648 for (AlignmentAnnotation alan : newap.av.getAlignment()
2649 .getAlignmentAnnotation())
2651 if (!alan.autoCalculated)
2653 newap.av.getAlignment().deleteAnnotation(alan);
2659 newap.av.gatherViewsHere = false;
2661 if (viewport.viewName == null)
2663 viewport.viewName = "Original";
2666 newap.av.historyList = viewport.historyList;
2667 newap.av.redoList = viewport.redoList;
2669 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2670 // make sure the new view has a unique name - this is essential for Jalview
2672 boolean addFirstIndex = false;
2673 if (viewTitle == null || viewTitle.trim().length() == 0)
2675 viewTitle = MessageManager.getString("action.view");
2676 addFirstIndex = true;
2680 index = 1;// we count from 1 if given a specific name
2682 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2683 Vector comps = (Vector) PaintRefresher.components.get(viewport
2684 .getSequenceSetId());
2685 Vector existingNames = new Vector();
2686 for (int i = 0; i < comps.size(); i++)
2688 if (comps.elementAt(i) instanceof AlignmentPanel)
2690 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2691 if (!existingNames.contains(ap.av.viewName))
2693 existingNames.addElement(ap.av.viewName);
2698 while (existingNames.contains(newViewName))
2700 newViewName = viewTitle + " " + (++index);
2703 newap.av.viewName = newViewName;
2705 addAlignmentPanel(newap, true);
2706 newap.alignmentChanged();
2708 if (alignPanels.size() == 2)
2710 viewport.gatherViewsHere = true;
2712 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2717 public void expandViews_actionPerformed(ActionEvent e)
2719 Desktop.instance.explodeViews(this);
2723 public void gatherViews_actionPerformed(ActionEvent e)
2725 Desktop.instance.gatherViews(this);
2735 public void font_actionPerformed(ActionEvent e)
2737 new FontChooser(alignPanel);
2747 protected void seqLimit_actionPerformed(ActionEvent e)
2749 viewport.setShowJVSuffix(seqLimits.isSelected());
2751 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2752 .calculateIdWidth());
2753 alignPanel.paintAlignment(true);
2757 public void idRightAlign_actionPerformed(ActionEvent e)
2759 viewport.rightAlignIds = idRightAlign.isSelected();
2760 alignPanel.paintAlignment(true);
2764 public void centreColumnLabels_actionPerformed(ActionEvent e)
2766 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2767 alignPanel.paintAlignment(true);
2773 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2776 protected void followHighlight_actionPerformed()
2778 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2780 alignPanel.scrollToPosition(
2781 alignPanel.seqPanel.seqCanvas.searchResults, false);
2792 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2794 viewport.setColourText(colourTextMenuItem.isSelected());
2795 alignPanel.paintAlignment(true);
2805 public void wrapMenuItem_actionPerformed(ActionEvent e)
2807 scaleAbove.setVisible(wrapMenuItem.isSelected());
2808 scaleLeft.setVisible(wrapMenuItem.isSelected());
2809 scaleRight.setVisible(wrapMenuItem.isSelected());
2810 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2811 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2815 public void showAllSeqs_actionPerformed(ActionEvent e)
2817 viewport.showAllHiddenSeqs();
2821 public void showAllColumns_actionPerformed(ActionEvent e)
2823 viewport.showAllHiddenColumns();
2828 public void hideSelSequences_actionPerformed(ActionEvent e)
2830 viewport.hideAllSelectedSeqs();
2831 alignPanel.paintAlignment(true);
2835 * called by key handler and the hide all/show all menu items
2840 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2843 boolean hide = false;
2844 SequenceGroup sg = viewport.getSelectionGroup();
2845 if (!toggleSeqs && !toggleCols)
2847 // Hide everything by the current selection - this is a hack - we do the
2848 // invert and then hide
2849 // first check that there will be visible columns after the invert.
2850 if ((viewport.getColumnSelection() != null
2851 && viewport.getColumnSelection().getSelected() != null && viewport
2852 .getColumnSelection().getSelected().size() > 0)
2853 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2856 // now invert the sequence set, if required - empty selection implies
2857 // that no hiding is required.
2860 invertSequenceMenuItem_actionPerformed(null);
2861 sg = viewport.getSelectionGroup();
2865 viewport.expandColSelection(sg, true);
2866 // finally invert the column selection and get the new sequence
2868 invertColSel_actionPerformed(null);
2875 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2877 hideSelSequences_actionPerformed(null);
2880 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2883 showAllSeqs_actionPerformed(null);
2889 if (viewport.getColumnSelection().getSelected().size() > 0)
2891 hideSelColumns_actionPerformed(null);
2894 viewport.setSelectionGroup(sg);
2899 showAllColumns_actionPerformed(null);
2908 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2909 * event.ActionEvent)
2912 public void hideAllButSelection_actionPerformed(ActionEvent e)
2914 toggleHiddenRegions(false, false);
2921 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2925 public void hideAllSelection_actionPerformed(ActionEvent e)
2927 SequenceGroup sg = viewport.getSelectionGroup();
2928 viewport.expandColSelection(sg, false);
2929 viewport.hideAllSelectedSeqs();
2930 viewport.hideSelectedColumns();
2931 alignPanel.paintAlignment(true);
2938 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2942 public void showAllhidden_actionPerformed(ActionEvent e)
2944 viewport.showAllHiddenColumns();
2945 viewport.showAllHiddenSeqs();
2946 alignPanel.paintAlignment(true);
2950 public void hideSelColumns_actionPerformed(ActionEvent e)
2952 viewport.hideSelectedColumns();
2953 alignPanel.paintAlignment(true);
2957 public void hiddenMarkers_actionPerformed(ActionEvent e)
2959 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2970 protected void scaleAbove_actionPerformed(ActionEvent e)
2972 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2973 alignPanel.paintAlignment(true);
2983 protected void scaleLeft_actionPerformed(ActionEvent e)
2985 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2986 alignPanel.paintAlignment(true);
2996 protected void scaleRight_actionPerformed(ActionEvent e)
2998 viewport.setScaleRightWrapped(scaleRight.isSelected());
2999 alignPanel.paintAlignment(true);
3009 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3011 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3012 alignPanel.paintAlignment(true);
3022 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3024 viewport.setShowText(viewTextMenuItem.isSelected());
3025 alignPanel.paintAlignment(true);
3035 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3037 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3038 alignPanel.paintAlignment(true);
3041 public FeatureSettings featureSettings;
3044 public void featureSettings_actionPerformed(ActionEvent e)
3046 if (featureSettings != null)
3048 featureSettings.close();
3049 featureSettings = null;
3051 if (!showSeqFeatures.isSelected())
3053 // make sure features are actually displayed
3054 showSeqFeatures.setSelected(true);
3055 showSeqFeatures_actionPerformed(null);
3057 featureSettings = new FeatureSettings(this);
3061 * Set or clear 'Show Sequence Features'
3067 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3069 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3070 alignPanel.paintAlignment(true);
3071 if (alignPanel.getOverviewPanel() != null)
3073 alignPanel.getOverviewPanel().updateOverviewImage();
3078 * Set or clear 'Show Sequence Features'
3084 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3086 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3088 if (viewport.getShowSequenceFeaturesHeight())
3090 // ensure we're actually displaying features
3091 viewport.setShowSequenceFeatures(true);
3092 showSeqFeatures.setSelected(true);
3094 alignPanel.paintAlignment(true);
3095 if (alignPanel.getOverviewPanel() != null)
3097 alignPanel.getOverviewPanel().updateOverviewImage();
3102 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3103 * the annotations panel as a whole.
3105 * The options to show/hide all annotations should be enabled when the panel
3106 * is shown, and disabled when the panel is hidden.
3111 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3113 final boolean setVisible = annotationPanelMenuItem.isSelected();
3114 viewport.setShowAnnotation(setVisible);
3115 alignPanel.setAnnotationVisible(setVisible);
3116 this.showAllSeqAnnotations.setEnabled(setVisible);
3117 this.hideAllSeqAnnotations.setEnabled(setVisible);
3118 this.showAllAlAnnotations.setEnabled(setVisible);
3119 this.hideAllAlAnnotations.setEnabled(setVisible);
3123 public void alignmentProperties()
3125 JEditorPane editPane = new JEditorPane("text/html", "");
3126 editPane.setEditable(false);
3127 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3129 editPane.setText(MessageManager.formatMessage("label.html_content",
3131 { contents.toString() }));
3132 JInternalFrame frame = new JInternalFrame();
3133 frame.getContentPane().add(new JScrollPane(editPane));
3135 Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage(
3136 "label.alignment_properties", new String[]
3137 { getTitle() }), 500, 400);
3147 public void overviewMenuItem_actionPerformed(ActionEvent e)
3149 if (alignPanel.overviewPanel != null)
3154 JInternalFrame frame = new JInternalFrame();
3155 OverviewPanel overview = new OverviewPanel(alignPanel);
3156 frame.setContentPane(overview);
3157 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3158 "label.overview_params", new String[]
3159 { this.getTitle() }), frame.getWidth(), frame.getHeight());
3161 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3162 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3165 public void internalFrameClosed(
3166 javax.swing.event.InternalFrameEvent evt)
3168 alignPanel.setOverviewPanel(null);
3172 alignPanel.setOverviewPanel(overview);
3176 public void textColour_actionPerformed(ActionEvent e)
3178 new TextColourChooser().chooseColour(alignPanel, null);
3188 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3200 public void clustalColour_actionPerformed(ActionEvent e)
3202 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3203 viewport.getHiddenRepSequences()));
3213 public void zappoColour_actionPerformed(ActionEvent e)
3215 changeColour(new ZappoColourScheme());
3225 public void taylorColour_actionPerformed(ActionEvent e)
3227 changeColour(new TaylorColourScheme());
3237 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3239 changeColour(new HydrophobicColourScheme());
3249 public void helixColour_actionPerformed(ActionEvent e)
3251 changeColour(new HelixColourScheme());
3261 public void strandColour_actionPerformed(ActionEvent e)
3263 changeColour(new StrandColourScheme());
3273 public void turnColour_actionPerformed(ActionEvent e)
3275 changeColour(new TurnColourScheme());
3285 public void buriedColour_actionPerformed(ActionEvent e)
3287 changeColour(new BuriedColourScheme());
3297 public void nucleotideColour_actionPerformed(ActionEvent e)
3299 changeColour(new NucleotideColourScheme());
3303 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3305 changeColour(new PurinePyrimidineColourScheme());
3309 * public void covariationColour_actionPerformed(ActionEvent e) {
3311 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3315 public void annotationColour_actionPerformed(ActionEvent e)
3317 new AnnotationColourChooser(viewport, alignPanel);
3321 public void rnahelicesColour_actionPerformed(ActionEvent e)
3323 new RNAHelicesColourChooser(viewport, alignPanel);
3333 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3335 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3344 public void changeColour(ColourSchemeI cs)
3346 // TODO: compare with applet and pull up to model method
3351 if (viewport.getAbovePIDThreshold())
3353 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3355 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3359 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3362 if (viewport.getConservationSelected())
3365 Alignment al = (Alignment) viewport.getAlignment();
3366 Conservation c = new Conservation("All",
3367 ResidueProperties.propHash, 3, al.getSequences(), 0,
3371 c.verdict(false, viewport.getConsPercGaps());
3373 cs.setConservation(c);
3375 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3380 cs.setConservation(null);
3383 cs.setConsensus(viewport.getSequenceConsensusHash());
3386 viewport.setGlobalColourScheme(cs);
3388 if (viewport.getColourAppliesToAllGroups())
3391 for (SequenceGroup sg : viewport.getAlignment().getGroups())
3399 if (cs instanceof ClustalxColourScheme)
3401 sg.cs = new ClustalxColourScheme(sg,
3402 viewport.getHiddenRepSequences());
3404 else if (cs instanceof UserColourScheme)
3406 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3412 sg.cs = cs.getClass().newInstance();
3413 } catch (Exception ex)
3418 if (viewport.getAbovePIDThreshold()
3419 || cs instanceof PIDColourScheme
3420 || cs instanceof Blosum62ColourScheme)
3422 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3424 sg.cs.setConsensus(AAFrequency.calculate(
3425 sg.getSequences(viewport.getHiddenRepSequences()),
3426 sg.getStartRes(), sg.getEndRes() + 1));
3430 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3433 if (viewport.getConservationSelected())
3435 Conservation c = new Conservation("Group",
3436 ResidueProperties.propHash, 3, sg.getSequences(viewport
3437 .getHiddenRepSequences()), sg.getStartRes(),
3438 sg.getEndRes() + 1);
3440 c.verdict(false, viewport.getConsPercGaps());
3441 sg.cs.setConservation(c);
3445 sg.cs.setConservation(null);
3450 if (alignPanel.getOverviewPanel() != null)
3452 alignPanel.getOverviewPanel().updateOverviewImage();
3455 alignPanel.paintAlignment(true);
3465 protected void modifyPID_actionPerformed(ActionEvent e)
3467 if (viewport.getAbovePIDThreshold()
3468 && viewport.getGlobalColourScheme() != null)
3470 SliderPanel.setPIDSliderSource(alignPanel,
3471 viewport.getGlobalColourScheme(), "Background");
3472 SliderPanel.showPIDSlider();
3483 protected void modifyConservation_actionPerformed(ActionEvent e)
3485 if (viewport.getConservationSelected()
3486 && viewport.getGlobalColourScheme() != null)
3488 SliderPanel.setConservationSlider(alignPanel,
3489 viewport.getGlobalColourScheme(), "Background");
3490 SliderPanel.showConservationSlider();
3501 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3503 viewport.setConservationSelected(conservationMenuItem.isSelected());
3505 viewport.setAbovePIDThreshold(false);
3506 abovePIDThreshold.setSelected(false);
3508 changeColour(viewport.getGlobalColourScheme());
3510 modifyConservation_actionPerformed(null);
3520 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3522 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3524 conservationMenuItem.setSelected(false);
3525 viewport.setConservationSelected(false);
3527 changeColour(viewport.getGlobalColourScheme());
3529 modifyPID_actionPerformed(null);
3539 public void userDefinedColour_actionPerformed(ActionEvent e)
3541 if (e.getActionCommand().equals(
3542 MessageManager.getString("action.user_defined")))
3544 new UserDefinedColours(alignPanel, null);
3548 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3549 .getUserColourSchemes().get(e.getActionCommand());
3555 public void updateUserColourMenu()
3558 Component[] menuItems = colourMenu.getMenuComponents();
3559 int i, iSize = menuItems.length;
3560 for (i = 0; i < iSize; i++)
3562 if (menuItems[i].getName() != null
3563 && menuItems[i].getName().equals("USER_DEFINED"))
3565 colourMenu.remove(menuItems[i]);
3569 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3571 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3572 .getUserColourSchemes().keys();
3574 while (userColours.hasMoreElements())
3576 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3577 userColours.nextElement().toString());
3578 radioItem.setName("USER_DEFINED");
3579 radioItem.addMouseListener(new MouseAdapter()
3582 public void mousePressed(MouseEvent evt)
3584 if (evt.isControlDown()
3585 || SwingUtilities.isRightMouseButton(evt))
3587 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3589 int option = JOptionPane.showInternalConfirmDialog(
3590 jalview.gui.Desktop.desktop,
3592 .getString("label.remove_from_default_list"),
3594 .getString("label.remove_user_defined_colour"),
3595 JOptionPane.YES_NO_OPTION);
3596 if (option == JOptionPane.YES_OPTION)
3598 jalview.gui.UserDefinedColours
3599 .removeColourFromDefaults(radioItem.getText());
3600 colourMenu.remove(radioItem);
3604 radioItem.addActionListener(new ActionListener()
3607 public void actionPerformed(ActionEvent evt)
3609 userDefinedColour_actionPerformed(evt);
3616 radioItem.addActionListener(new ActionListener()
3619 public void actionPerformed(ActionEvent evt)
3621 userDefinedColour_actionPerformed(evt);
3625 colourMenu.insert(radioItem, 15);
3626 colours.add(radioItem);
3638 public void PIDColour_actionPerformed(ActionEvent e)
3640 changeColour(new PIDColourScheme());
3650 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3652 changeColour(new Blosum62ColourScheme());
3662 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3664 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3665 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3666 .getAlignment().getSequenceAt(0), null);
3667 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3668 viewport.getAlignment()));
3669 alignPanel.paintAlignment(true);
3679 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3681 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3682 AlignmentSorter.sortByID(viewport.getAlignment());
3683 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3684 viewport.getAlignment()));
3685 alignPanel.paintAlignment(true);
3695 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3697 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3698 AlignmentSorter.sortByLength(viewport.getAlignment());
3699 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3700 viewport.getAlignment()));
3701 alignPanel.paintAlignment(true);
3711 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3713 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3714 AlignmentSorter.sortByGroup(viewport.getAlignment());
3715 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3716 viewport.getAlignment()));
3718 alignPanel.paintAlignment(true);
3728 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3730 new RedundancyPanel(alignPanel, this);
3740 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3742 if ((viewport.getSelectionGroup() == null)
3743 || (viewport.getSelectionGroup().getSize() < 2))
3745 JOptionPane.showInternalMessageDialog(this, MessageManager
3746 .getString("label.you_must_select_least_two_sequences"),
3747 MessageManager.getString("label.invalid_selection"),
3748 JOptionPane.WARNING_MESSAGE);
3752 JInternalFrame frame = new JInternalFrame();
3753 frame.setContentPane(new PairwiseAlignPanel(viewport));
3754 Desktop.addInternalFrame(frame,
3755 MessageManager.getString("action.pairwise_alignment"), 600,
3767 public void PCAMenuItem_actionPerformed(ActionEvent e)
3769 if (((viewport.getSelectionGroup() != null)
3770 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3771 .getSelectionGroup().getSize() > 0))
3772 || (viewport.getAlignment().getHeight() < 4))
3775 .showInternalMessageDialog(
3778 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3780 .getString("label.sequence_selection_insufficient"),
3781 JOptionPane.WARNING_MESSAGE);
3786 new PCAPanel(alignPanel);
3790 public void autoCalculate_actionPerformed(ActionEvent e)
3792 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3793 if (viewport.autoCalculateConsensus)
3795 viewport.firePropertyChange("alignment", null, viewport
3796 .getAlignment().getSequences());
3801 public void sortByTreeOption_actionPerformed(ActionEvent e)
3803 viewport.sortByTree = sortByTree.isSelected();
3807 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3809 viewport.followSelection = listenToViewSelections.isSelected();
3819 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3821 NewTreePanel("AV", "PID", "Average distance tree using PID");
3831 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3833 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3843 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3845 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3855 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3857 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3870 void NewTreePanel(String type, String pwType, String title)
3874 if (viewport.getSelectionGroup() != null
3875 && viewport.getSelectionGroup().getSize() > 0)
3877 if (viewport.getSelectionGroup().getSize() < 3)
3883 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3885 .getString("label.not_enough_sequences"),
3886 JOptionPane.WARNING_MESSAGE);
3890 SequenceGroup sg = viewport.getSelectionGroup();
3892 /* Decide if the selection is a column region */
3893 for (SequenceI _s : sg.getSequences())
3895 if (_s.getLength() < sg.getEndRes())
3901 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3903 .getString("label.sequences_selection_not_aligned"),
3904 JOptionPane.WARNING_MESSAGE);
3910 title = title + " on region";
3911 tp = new TreePanel(alignPanel, type, pwType);
3915 // are the visible sequences aligned?
3916 if (!viewport.getAlignment().isAligned(false))
3922 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3924 .getString("label.sequences_not_aligned"),
3925 JOptionPane.WARNING_MESSAGE);
3930 if (viewport.getAlignment().getHeight() < 2)
3935 tp = new TreePanel(alignPanel, type, pwType);
3940 if (viewport.viewName != null)
3942 title += viewport.viewName + " of ";
3945 title += this.title;
3947 Desktop.addInternalFrame(tp, title, 600, 500);
3958 public void addSortByOrderMenuItem(String title,
3959 final AlignmentOrder order)
3961 final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new String[]{title}));
3963 item.addActionListener(new java.awt.event.ActionListener()
3966 public void actionPerformed(ActionEvent e)
3968 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3970 // TODO: JBPNote - have to map order entries to curent SequenceI
3972 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3974 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3977 alignPanel.paintAlignment(true);
3983 * Add a new sort by annotation score menu item
3986 * the menu to add the option to
3988 * the label used to retrieve scores for each sequence on the
3991 public void addSortByAnnotScoreMenuItem(JMenu sort,
3992 final String scoreLabel)
3994 final JMenuItem item = new JMenuItem(scoreLabel);
3996 item.addActionListener(new java.awt.event.ActionListener()
3999 public void actionPerformed(ActionEvent e)
4001 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4002 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4003 viewport.getAlignment());// ,viewport.getSelectionGroup());
4004 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4005 viewport.getAlignment()));
4006 alignPanel.paintAlignment(true);
4012 * last hash for alignment's annotation array - used to minimise cost of
4015 protected int _annotationScoreVectorHash;
4018 * search the alignment and rebuild the sort by annotation score submenu the
4019 * last alignment annotation vector hash is stored to minimize cost of
4020 * rebuilding in subsequence calls.
4024 public void buildSortByAnnotationScoresMenu()
4026 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4031 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4033 sortByAnnotScore.removeAll();
4034 // almost certainly a quicker way to do this - but we keep it simple
4035 Hashtable scoreSorts = new Hashtable();
4036 AlignmentAnnotation aann[];
4037 for (SequenceI sqa : viewport.getAlignment().getSequences())
4039 aann = sqa.getAnnotation();
4040 for (int i = 0; aann != null && i < aann.length; i++)
4042 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4044 scoreSorts.put(aann[i].label, aann[i].label);
4048 Enumeration labels = scoreSorts.keys();
4049 while (labels.hasMoreElements())
4051 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4052 (String) labels.nextElement());
4054 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4057 _annotationScoreVectorHash = viewport.getAlignment()
4058 .getAlignmentAnnotation().hashCode();
4063 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4064 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4065 * call. Listeners are added to remove the menu item when the treePanel is
4066 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4070 * Displayed tree window.
4072 * SortBy menu item title.
4075 public void buildTreeMenu()
4077 calculateTree.removeAll();
4078 // build the calculate menu
4080 for (final String type : new String[]
4083 String treecalcnm = MessageManager.getString("label.tree_calc_"
4084 + type.toLowerCase());
4085 for (final Object pwtype : ResidueProperties.scoreMatrices.keySet())
4087 JMenuItem tm = new JMenuItem();
4088 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4089 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4091 String smn = MessageManager.getStringOrReturn(
4092 "label.score_model_", sm.getName());
4093 final String title = MessageManager.formatMessage(
4094 "label.treecalc_title", treecalcnm, smn);
4095 tm.setText(title);//
4096 tm.addActionListener(new java.awt.event.ActionListener()
4099 public void actionPerformed(ActionEvent e)
4101 NewTreePanel(type, (String) pwtype, title);
4104 calculateTree.add(tm);
4109 sortByTreeMenu.removeAll();
4111 Vector comps = (Vector) PaintRefresher.components.get(viewport
4112 .getSequenceSetId());
4113 Vector treePanels = new Vector();
4114 int i, iSize = comps.size();
4115 for (i = 0; i < iSize; i++)
4117 if (comps.elementAt(i) instanceof TreePanel)
4119 treePanels.add(comps.elementAt(i));
4123 iSize = treePanels.size();
4127 sortByTreeMenu.setVisible(false);
4131 sortByTreeMenu.setVisible(true);
4133 for (i = 0; i < treePanels.size(); i++)
4135 final TreePanel tp = (TreePanel) treePanels.elementAt(i);
4136 final JMenuItem item = new JMenuItem(tp.getTitle());
4137 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
4138 item.addActionListener(new java.awt.event.ActionListener()
4141 public void actionPerformed(ActionEvent e)
4143 tp.sortByTree_actionPerformed(null);
4144 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4149 sortByTreeMenu.add(item);
4153 public boolean sortBy(AlignmentOrder alorder, String undoname)
4155 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4156 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4157 if (undoname != null)
4159 addHistoryItem(new OrderCommand(undoname, oldOrder,
4160 viewport.getAlignment()));
4162 alignPanel.paintAlignment(true);
4167 * Work out whether the whole set of sequences or just the selected set will
4168 * be submitted for multiple alignment.
4171 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4173 // Now, check we have enough sequences
4174 AlignmentView msa = null;
4176 if ((viewport.getSelectionGroup() != null)
4177 && (viewport.getSelectionGroup().getSize() > 1))
4179 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4180 // some common interface!
4182 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4183 * SequenceI[sz = seqs.getSize(false)];
4185 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4186 * seqs.getSequenceAt(i); }
4188 msa = viewport.getAlignmentView(true);
4193 * Vector seqs = viewport.getAlignment().getSequences();
4195 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
4197 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
4198 * seqs.elementAt(i); } }
4200 msa = viewport.getAlignmentView(false);
4206 * Decides what is submitted to a secondary structure prediction service: the
4207 * first sequence in the alignment, or in the current selection, or, if the
4208 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4209 * region or the whole alignment. (where the first sequence in the set is the
4210 * one that the prediction will be for).
4212 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4214 AlignmentView seqs = null;
4216 if ((viewport.getSelectionGroup() != null)
4217 && (viewport.getSelectionGroup().getSize() > 0))
4219 seqs = viewport.getAlignmentView(true);
4223 seqs = viewport.getAlignmentView(false);
4225 // limit sequences - JBPNote in future - could spawn multiple prediction
4227 // TODO: viewport.getAlignment().isAligned is a global state - the local
4228 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4229 if (!viewport.getAlignment().isAligned(false))
4231 seqs.setSequences(new SeqCigar[]
4232 { seqs.getSequences()[0] });
4233 // TODO: if seqs.getSequences().length>1 then should really have warned
4247 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
4249 // Pick the tree file
4250 JalviewFileChooser chooser = new JalviewFileChooser(
4251 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4252 chooser.setFileView(new JalviewFileView());
4253 chooser.setDialogTitle(MessageManager
4254 .getString("label.select_newick_like_tree_file"));
4255 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4257 int value = chooser.showOpenDialog(null);
4259 if (value == JalviewFileChooser.APPROVE_OPTION)
4261 String choice = chooser.getSelectedFile().getPath();
4262 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4263 jalview.io.NewickFile fin = null;
4266 fin = new jalview.io.NewickFile(choice, "File");
4267 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4268 } catch (Exception ex)
4275 .getString("label.problem_reading_tree_file"),
4276 JOptionPane.WARNING_MESSAGE);
4277 ex.printStackTrace();
4279 if (fin != null && fin.hasWarningMessage())
4281 JOptionPane.showMessageDialog(Desktop.desktop, fin
4282 .getWarningMessage(), MessageManager
4283 .getString("label.possible_problem_with_tree_file"),
4284 JOptionPane.WARNING_MESSAGE);
4290 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4292 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4295 public TreePanel ShowNewickTree(NewickFile nf, String title)
4297 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4300 public TreePanel ShowNewickTree(NewickFile nf, String title,
4301 AlignmentView input)
4303 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4306 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4307 int h, int x, int y)
4309 return ShowNewickTree(nf, title, null, w, h, x, y);
4313 * Add a treeviewer for the tree extracted from a newick file object to the
4314 * current alignment view
4321 * Associated alignment input data (or null)
4330 * @return TreePanel handle
4332 public TreePanel ShowNewickTree(NewickFile nf, String title,
4333 AlignmentView input, int w, int h, int x, int y)
4335 TreePanel tp = null;
4341 if (nf.getTree() != null)
4343 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4349 tp.setLocation(x, y);
4352 Desktop.addInternalFrame(tp, title, w, h);
4354 } catch (Exception ex)
4356 ex.printStackTrace();
4362 private boolean buildingMenu = false;
4365 * Generates menu items and listener event actions for web service clients
4368 public void BuildWebServiceMenu()
4370 while (buildingMenu)
4374 System.err.println("Waiting for building menu to finish.");
4376 } catch (Exception e)
4381 final AlignFrame me = this;
4382 buildingMenu = true;
4383 new Thread(new Runnable()
4388 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4391 System.err.println("Building ws menu again "
4392 + Thread.currentThread());
4393 // TODO: add support for context dependent disabling of services based
4395 // alignment and current selection
4396 // TODO: add additional serviceHandle parameter to specify abstract
4398 // class independently of AbstractName
4399 // TODO: add in rediscovery GUI function to restart discoverer
4400 // TODO: group services by location as well as function and/or
4402 // object broker mechanism.
4403 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4404 final IProgressIndicator af = me;
4405 final JMenu msawsmenu = new JMenu("Alignment");
4406 final JMenu secstrmenu = new JMenu(
4407 "Secondary Structure Prediction");
4408 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4409 final JMenu analymenu = new JMenu("Analysis");
4410 final JMenu dismenu = new JMenu("Protein Disorder");
4411 // final JMenu msawsmenu = new
4412 // JMenu(MessageManager.getString("label.alignment"));
4413 // final JMenu secstrmenu = new
4414 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4415 // final JMenu seqsrchmenu = new
4416 // JMenu(MessageManager.getString("label.sequence_database_search"));
4417 // final JMenu analymenu = new
4418 // JMenu(MessageManager.getString("label.analysis"));
4419 // final JMenu dismenu = new
4420 // JMenu(MessageManager.getString("label.protein_disorder"));
4421 // JAL-940 - only show secondary structure prediction services from
4422 // the legacy server
4423 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4425 Discoverer.services != null && (Discoverer.services.size() > 0))
4427 // TODO: refactor to allow list of AbstractName/Handler bindings to
4429 // stored or retrieved from elsewhere
4430 // No MSAWS used any more:
4431 // Vector msaws = null; // (Vector)
4432 // Discoverer.services.get("MsaWS");
4433 Vector secstrpr = (Vector) Discoverer.services
4435 if (secstrpr != null)
4437 // Add any secondary structure prediction services
4438 for (int i = 0, j = secstrpr.size(); i < j; i++)
4440 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4442 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4443 .getServiceClient(sh);
4444 int p = secstrmenu.getItemCount();
4445 impl.attachWSMenuEntry(secstrmenu, me);
4446 int q = secstrmenu.getItemCount();
4447 for (int litm = p; litm < q; litm++)
4449 legacyItems.add(secstrmenu.getItem(litm));
4455 // Add all submenus in the order they should appear on the web
4457 wsmenu.add(msawsmenu);
4458 wsmenu.add(secstrmenu);
4459 wsmenu.add(dismenu);
4460 wsmenu.add(analymenu);
4461 // No search services yet
4462 // wsmenu.add(seqsrchmenu);
4464 javax.swing.SwingUtilities.invokeLater(new Runnable()
4471 webService.removeAll();
4472 // first, add discovered services onto the webservices menu
4473 if (wsmenu.size() > 0)
4475 for (int i = 0, j = wsmenu.size(); i < j; i++)
4477 webService.add(wsmenu.get(i));
4482 webService.add(me.webServiceNoServices);
4484 // TODO: move into separate menu builder class.
4485 boolean new_sspred = false;
4486 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4488 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4489 if (jws2servs != null)
4491 if (jws2servs.hasServices())
4493 jws2servs.attachWSMenuEntry(webService, me);
4494 for (Jws2Instance sv : jws2servs.getServices())
4496 if (sv.description.toLowerCase().contains("jpred"))
4498 for (JMenuItem jmi : legacyItems)
4500 jmi.setVisible(false);
4506 if (jws2servs.isRunning())
4508 JMenuItem tm = new JMenuItem(
4509 "Still discovering JABA Services");
4510 tm.setEnabled(false);
4515 build_urlServiceMenu(me.webService);
4516 build_fetchdbmenu(webService);
4517 for (JMenu item : wsmenu)
4519 if (item.getItemCount() == 0)
4521 item.setEnabled(false);
4525 item.setEnabled(true);
4528 } catch (Exception e)
4531 .debug("Exception during web service menu building process.",
4537 } catch (Exception e)
4542 buildingMenu = false;
4549 * construct any groupURL type service menu entries.
4553 private void build_urlServiceMenu(JMenu webService)
4555 // TODO: remove this code when 2.7 is released
4556 // DEBUG - alignmentView
4558 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4559 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4561 * @Override public void actionPerformed(ActionEvent e) {
4562 * jalview.datamodel.AlignmentView
4563 * .testSelectionViews(af.viewport.getAlignment(),
4564 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4566 * }); webService.add(testAlView);
4568 // TODO: refactor to RestClient discoverer and merge menu entries for
4569 // rest-style services with other types of analysis/calculation service
4570 // SHmmr test client - still being implemented.
4571 // DEBUG - alignmentView
4573 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4576 client.attachWSMenuEntry(
4577 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4583 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4584 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4585 * getProperty("LAST_DIRECTORY"));
4587 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4588 * to Vamsas file"); chooser.setToolTipText("Export");
4590 * int value = chooser.showSaveDialog(this);
4592 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4593 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4594 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4595 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4598 * prototype of an automatically enabled/disabled analysis function
4601 protected void setShowProductsEnabled()
4603 SequenceI[] selection = viewport.getSequenceSelection();
4604 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4605 viewport.getAlignment().getDataset()))
4607 showProducts.setEnabled(true);
4612 showProducts.setEnabled(false);
4617 * search selection for sequence xRef products and build the show products
4622 * @return true if showProducts menu should be enabled.
4624 public boolean canShowProducts(SequenceI[] selection,
4625 boolean isRegionSelection, Alignment dataset)
4627 boolean showp = false;
4630 showProducts.removeAll();
4631 final boolean dna = viewport.getAlignment().isNucleotide();
4632 final Alignment ds = dataset;
4633 String[] ptypes = (selection == null || selection.length == 0) ? null
4634 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4636 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4637 // selection, dataset, true);
4638 final SequenceI[] sel = selection;
4639 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4642 final boolean isRegSel = isRegionSelection;
4643 final AlignFrame af = this;
4644 final String source = ptypes[t];
4645 JMenuItem xtype = new JMenuItem(ptypes[t]);
4646 xtype.addActionListener(new ActionListener()
4650 public void actionPerformed(ActionEvent e)
4652 // TODO: new thread for this call with vis-delay
4653 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4654 isRegSel, dna, source);
4658 showProducts.add(xtype);
4660 showProducts.setVisible(showp);
4661 showProducts.setEnabled(showp);
4662 } catch (Exception e)
4664 jalview.bin.Cache.log
4665 .warn("canTranslate threw an exception - please report to help@jalview.org",
4672 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4673 boolean isRegSel, boolean dna, String source)
4675 final boolean fisRegSel = isRegSel;
4676 final boolean fdna = dna;
4677 final String fsrc = source;
4678 final AlignFrame ths = this;
4679 final SequenceI[] fsel = sel;
4680 Runnable foo = new Runnable()
4686 final long sttime = System.currentTimeMillis();
4687 ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{fsrc}), sttime);
4690 Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4694 Alignment prods = CrossRef
4695 .findXrefSequences(fsel, fdna, fsrc, ds);
4698 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4699 for (int s = 0; s < sprods.length; s++)
4701 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4702 if (ds.getSequences() == null
4703 || !ds.getSequences().contains(
4704 sprods[s].getDatasetSequence()))
4706 ds.addSequence(sprods[s].getDatasetSequence());
4708 sprods[s].updatePDBIds();
4710 Alignment al = new Alignment(sprods);
4711 AlignedCodonFrame[] cf = prods.getCodonFrames();
4713 for (int s = 0; cf != null && s < cf.length; s++)
4715 al.addCodonFrame(cf[s]);
4718 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4720 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4721 + " for " + ((fisRegSel) ? "selected region of " : "")
4723 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4728 System.err.println("No Sequences generated for xRef type "
4731 } catch (Exception e)
4733 jalview.bin.Cache.log.error(
4734 "Exception when finding crossreferences", e);
4735 } catch (OutOfMemoryError e)
4737 new OOMWarning("whilst fetching crossreferences", e);
4740 jalview.bin.Cache.log.error("Error when finding crossreferences",
4743 ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{fsrc}),
4748 Thread frunner = new Thread(foo);
4752 public boolean canShowTranslationProducts(SequenceI[] selection,
4753 AlignmentI alignment)
4758 return (jalview.analysis.Dna.canTranslate(selection,
4759 viewport.getViewAsVisibleContigs(true)));
4760 } catch (Exception e)
4762 jalview.bin.Cache.log
4763 .warn("canTranslate threw an exception - please report to help@jalview.org",
4770 public void showProducts_actionPerformed(ActionEvent e)
4772 // /////////////////////////////
4773 // Collect Data to be translated/transferred
4775 SequenceI[] selection = viewport.getSequenceSelection();
4776 AlignmentI al = null;
4779 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4780 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4781 viewport.getAlignment().getDataset());
4782 } catch (Exception ex)
4785 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4793 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4794 MessageManager.getString("label.translation_failed"),
4795 JOptionPane.WARNING_MESSAGE);
4799 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4800 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4801 "label.translation_of_params", new String[]
4802 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4807 public void showTranslation_actionPerformed(ActionEvent e)
4809 // /////////////////////////////
4810 // Collect Data to be translated/transferred
4812 SequenceI[] selection = viewport.getSequenceSelection();
4813 String[] seqstring = viewport.getViewAsString(true);
4814 AlignmentI al = null;
4817 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4818 viewport.getViewAsVisibleContigs(true), viewport
4819 .getGapCharacter(), viewport.getAlignment()
4820 .getAlignmentAnnotation(), viewport.getAlignment()
4821 .getWidth(), viewport.getAlignment().getDataset());
4822 } catch (Exception ex)
4825 jalview.bin.Cache.log.error(
4826 "Exception during translation. Please report this !", ex);
4831 .getString("label.error_when_translating_sequences_submit_bug_report"),
4833 .getString("label.implementation_error")
4835 .getString("translation_failed"),
4836 JOptionPane.ERROR_MESSAGE);
4845 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4846 MessageManager.getString("label.translation_failed"),
4847 JOptionPane.WARNING_MESSAGE);
4851 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4852 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4853 "label.translation_of_params", new String[]
4854 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4859 * Try to load a features file onto the alignment.
4862 * contents or path to retrieve file
4864 * access mode of file (see jalview.io.AlignFile)
4865 * @return true if features file was parsed corectly.
4867 public boolean parseFeaturesFile(String file, String type)
4869 boolean featuresFile = false;
4872 featuresFile = new FeaturesFile(file, type).parse(viewport
4873 .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4874 .getFeatureRenderer().featureColours, false,
4875 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4876 } catch (Exception ex)
4878 ex.printStackTrace();
4883 viewport.showSequenceFeatures = true;
4884 showSeqFeatures.setSelected(true);
4885 if (alignPanel.seqPanel.seqCanvas.fr != null)
4887 // update the min/max ranges where necessary
4888 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4890 if (featureSettings != null)
4892 featureSettings.setTableData();
4894 alignPanel.paintAlignment(true);
4897 return featuresFile;
4901 public void dragEnter(DropTargetDragEvent evt)
4906 public void dragExit(DropTargetEvent evt)
4911 public void dragOver(DropTargetDragEvent evt)
4916 public void dropActionChanged(DropTargetDragEvent evt)
4921 public void drop(DropTargetDropEvent evt)
4923 Transferable t = evt.getTransferable();
4924 java.util.List files = null;
4928 DataFlavor uriListFlavor = new DataFlavor(
4929 "text/uri-list;class=java.lang.String");
4930 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4932 // Works on Windows and MacOSX
4933 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4934 files = (java.util.List) t
4935 .getTransferData(DataFlavor.javaFileListFlavor);
4937 else if (t.isDataFlavorSupported(uriListFlavor))
4939 // This is used by Unix drag system
4940 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4941 String data = (String) t.getTransferData(uriListFlavor);
4942 files = new java.util.ArrayList(1);
4943 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4944 data, "\r\n"); st.hasMoreTokens();)
4946 String s = st.nextToken();
4947 if (s.startsWith("#"))
4949 // the line is a comment (as per the RFC 2483)
4953 java.net.URI uri = new java.net.URI(s);
4954 // check to see if we can handle this kind of URI
4955 if (uri.getScheme().toLowerCase().startsWith("http"))
4957 files.add(uri.toString());
4961 // otherwise preserve old behaviour: catch all for file objects
4962 java.io.File file = new java.io.File(uri);
4963 files.add(file.toString());
4967 } catch (Exception e)
4969 e.printStackTrace();
4975 // check to see if any of these files have names matching sequences in
4977 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4978 .getAlignment().getSequencesArray());
4980 * Object[] { String,SequenceI}
4982 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4983 ArrayList<String> filesnotmatched = new ArrayList<String>();
4984 for (int i = 0; i < files.size(); i++)
4986 String file = files.get(i).toString();
4988 String protocol = FormatAdapter.checkProtocol(file);
4989 if (protocol == jalview.io.FormatAdapter.FILE)
4991 File fl = new File(file);
4992 pdbfn = fl.getName();
4994 else if (protocol == jalview.io.FormatAdapter.URL)
4996 URL url = new URL(file);
4997 pdbfn = url.getFile();
4999 if (pdbfn.length() > 0)
5001 // attempt to find a match in the alignment
5002 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5003 int l = 0, c = pdbfn.indexOf(".");
5004 while (mtch == null && c != -1)
5009 } while ((c = pdbfn.indexOf(".", l)) > l);
5012 pdbfn = pdbfn.substring(0, l);
5014 mtch = idm.findAllIdMatches(pdbfn);
5021 type = new IdentifyFile().Identify(file, protocol);
5022 } catch (Exception ex)
5028 if (type.equalsIgnoreCase("PDB"))
5030 filesmatched.add(new Object[]
5031 { file, protocol, mtch });
5036 // File wasn't named like one of the sequences or wasn't a PDB file.
5037 filesnotmatched.add(file);
5041 if (filesmatched.size() > 0)
5043 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5049 "label.automatically_associate_pdb_files_with_sequences_same_name",
5056 .getString("label.automatically_associate_pdb_files_by_name"),
5057 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5060 for (Object[] fm : filesmatched)
5062 // try and associate
5063 // TODO: may want to set a standard ID naming formalism for
5064 // associating PDB files which have no IDs.
5065 for (SequenceI toassoc : (SequenceI[]) fm[2])
5067 PDBEntry pe = new AssociatePdbFileWithSeq()
5068 .associatePdbWithSeq((String) fm[0],
5069 (String) fm[1], toassoc, false,
5073 System.err.println("Associated file : "
5074 + ((String) fm[0]) + " with "
5075 + toassoc.getDisplayId(true));
5079 alignPanel.paintAlignment(true);
5083 if (filesnotmatched.size() > 0)
5086 && (Cache.getDefault(
5087 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5090 "<html>"+MessageManager
5092 "label.ignore_unmatched_dropped_files_info",
5097 .toString() })+"</html>",
5099 .getString("label.ignore_unmatched_dropped_files"),
5100 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5104 for (String fn : filesnotmatched)
5106 loadJalviewDataFile(fn, null, null, null);
5110 } catch (Exception ex)
5112 ex.printStackTrace();
5118 * Attempt to load a "dropped" file or URL string: First by testing whether
5119 * it's and Annotation file, then a JNet file, and finally a features file. If
5120 * all are false then the user may have dropped an alignment file onto this
5124 * either a filename or a URL string.
5126 public void loadJalviewDataFile(String file, String protocol,
5127 String format, SequenceI assocSeq)
5131 if (protocol == null)
5133 protocol = jalview.io.FormatAdapter.checkProtocol(file);
5135 // if the file isn't identified, or not positively identified as some
5136 // other filetype (PFAM is default unidentified alignment file type) then
5137 // try to parse as annotation.
5138 boolean isAnnotation = (format == null || format
5139 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5140 .readAnnotationFile(viewport.getAlignment(), file, protocol)
5145 // first see if its a T-COFFEE score file
5146 TCoffeeScoreFile tcf = null;
5149 tcf = new TCoffeeScoreFile(file, protocol);
5152 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5154 tcoffeeColour.setEnabled(true);
5155 tcoffeeColour.setSelected(true);
5156 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5157 isAnnotation = true;
5159 .setText(MessageManager
5160 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5164 // some problem - if no warning its probable that the ID matching
5165 // process didn't work
5169 tcf.getWarningMessage() == null ? MessageManager
5170 .getString("label.check_file_matches_sequence_ids_alignment")
5171 : tcf.getWarningMessage(),
5173 .getString("label.problem_reading_tcoffee_score_file"),
5174 JOptionPane.WARNING_MESSAGE);
5181 } catch (Exception x)
5184 .debug("Exception when processing data source as T-COFFEE score file",
5190 // try to see if its a JNet 'concise' style annotation file *before*
5192 // try to parse it as a features file
5195 format = new IdentifyFile().Identify(file, protocol);
5197 if (format.equalsIgnoreCase("JnetFile"))
5199 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5201 new JnetAnnotationMaker().add_annotation(predictions,
5202 viewport.getAlignment(), 0, false);
5203 isAnnotation = true;
5208 * if (format.equalsIgnoreCase("PDB")) {
5210 * String pdbfn = ""; // try to match up filename with sequence id
5211 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5212 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5213 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5214 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5215 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5216 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5217 * // attempt to find a match in the alignment SequenceI mtch =
5218 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5219 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5220 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5221 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5222 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5223 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5224 * { System.err.println("Associated file : " + file + " with " +
5225 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5226 * TODO: maybe need to load as normal otherwise return; } }
5228 // try to parse it as a features file
5229 boolean isGroupsFile = parseFeaturesFile(file, protocol);
5230 // if it wasn't a features file then we just treat it as a general
5231 // alignment file to load into the current view.
5234 new FileLoader().LoadFile(viewport, file, protocol, format);
5238 alignPanel.paintAlignment(true);
5246 alignPanel.adjustAnnotationHeight();
5247 viewport.updateSequenceIdColours();
5248 buildSortByAnnotationScoresMenu();
5249 alignPanel.paintAlignment(true);
5251 } catch (Exception ex)
5253 ex.printStackTrace();
5254 } catch (OutOfMemoryError oom)
5259 } catch (Exception x)
5265 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5266 : "using " + protocol + " from " + file)
5268 + (format != null ? "(parsing as '" + format
5269 + "' file)" : ""), oom, Desktop.desktop);
5274 public void tabSelectionChanged(int index)
5278 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
5279 viewport = alignPanel.av;
5280 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5281 setMenusFromViewport(viewport);
5286 public void tabbedPane_mousePressed(MouseEvent e)
5288 if (SwingUtilities.isRightMouseButton(e))
5290 String reply = JOptionPane.showInternalInputDialog(this,
5291 MessageManager.getString("label.enter_view_name"),
5292 MessageManager.getString("label.enter_view_name"),
5293 JOptionPane.QUESTION_MESSAGE);
5297 viewport.viewName = reply;
5298 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5303 public AlignViewport getCurrentView()
5309 * Open the dialog for regex description parsing.
5312 protected void extractScores_actionPerformed(ActionEvent e)
5314 ParseProperties pp = new jalview.analysis.ParseProperties(
5315 viewport.getAlignment());
5316 // TODO: verify regex and introduce GUI dialog for version 2.5
5317 // if (pp.getScoresFromDescription("col", "score column ",
5318 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5320 if (pp.getScoresFromDescription("description column",
5321 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5323 buildSortByAnnotationScoresMenu();
5331 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5335 protected void showDbRefs_actionPerformed(ActionEvent e)
5337 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
5343 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5347 protected void showNpFeats_actionPerformed(ActionEvent e)
5349 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
5353 * find the viewport amongst the tabs in this alignment frame and close that
5358 public boolean closeView(AlignViewport av)
5362 this.closeMenuItem_actionPerformed(false);
5365 Component[] comp = tabbedPane.getComponents();
5366 for (int i = 0; comp != null && i < comp.length; i++)
5368 if (comp[i] instanceof AlignmentPanel)
5370 if (((AlignmentPanel) comp[i]).av == av)
5373 closeView((AlignmentPanel) comp[i]);
5381 protected void build_fetchdbmenu(JMenu webService)
5383 // Temporary hack - DBRef Fetcher always top level ws entry.
5384 // TODO We probably want to store a sequence database checklist in
5385 // preferences and have checkboxes.. rather than individual sources selected
5387 final JMenu rfetch = new JMenu(
5388 MessageManager.getString("action.fetch_db_references"));
5389 rfetch.setToolTipText(MessageManager
5390 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5391 webService.add(rfetch);
5393 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5394 MessageManager.getString("option.trim_retrieved_seqs"));
5395 trimrs.setToolTipText(MessageManager
5396 .getString("label.trim_retrieved_sequences"));
5397 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5398 trimrs.addActionListener(new ActionListener()
5401 public void actionPerformed(ActionEvent e)
5403 trimrs.setSelected(trimrs.isSelected());
5404 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5405 Boolean.valueOf(trimrs.isSelected()).toString());
5409 JMenuItem fetchr = new JMenuItem(
5410 MessageManager.getString("label.standard_databases"));
5411 fetchr.setToolTipText(MessageManager
5412 .getString("label.fetch_embl_uniprot"));
5413 fetchr.addActionListener(new ActionListener()
5417 public void actionPerformed(ActionEvent e)
5419 new Thread(new Runnable()
5425 new jalview.ws.DBRefFetcher(alignPanel.av
5426 .getSequenceSelection(), alignPanel.alignFrame)
5427 .fetchDBRefs(false);
5435 final AlignFrame me = this;
5436 new Thread(new Runnable()
5441 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5442 .getSequenceFetcherSingleton(me);
5443 javax.swing.SwingUtilities.invokeLater(new Runnable()
5448 String[] dbclasses = sf.getOrderedSupportedSources();
5449 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5450 // jalview.util.QuickSort.sort(otherdb, otherdb);
5451 List<DbSourceProxy> otherdb;
5452 JMenu dfetch = new JMenu();
5453 JMenu ifetch = new JMenu();
5454 JMenuItem fetchr = null;
5455 int comp = 0, icomp = 0, mcomp = 15;
5456 String mname = null;
5458 for (String dbclass : dbclasses)
5460 otherdb = sf.getSourceProxy(dbclass);
5461 // add a single entry for this class, or submenu allowing 'fetch
5463 if (otherdb == null || otherdb.size() < 1)
5467 // List<DbSourceProxy> dbs=otherdb;
5468 // otherdb=new ArrayList<DbSourceProxy>();
5469 // for (DbSourceProxy db:dbs)
5471 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5475 mname = "From " + dbclass;
5477 if (otherdb.size() == 1)
5479 final DbSourceProxy[] dassource = otherdb
5480 .toArray(new DbSourceProxy[0]);
5481 DbSourceProxy src = otherdb.get(0);
5482 fetchr = new JMenuItem(src.getDbSource());
5483 fetchr.addActionListener(new ActionListener()
5487 public void actionPerformed(ActionEvent e)
5489 new Thread(new Runnable()
5495 new jalview.ws.DBRefFetcher(alignPanel.av
5496 .getSequenceSelection(),
5497 alignPanel.alignFrame, dassource)
5498 .fetchDBRefs(false);
5504 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{src.getDbName()})));
5510 final DbSourceProxy[] dassource = otherdb
5511 .toArray(new DbSourceProxy[0]);
5513 DbSourceProxy src = otherdb.get(0);
5514 fetchr = new JMenuItem(MessageManager.formatMessage(
5515 "label.fetch_all_param", new String[]
5516 { src.getDbSource() }));
5517 fetchr.addActionListener(new ActionListener()
5520 public void actionPerformed(ActionEvent e)
5522 new Thread(new Runnable()
5528 new jalview.ws.DBRefFetcher(alignPanel.av
5529 .getSequenceSelection(),
5530 alignPanel.alignFrame, dassource)
5531 .fetchDBRefs(false);
5537 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new String[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
5540 // and then build the rest of the individual menus
5541 ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new String[]{src.getDbSource()}));
5543 String imname = null;
5545 for (DbSourceProxy sproxy : otherdb)
5547 String dbname = sproxy.getDbName();
5548 String sname = dbname.length() > 5 ? dbname.substring(0,
5549 5) + "..." : dbname;
5550 String msname = dbname.length() > 10 ? dbname.substring(
5551 0, 10) + "..." : dbname;
5554 imname = MessageManager.formatMessage("label.from_msname", new String[]{sname});
5556 fetchr = new JMenuItem(msname);
5557 final DbSourceProxy[] dassrc =
5559 fetchr.addActionListener(new ActionListener()
5563 public void actionPerformed(ActionEvent e)
5565 new Thread(new Runnable()
5571 new jalview.ws.DBRefFetcher(alignPanel.av
5572 .getSequenceSelection(),
5573 alignPanel.alignFrame, dassrc)
5574 .fetchDBRefs(false);
5580 fetchr.setToolTipText("<html>"
5581 + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname}));
5584 if (++icomp >= mcomp || i == (otherdb.size()))
5586 ifetch.setText(MessageManager.formatMessage(
5587 "label.source_to_target", imname, sname));
5589 ifetch = new JMenu();
5597 if (comp >= mcomp || dbi >= (dbclasses.length))
5599 dfetch.setText(MessageManager.formatMessage(
5600 "label.source_to_target", mname, dbclass));
5602 dfetch = new JMenu();
5615 * Left justify the whole alignment.
5618 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5620 AlignmentI al = viewport.getAlignment();
5622 viewport.firePropertyChange("alignment", null, al);
5626 * Right justify the whole alignment.
5629 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5631 AlignmentI al = viewport.getAlignment();
5633 viewport.firePropertyChange("alignment", null, al);
5636 public void setShowSeqFeatures(boolean b)
5638 showSeqFeatures.setSelected(true);
5639 viewport.setShowSequenceFeatures(true);
5646 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5647 * awt.event.ActionEvent)
5650 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5652 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5653 alignPanel.paintAlignment(true);
5660 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5664 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5666 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5667 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5675 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5676 * .event.ActionEvent)
5679 protected void showGroupConservation_actionPerformed(ActionEvent e)
5681 viewport.setShowGroupConservation(showGroupConservation.getState());
5682 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5689 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5690 * .event.ActionEvent)
5693 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5695 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5696 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5703 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5704 * .event.ActionEvent)
5707 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5709 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5710 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5714 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5716 showSequenceLogo.setState(true);
5717 viewport.setShowSequenceLogo(true);
5718 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5719 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5723 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5725 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5732 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5733 * .event.ActionEvent)
5736 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5738 if (avc.makeGroupsFromSelection())
5740 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5741 alignPanel.updateAnnotation();
5742 alignPanel.paintAlignment(true);
5747 protected void createGroup_actionPerformed(ActionEvent e)
5749 if (avc.createGroup())
5751 alignPanel.alignmentChanged();
5756 protected void unGroup_actionPerformed(ActionEvent e)
5760 alignPanel.alignmentChanged();
5765 * make the given alignmentPanel the currently selected tab
5767 * @param alignmentPanel
5769 public void setDisplayedView(AlignmentPanel alignmentPanel)
5771 if (!viewport.getSequenceSetId().equals(
5772 alignmentPanel.av.getSequenceSetId()))
5774 throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
5776 if (tabbedPane != null
5777 & alignPanels.indexOf(alignmentPanel) != tabbedPane
5778 .getSelectedIndex())
5780 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5785 * Action on selection of menu options to Show or Hide annotations.
5788 * @param forSequences
5789 * update sequence-related annotations
5790 * @param forAlignment
5791 * update non-sequence-related annotations
5794 protected void setAnnotationsVisibility(boolean visible,
5795 boolean forSequences, boolean forAlignment)
5797 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5798 .getAlignmentAnnotation())
5800 boolean apply = (aa.sequenceRef == null && forAlignment)
5801 || (aa.sequenceRef != null && forSequences);
5804 aa.visible = visible;
5807 this.alignPanel.paintAlignment(true);
5811 * Store selected annotation sort order for the view and repaint.
5814 protected void sortAnnotations_actionPerformed()
5816 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5818 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5819 alignPanel.paintAlignment(true);
5823 class PrintThread extends Thread
5827 public PrintThread(AlignmentPanel ap)
5832 static PageFormat pf;
5837 PrinterJob printJob = PrinterJob.getPrinterJob();
5841 printJob.setPrintable(ap, pf);
5845 printJob.setPrintable(ap);
5848 if (printJob.printDialog())
5853 } catch (Exception PrintException)
5855 PrintException.printStackTrace();