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.EditCommand.Action;
38 import jalview.commands.OrderCommand;
39 import jalview.commands.RemoveGapColCommand;
40 import jalview.commands.RemoveGapsCommand;
41 import jalview.commands.SlideSequencesCommand;
42 import jalview.commands.TrimRegionCommand;
43 import jalview.datamodel.AlignedCodonFrame;
44 import jalview.datamodel.Alignment;
45 import jalview.datamodel.AlignmentAnnotation;
46 import jalview.datamodel.AlignmentI;
47 import jalview.datamodel.AlignmentOrder;
48 import jalview.datamodel.AlignmentView;
49 import jalview.datamodel.ColumnSelection;
50 import jalview.datamodel.PDBEntry;
51 import jalview.datamodel.SeqCigar;
52 import jalview.datamodel.Sequence;
53 import jalview.datamodel.SequenceGroup;
54 import jalview.datamodel.SequenceI;
55 import jalview.io.AlignmentProperties;
56 import jalview.io.AnnotationFile;
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());
1235 public void createImageMap(File file, String image)
1237 alignPanel.makePNGImageMap(file, image);
1247 public void createPNG(File f)
1249 alignPanel.makePNG(f);
1259 public void createEPS(File f)
1261 alignPanel.makeEPS(f);
1264 public void createSVG(File f)
1266 alignPanel.makeSVG(f);
1269 public void pageSetup_actionPerformed(ActionEvent e)
1271 PrinterJob printJob = PrinterJob.getPrinterJob();
1272 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1282 public void printMenuItem_actionPerformed(ActionEvent e)
1284 // Putting in a thread avoids Swing painting problems
1285 PrintThread thread = new PrintThread(alignPanel);
1290 public void exportFeatures_actionPerformed(ActionEvent e)
1292 new AnnotationExporter().exportFeatures(alignPanel);
1296 public void exportAnnotations_actionPerformed(ActionEvent e)
1298 new AnnotationExporter().exportAnnotations(alignPanel,
1299 viewport.showAnnotation ? viewport.getAlignment()
1300 .getAlignmentAnnotation() : null, viewport
1301 .getAlignment().getGroups(), ((Alignment) viewport
1302 .getAlignment()).alignmentProperties);
1306 public void associatedData_actionPerformed(ActionEvent e)
1308 // Pick the tree file
1309 JalviewFileChooser chooser = new JalviewFileChooser(
1310 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1311 chooser.setFileView(new JalviewFileView());
1312 chooser.setDialogTitle(MessageManager
1313 .getString("label.load_jalview_annotations"));
1314 chooser.setToolTipText(MessageManager
1315 .getString("label.load_jalview_annotations"));
1317 int value = chooser.showOpenDialog(null);
1319 if (value == JalviewFileChooser.APPROVE_OPTION)
1321 String choice = chooser.getSelectedFile().getPath();
1322 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1323 loadJalviewDataFile(choice, null, null, null);
1329 * Close the current view or all views in the alignment frame. If the frame
1330 * only contains one view then the alignment will be removed from memory.
1332 * @param closeAllTabs
1335 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1337 if (alignPanels != null && alignPanels.size() < 2)
1339 closeAllTabs = true;
1344 if (alignPanels != null)
1348 if (this.isClosed())
1350 // really close all the windows - otherwise wait till
1351 // setClosed(true) is called
1352 for (int i = 0; i < alignPanels.size(); i++)
1354 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1361 closeView(alignPanel);
1367 this.setClosed(true);
1369 } catch (Exception ex)
1371 ex.printStackTrace();
1376 * close alignPanel2 and shuffle tabs appropriately.
1378 * @param alignPanel2
1380 public void closeView(AlignmentPanel alignPanel2)
1382 int index = tabbedPane.getSelectedIndex();
1383 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1384 alignPanels.removeElement(alignPanel2);
1386 // if (viewport == alignPanel2.av)
1390 alignPanel2.closePanel();
1393 tabbedPane.removeTabAt(closedindex);
1394 tabbedPane.validate();
1396 if (index > closedindex || index == tabbedPane.getTabCount())
1398 // modify currently selected tab index if necessary.
1402 this.tabSelectionChanged(index);
1408 void updateEditMenuBar()
1411 if (viewport.historyList.size() > 0)
1413 undoMenuItem.setEnabled(true);
1414 CommandI command = viewport.historyList.peek();
1415 undoMenuItem.setText(MessageManager.formatMessage(
1416 "label.undo_command", new String[]
1417 { command.getDescription() }));
1421 undoMenuItem.setEnabled(false);
1422 undoMenuItem.setText(MessageManager.getString("action.undo"));
1425 if (viewport.redoList.size() > 0)
1427 redoMenuItem.setEnabled(true);
1429 CommandI command = viewport.redoList.peek();
1430 redoMenuItem.setText(MessageManager.formatMessage(
1431 "label.redo_command", new String[]
1432 { command.getDescription() }));
1436 redoMenuItem.setEnabled(false);
1437 redoMenuItem.setText(MessageManager.getString("action.redo"));
1441 public void addHistoryItem(CommandI command)
1443 if (command.getSize() > 0)
1445 viewport.historyList.push(command);
1446 viewport.redoList.clear();
1447 updateEditMenuBar();
1448 viewport.updateHiddenColumns();
1449 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1450 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1451 // viewport.getColumnSelection()
1452 // .getHiddenColumns().size() > 0);
1458 * @return alignment objects for all views
1460 AlignmentI[] getViewAlignments()
1462 if (alignPanels != null)
1464 Enumeration e = alignPanels.elements();
1465 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1466 for (int i = 0; e.hasMoreElements(); i++)
1468 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1472 if (viewport != null)
1474 return new AlignmentI[]
1475 { viewport.getAlignment() };
1487 protected void undoMenuItem_actionPerformed(ActionEvent e)
1489 if (viewport.historyList.empty())
1493 CommandI command = viewport.historyList.pop();
1494 viewport.redoList.push(command);
1495 command.undoCommand(getViewAlignments());
1497 AlignViewport originalSource = getOriginatingSource(command);
1498 updateEditMenuBar();
1500 if (originalSource != null)
1502 if (originalSource != viewport)
1505 .warn("Implementation worry: mismatch of viewport origin for undo");
1507 originalSource.updateHiddenColumns();
1508 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1510 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1511 // viewport.getColumnSelection()
1512 // .getHiddenColumns().size() > 0);
1513 originalSource.firePropertyChange("alignment", null, originalSource
1514 .getAlignment().getSequences());
1525 protected void redoMenuItem_actionPerformed(ActionEvent e)
1527 if (viewport.redoList.size() < 1)
1532 CommandI command = viewport.redoList.pop();
1533 viewport.historyList.push(command);
1534 command.doCommand(getViewAlignments());
1536 AlignViewport originalSource = getOriginatingSource(command);
1537 updateEditMenuBar();
1539 if (originalSource != null)
1542 if (originalSource != viewport)
1545 .warn("Implementation worry: mismatch of viewport origin for redo");
1547 originalSource.updateHiddenColumns();
1548 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1550 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1551 // viewport.getColumnSelection()
1552 // .getHiddenColumns().size() > 0);
1553 originalSource.firePropertyChange("alignment", null, originalSource
1554 .getAlignment().getSequences());
1558 AlignViewport getOriginatingSource(CommandI command)
1560 AlignViewport originalSource = null;
1561 // For sequence removal and addition, we need to fire
1562 // the property change event FROM the viewport where the
1563 // original alignment was altered
1564 AlignmentI al = null;
1565 if (command instanceof EditCommand)
1567 EditCommand editCommand = (EditCommand) command;
1568 al = editCommand.getAlignment();
1569 Vector comps = (Vector) PaintRefresher.components.get(viewport
1570 .getSequenceSetId());
1572 for (int i = 0; i < comps.size(); i++)
1574 if (comps.elementAt(i) instanceof AlignmentPanel)
1576 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1578 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1585 if (originalSource == null)
1587 // The original view is closed, we must validate
1588 // the current view against the closed view first
1591 PaintRefresher.validateSequences(al, viewport.getAlignment());
1594 originalSource = viewport;
1597 return originalSource;
1606 public void moveSelectedSequences(boolean up)
1608 SequenceGroup sg = viewport.getSelectionGroup();
1614 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1615 viewport.getHiddenRepSequences(), up);
1616 alignPanel.paintAlignment(true);
1619 synchronized void slideSequences(boolean right, int size)
1621 List<SequenceI> sg = new Vector();
1622 if (viewport.cursorMode)
1624 sg.add(viewport.getAlignment().getSequenceAt(
1625 alignPanel.seqPanel.seqCanvas.cursorY));
1627 else if (viewport.getSelectionGroup() != null
1628 && viewport.getSelectionGroup().getSize() != viewport
1629 .getAlignment().getHeight())
1631 sg = viewport.getSelectionGroup().getSequences(
1632 viewport.getHiddenRepSequences());
1640 Vector invertGroup = new Vector();
1642 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1644 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1646 invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1650 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1652 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1653 for (int i = 0; i < invertGroup.size(); i++)
1655 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1658 SlideSequencesCommand ssc;
1661 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1662 size, viewport.getGapCharacter());
1666 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1667 size, viewport.getGapCharacter());
1670 int groupAdjustment = 0;
1671 if (ssc.getGapsInsertedBegin() && right)
1673 if (viewport.cursorMode)
1675 alignPanel.seqPanel.moveCursor(size, 0);
1679 groupAdjustment = size;
1682 else if (!ssc.getGapsInsertedBegin() && !right)
1684 if (viewport.cursorMode)
1686 alignPanel.seqPanel.moveCursor(-size, 0);
1690 groupAdjustment = -size;
1694 if (groupAdjustment != 0)
1696 viewport.getSelectionGroup().setStartRes(
1697 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1698 viewport.getSelectionGroup().setEndRes(
1699 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1702 boolean appendHistoryItem = false;
1703 if (viewport.historyList != null && viewport.historyList.size() > 0
1704 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1706 appendHistoryItem = ssc
1707 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1711 if (!appendHistoryItem)
1713 addHistoryItem(ssc);
1726 protected void copy_actionPerformed(ActionEvent e)
1729 if (viewport.getSelectionGroup() == null)
1733 // TODO: preserve the ordering of displayed alignment annotation in any
1734 // internal paste (particularly sequence associated annotation)
1735 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1736 String[] omitHidden = null;
1738 if (viewport.hasHiddenColumns())
1740 omitHidden = viewport.getViewAsString(true);
1743 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1746 StringSelection ss = new StringSelection(output);
1750 jalview.gui.Desktop.internalCopy = true;
1751 // Its really worth setting the clipboard contents
1752 // to empty before setting the large StringSelection!!
1753 Toolkit.getDefaultToolkit().getSystemClipboard()
1754 .setContents(new StringSelection(""), null);
1756 Toolkit.getDefaultToolkit().getSystemClipboard()
1757 .setContents(ss, Desktop.instance);
1758 } catch (OutOfMemoryError er)
1760 new OOMWarning("copying region", er);
1764 Vector hiddenColumns = null;
1765 if (viewport.hasHiddenColumns())
1767 hiddenColumns = new Vector();
1768 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1769 .getSelectionGroup().getEndRes();
1770 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1773 int[] region = (int[]) viewport.getColumnSelection()
1774 .getHiddenColumns().elementAt(i);
1775 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1777 hiddenColumns.addElement(new int[]
1778 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1783 Desktop.jalviewClipboard = new Object[]
1784 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1785 statusBar.setText(MessageManager.formatMessage(
1786 "label.copied_sequences_to_clipboard", new String[]
1787 { Integer.valueOf(seqs.length).toString() }));
1797 protected void pasteNew_actionPerformed(ActionEvent e)
1809 protected void pasteThis_actionPerformed(ActionEvent e)
1815 * Paste contents of Jalview clipboard
1817 * @param newAlignment
1818 * true to paste to a new alignment, otherwise add to this.
1820 void paste(boolean newAlignment)
1822 boolean externalPaste = true;
1825 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1826 Transferable contents = c.getContents(this);
1828 if (contents == null)
1836 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1837 if (str.length() < 1)
1842 format = new IdentifyFile().Identify(str, "Paste");
1844 } catch (OutOfMemoryError er)
1846 new OOMWarning("Out of memory pasting sequences!!", er);
1850 SequenceI[] sequences;
1851 boolean annotationAdded = false;
1852 AlignmentI alignment = null;
1854 if (Desktop.jalviewClipboard != null)
1856 // The clipboard was filled from within Jalview, we must use the
1858 // And dataset from the copied alignment
1859 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1860 // be doubly sure that we create *new* sequence objects.
1861 sequences = new SequenceI[newseq.length];
1862 for (int i = 0; i < newseq.length; i++)
1864 sequences[i] = new Sequence(newseq[i]);
1866 alignment = new Alignment(sequences);
1867 externalPaste = false;
1871 // parse the clipboard as an alignment.
1872 alignment = new FormatAdapter().readFile(str, "Paste", format);
1873 sequences = alignment.getSequencesArray();
1877 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1883 if (Desktop.jalviewClipboard != null)
1885 // dataset is inherited
1886 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1890 // new dataset is constructed
1891 alignment.setDataset(null);
1893 alwidth = alignment.getWidth() + 1;
1897 AlignmentI pastedal = alignment; // preserve pasted alignment object
1898 // Add pasted sequences and dataset into existing alignment.
1899 alignment = viewport.getAlignment();
1900 alwidth = alignment.getWidth() + 1;
1901 // decide if we need to import sequences from an existing dataset
1902 boolean importDs = Desktop.jalviewClipboard != null
1903 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1904 // importDs==true instructs us to copy over new dataset sequences from
1905 // an existing alignment
1906 Vector newDs = (importDs) ? new Vector() : null; // used to create
1907 // minimum dataset set
1909 for (int i = 0; i < sequences.length; i++)
1913 newDs.addElement(null);
1915 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1917 if (importDs && ds != null)
1919 if (!newDs.contains(ds))
1921 newDs.setElementAt(ds, i);
1922 ds = new Sequence(ds);
1923 // update with new dataset sequence
1924 sequences[i].setDatasetSequence(ds);
1928 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1933 // copy and derive new dataset sequence
1934 sequences[i] = sequences[i].deriveSequence();
1935 alignment.getDataset().addSequence(
1936 sequences[i].getDatasetSequence());
1937 // TODO: avoid creation of duplicate dataset sequences with a
1938 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1940 alignment.addSequence(sequences[i]); // merges dataset
1944 newDs.clear(); // tidy up
1946 if (alignment.getAlignmentAnnotation() != null)
1948 for (AlignmentAnnotation alan : alignment
1949 .getAlignmentAnnotation())
1951 if (alan.graphGroup > fgroup)
1953 fgroup = alan.graphGroup;
1957 if (pastedal.getAlignmentAnnotation() != null)
1959 // Add any annotation attached to alignment.
1960 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1961 for (int i = 0; i < alann.length; i++)
1963 annotationAdded = true;
1964 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1966 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1967 if (newann.graphGroup > -1)
1969 if (newGraphGroups.size() <= newann.graphGroup
1970 || newGraphGroups.get(newann.graphGroup) == null)
1972 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1974 newGraphGroups.add(q, null);
1976 newGraphGroups.set(newann.graphGroup, new Integer(
1979 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1983 newann.padAnnotation(alwidth);
1984 alignment.addAnnotation(newann);
1994 addHistoryItem(new EditCommand(
1995 MessageManager.getString("label.add_sequences"),
1997 sequences, 0, alignment.getWidth(), alignment));
1999 // Add any annotations attached to sequences
2000 for (int i = 0; i < sequences.length; i++)
2002 if (sequences[i].getAnnotation() != null)
2004 AlignmentAnnotation newann;
2005 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2007 annotationAdded = true;
2008 newann = sequences[i].getAnnotation()[a];
2009 newann.adjustForAlignment();
2010 newann.padAnnotation(alwidth);
2011 if (newann.graphGroup > -1)
2013 if (newann.graphGroup > -1)
2015 if (newGraphGroups.size() <= newann.graphGroup
2016 || newGraphGroups.get(newann.graphGroup) == null)
2018 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2020 newGraphGroups.add(q, null);
2022 newGraphGroups.set(newann.graphGroup, new Integer(
2025 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2029 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2034 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2041 // propagate alignment changed.
2042 viewport.setEndSeq(alignment.getHeight());
2043 if (annotationAdded)
2045 // Duplicate sequence annotation in all views.
2046 AlignmentI[] alview = this.getViewAlignments();
2047 for (int i = 0; i < sequences.length; i++)
2049 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2054 for (int avnum = 0; avnum < alview.length; avnum++)
2056 if (alview[avnum] != alignment)
2058 // duplicate in a view other than the one with input focus
2059 int avwidth = alview[avnum].getWidth() + 1;
2060 // this relies on sann being preserved after we
2061 // modify the sequence's annotation array for each duplication
2062 for (int a = 0; a < sann.length; a++)
2064 AlignmentAnnotation newann = new AlignmentAnnotation(
2066 sequences[i].addAlignmentAnnotation(newann);
2067 newann.padAnnotation(avwidth);
2068 alview[avnum].addAnnotation(newann); // annotation was
2069 // duplicated earlier
2070 // TODO JAL-1145 graphGroups are not updated for sequence
2071 // annotation added to several views. This may cause
2073 alview[avnum].setAnnotationIndex(newann, a);
2078 buildSortByAnnotationScoresMenu();
2080 viewport.firePropertyChange("alignment", null,
2081 alignment.getSequences());
2082 if (alignPanels != null)
2084 for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
2086 ap.validateAnnotationDimensions(false);
2091 alignPanel.validateAnnotationDimensions(false);
2097 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2099 String newtitle = new String("Copied sequences");
2101 if (Desktop.jalviewClipboard != null
2102 && Desktop.jalviewClipboard[2] != null)
2104 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2105 for (int i = 0; i < hc.size(); i++)
2107 int[] region = (int[]) hc.elementAt(i);
2108 af.viewport.hideColumns(region[0], region[1]);
2112 // >>>This is a fix for the moment, until a better solution is
2114 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2116 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2118 // TODO: maintain provenance of an alignment, rather than just make the
2119 // title a concatenation of operations.
2122 if (title.startsWith("Copied sequences"))
2128 newtitle = newtitle.concat("- from " + title);
2133 newtitle = new String("Pasted sequences");
2136 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2141 } catch (Exception ex)
2143 ex.printStackTrace();
2144 System.out.println("Exception whilst pasting: " + ex);
2145 // could be anything being pasted in here
2151 protected void expand_newalign(ActionEvent e)
2155 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2156 .getAlignment(), -1);
2157 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2159 String newtitle = new String("Flanking alignment");
2161 if (Desktop.jalviewClipboard != null
2162 && Desktop.jalviewClipboard[2] != null)
2164 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2165 for (int i = 0; i < hc.size(); i++)
2167 int[] region = (int[]) hc.elementAt(i);
2168 af.viewport.hideColumns(region[0], region[1]);
2172 // >>>This is a fix for the moment, until a better solution is
2174 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2176 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2178 // TODO: maintain provenance of an alignment, rather than just make the
2179 // title a concatenation of operations.
2181 if (title.startsWith("Copied sequences"))
2187 newtitle = newtitle.concat("- from " + title);
2191 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2193 } catch (Exception ex)
2195 ex.printStackTrace();
2196 System.out.println("Exception whilst pasting: " + ex);
2197 // could be anything being pasted in here
2198 } catch (OutOfMemoryError oom)
2200 new OOMWarning("Viewing flanking region of alignment", oom);
2211 protected void cut_actionPerformed(ActionEvent e)
2213 copy_actionPerformed(null);
2214 delete_actionPerformed(null);
2224 protected void delete_actionPerformed(ActionEvent evt)
2227 SequenceGroup sg = viewport.getSelectionGroup();
2233 List<SequenceI> seqs = new ArrayList<SequenceI>(sg.getSize());
2235 for (int i = 0; i < sg.getSize(); i++)
2237 seq = sg.getSequenceAt(i);
2241 // If the cut affects all sequences, warn, remove highlighted columns
2242 if (sg.getSize() == viewport.getAlignment().getHeight())
2244 int confirm = JOptionPane.showConfirmDialog(this,
2245 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2246 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2247 JOptionPane.OK_CANCEL_OPTION);
2249 if (confirm == JOptionPane.CANCEL_OPTION
2250 || confirm == JOptionPane.CLOSED_OPTION)
2254 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2255 sg.getEndRes() + 1);
2258 SequenceI[] cut = new SequenceI[seqs.size()];
2259 for (int i = 0; i < seqs.size(); i++)
2261 cut[i] = seqs.get(i);
2265 * //ADD HISTORY ITEM
2267 addHistoryItem(new EditCommand(
2268 MessageManager.getString("label.cut_sequences"), Action.CUT,
2269 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2270 viewport.getAlignment()));
2272 viewport.setSelectionGroup(null);
2273 viewport.sendSelection();
2274 viewport.getAlignment().deleteGroup(sg);
2276 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2278 if (viewport.getAlignment().getHeight() < 1)
2282 this.setClosed(true);
2283 } catch (Exception ex)
2296 protected void deleteGroups_actionPerformed(ActionEvent e)
2298 if (avc.deleteGroups())
2300 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2301 alignPanel.updateAnnotation();
2302 alignPanel.paintAlignment(true);
2313 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2315 SequenceGroup sg = new SequenceGroup();
2317 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2319 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2322 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2323 viewport.setSelectionGroup(sg);
2324 viewport.sendSelection();
2325 alignPanel.paintAlignment(true);
2326 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2336 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2338 if (viewport.cursorMode)
2340 alignPanel.seqPanel.keyboardNo1 = null;
2341 alignPanel.seqPanel.keyboardNo2 = null;
2343 viewport.setSelectionGroup(null);
2344 viewport.getColumnSelection().clear();
2345 viewport.setSelectionGroup(null);
2346 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2347 alignPanel.idPanel.idCanvas.searchResults = null;
2348 alignPanel.paintAlignment(true);
2349 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2350 viewport.sendSelection();
2360 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2362 SequenceGroup sg = viewport.getSelectionGroup();
2366 selectAllSequenceMenuItem_actionPerformed(null);
2371 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2373 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2376 alignPanel.paintAlignment(true);
2377 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2378 viewport.sendSelection();
2382 public void invertColSel_actionPerformed(ActionEvent e)
2384 viewport.invertColumnSelection();
2385 alignPanel.paintAlignment(true);
2386 viewport.sendSelection();
2396 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2398 trimAlignment(true);
2408 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2410 trimAlignment(false);
2413 void trimAlignment(boolean trimLeft)
2415 ColumnSelection colSel = viewport.getColumnSelection();
2418 if (colSel.size() > 0)
2422 column = colSel.getMin();
2426 column = colSel.getMax();
2430 if (viewport.getSelectionGroup() != null)
2432 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2433 viewport.getHiddenRepSequences());
2437 seqs = viewport.getAlignment().getSequencesArray();
2440 TrimRegionCommand trimRegion;
2443 trimRegion = new TrimRegionCommand("Remove Left",
2444 TrimRegionCommand.TRIM_LEFT, seqs, column,
2445 viewport.getAlignment(), viewport.getColumnSelection(),
2446 viewport.getSelectionGroup());
2447 viewport.setStartRes(0);
2451 trimRegion = new TrimRegionCommand("Remove Right",
2452 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2453 viewport.getAlignment(), viewport.getColumnSelection(),
2454 viewport.getSelectionGroup());
2457 statusBar.setText(MessageManager.formatMessage(
2458 "label.removed_columns", new String[]
2459 { Integer.valueOf(trimRegion.getSize()).toString() }));
2461 addHistoryItem(trimRegion);
2463 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2465 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2466 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2468 viewport.getAlignment().deleteGroup(sg);
2472 viewport.firePropertyChange("alignment", null, viewport
2473 .getAlignment().getSequences());
2484 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2486 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2489 if (viewport.getSelectionGroup() != null)
2491 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2492 viewport.getHiddenRepSequences());
2493 start = viewport.getSelectionGroup().getStartRes();
2494 end = viewport.getSelectionGroup().getEndRes();
2498 seqs = viewport.getAlignment().getSequencesArray();
2501 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2502 "Remove Gapped Columns", seqs, start, end,
2503 viewport.getAlignment());
2505 addHistoryItem(removeGapCols);
2507 statusBar.setText(MessageManager.formatMessage(
2508 "label.removed_empty_columns", new String[]
2509 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2511 // This is to maintain viewport position on first residue
2512 // of first sequence
2513 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2514 int startRes = seq.findPosition(viewport.startRes);
2515 // ShiftList shifts;
2516 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2517 // edit.alColumnChanges=shifts.getInverse();
2518 // if (viewport.hasHiddenColumns)
2519 // viewport.getColumnSelection().compensateForEdits(shifts);
2520 viewport.setStartRes(seq.findIndex(startRes) - 1);
2521 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2533 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2535 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2538 if (viewport.getSelectionGroup() != null)
2540 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2541 viewport.getHiddenRepSequences());
2542 start = viewport.getSelectionGroup().getStartRes();
2543 end = viewport.getSelectionGroup().getEndRes();
2547 seqs = viewport.getAlignment().getSequencesArray();
2550 // This is to maintain viewport position on first residue
2551 // of first sequence
2552 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2553 int startRes = seq.findPosition(viewport.startRes);
2555 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2556 viewport.getAlignment()));
2558 viewport.setStartRes(seq.findIndex(startRes) - 1);
2560 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2572 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2574 viewport.setPadGaps(padGapsMenuitem.isSelected());
2575 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2581 // if (justifySeqs>0)
2583 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2596 public void findMenuItem_actionPerformed(ActionEvent e)
2602 public void newView_actionPerformed(ActionEvent e)
2609 * @param copyAnnotation
2610 * if true then duplicate all annnotation, groups and settings
2611 * @return new alignment panel, already displayed.
2613 public AlignmentPanel newView(boolean copyAnnotation)
2615 return newView(null, copyAnnotation);
2621 * title of newly created view
2622 * @return new alignment panel, already displayed.
2624 public AlignmentPanel newView(String viewTitle)
2626 return newView(viewTitle, true);
2632 * title of newly created view
2633 * @param copyAnnotation
2634 * if true then duplicate all annnotation, groups and settings
2635 * @return new alignment panel, already displayed.
2637 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2639 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2641 if (!copyAnnotation)
2643 // just remove all the current annotation except for the automatic stuff
2644 newap.av.getAlignment().deleteAllGroups();
2645 for (AlignmentAnnotation alan : newap.av.getAlignment()
2646 .getAlignmentAnnotation())
2648 if (!alan.autoCalculated)
2650 newap.av.getAlignment().deleteAnnotation(alan);
2656 newap.av.gatherViewsHere = false;
2658 if (viewport.viewName == null)
2660 viewport.viewName = "Original";
2663 newap.av.historyList = viewport.historyList;
2664 newap.av.redoList = viewport.redoList;
2666 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2667 // make sure the new view has a unique name - this is essential for Jalview
2669 boolean addFirstIndex = false;
2670 if (viewTitle == null || viewTitle.trim().length() == 0)
2672 viewTitle = MessageManager.getString("action.view");
2673 addFirstIndex = true;
2677 index = 1;// we count from 1 if given a specific name
2679 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2680 Vector comps = (Vector) PaintRefresher.components.get(viewport
2681 .getSequenceSetId());
2682 Vector existingNames = new Vector();
2683 for (int i = 0; i < comps.size(); i++)
2685 if (comps.elementAt(i) instanceof AlignmentPanel)
2687 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2688 if (!existingNames.contains(ap.av.viewName))
2690 existingNames.addElement(ap.av.viewName);
2695 while (existingNames.contains(newViewName))
2697 newViewName = viewTitle + " " + (++index);
2700 newap.av.viewName = newViewName;
2702 addAlignmentPanel(newap, true);
2703 newap.alignmentChanged();
2705 if (alignPanels.size() == 2)
2707 viewport.gatherViewsHere = true;
2709 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2714 public void expandViews_actionPerformed(ActionEvent e)
2716 Desktop.instance.explodeViews(this);
2720 public void gatherViews_actionPerformed(ActionEvent e)
2722 Desktop.instance.gatherViews(this);
2732 public void font_actionPerformed(ActionEvent e)
2734 new FontChooser(alignPanel);
2744 protected void seqLimit_actionPerformed(ActionEvent e)
2746 viewport.setShowJVSuffix(seqLimits.isSelected());
2748 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2749 .calculateIdWidth());
2750 alignPanel.paintAlignment(true);
2754 public void idRightAlign_actionPerformed(ActionEvent e)
2756 viewport.rightAlignIds = idRightAlign.isSelected();
2757 alignPanel.paintAlignment(true);
2761 public void centreColumnLabels_actionPerformed(ActionEvent e)
2763 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2764 alignPanel.paintAlignment(true);
2770 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2773 protected void followHighlight_actionPerformed()
2775 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2777 alignPanel.scrollToPosition(
2778 alignPanel.seqPanel.seqCanvas.searchResults, false);
2789 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2791 viewport.setColourText(colourTextMenuItem.isSelected());
2792 alignPanel.paintAlignment(true);
2802 public void wrapMenuItem_actionPerformed(ActionEvent e)
2804 scaleAbove.setVisible(wrapMenuItem.isSelected());
2805 scaleLeft.setVisible(wrapMenuItem.isSelected());
2806 scaleRight.setVisible(wrapMenuItem.isSelected());
2807 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2808 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2812 public void showAllSeqs_actionPerformed(ActionEvent e)
2814 viewport.showAllHiddenSeqs();
2818 public void showAllColumns_actionPerformed(ActionEvent e)
2820 viewport.showAllHiddenColumns();
2825 public void hideSelSequences_actionPerformed(ActionEvent e)
2827 viewport.hideAllSelectedSeqs();
2828 alignPanel.paintAlignment(true);
2832 * called by key handler and the hide all/show all menu items
2837 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2840 boolean hide = false;
2841 SequenceGroup sg = viewport.getSelectionGroup();
2842 if (!toggleSeqs && !toggleCols)
2844 // Hide everything by the current selection - this is a hack - we do the
2845 // invert and then hide
2846 // first check that there will be visible columns after the invert.
2847 if ((viewport.getColumnSelection() != null
2848 && viewport.getColumnSelection().getSelected() != null && viewport
2849 .getColumnSelection().getSelected().size() > 0)
2850 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2853 // now invert the sequence set, if required - empty selection implies
2854 // that no hiding is required.
2857 invertSequenceMenuItem_actionPerformed(null);
2858 sg = viewport.getSelectionGroup();
2862 viewport.expandColSelection(sg, true);
2863 // finally invert the column selection and get the new sequence
2865 invertColSel_actionPerformed(null);
2872 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2874 hideSelSequences_actionPerformed(null);
2877 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2880 showAllSeqs_actionPerformed(null);
2886 if (viewport.getColumnSelection().getSelected().size() > 0)
2888 hideSelColumns_actionPerformed(null);
2891 viewport.setSelectionGroup(sg);
2896 showAllColumns_actionPerformed(null);
2905 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2906 * event.ActionEvent)
2909 public void hideAllButSelection_actionPerformed(ActionEvent e)
2911 toggleHiddenRegions(false, false);
2918 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2922 public void hideAllSelection_actionPerformed(ActionEvent e)
2924 SequenceGroup sg = viewport.getSelectionGroup();
2925 viewport.expandColSelection(sg, false);
2926 viewport.hideAllSelectedSeqs();
2927 viewport.hideSelectedColumns();
2928 alignPanel.paintAlignment(true);
2935 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2939 public void showAllhidden_actionPerformed(ActionEvent e)
2941 viewport.showAllHiddenColumns();
2942 viewport.showAllHiddenSeqs();
2943 alignPanel.paintAlignment(true);
2947 public void hideSelColumns_actionPerformed(ActionEvent e)
2949 viewport.hideSelectedColumns();
2950 alignPanel.paintAlignment(true);
2954 public void hiddenMarkers_actionPerformed(ActionEvent e)
2956 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2967 protected void scaleAbove_actionPerformed(ActionEvent e)
2969 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2970 alignPanel.paintAlignment(true);
2980 protected void scaleLeft_actionPerformed(ActionEvent e)
2982 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2983 alignPanel.paintAlignment(true);
2993 protected void scaleRight_actionPerformed(ActionEvent e)
2995 viewport.setScaleRightWrapped(scaleRight.isSelected());
2996 alignPanel.paintAlignment(true);
3006 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3008 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3009 alignPanel.paintAlignment(true);
3019 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3021 viewport.setShowText(viewTextMenuItem.isSelected());
3022 alignPanel.paintAlignment(true);
3032 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3034 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3035 alignPanel.paintAlignment(true);
3038 public FeatureSettings featureSettings;
3041 public void featureSettings_actionPerformed(ActionEvent e)
3043 if (featureSettings != null)
3045 featureSettings.close();
3046 featureSettings = null;
3048 if (!showSeqFeatures.isSelected())
3050 // make sure features are actually displayed
3051 showSeqFeatures.setSelected(true);
3052 showSeqFeatures_actionPerformed(null);
3054 featureSettings = new FeatureSettings(this);
3058 * Set or clear 'Show Sequence Features'
3064 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3066 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3067 alignPanel.paintAlignment(true);
3068 if (alignPanel.getOverviewPanel() != null)
3070 alignPanel.getOverviewPanel().updateOverviewImage();
3075 * Set or clear 'Show Sequence Features'
3081 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3083 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3085 if (viewport.getShowSequenceFeaturesHeight())
3087 // ensure we're actually displaying features
3088 viewport.setShowSequenceFeatures(true);
3089 showSeqFeatures.setSelected(true);
3091 alignPanel.paintAlignment(true);
3092 if (alignPanel.getOverviewPanel() != null)
3094 alignPanel.getOverviewPanel().updateOverviewImage();
3099 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3100 * the annotations panel as a whole.
3102 * The options to show/hide all annotations should be enabled when the panel
3103 * is shown, and disabled when the panel is hidden.
3108 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3110 final boolean setVisible = annotationPanelMenuItem.isSelected();
3111 viewport.setShowAnnotation(setVisible);
3112 alignPanel.setAnnotationVisible(setVisible);
3113 this.showAllSeqAnnotations.setEnabled(setVisible);
3114 this.hideAllSeqAnnotations.setEnabled(setVisible);
3115 this.showAllAlAnnotations.setEnabled(setVisible);
3116 this.hideAllAlAnnotations.setEnabled(setVisible);
3120 public void alignmentProperties()
3122 JEditorPane editPane = new JEditorPane("text/html", "");
3123 editPane.setEditable(false);
3124 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3126 editPane.setText(MessageManager.formatMessage("label.html_content",
3128 { contents.toString() }));
3129 JInternalFrame frame = new JInternalFrame();
3130 frame.getContentPane().add(new JScrollPane(editPane));
3132 Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage(
3133 "label.alignment_properties", new String[]
3134 { getTitle() }), 500, 400);
3144 public void overviewMenuItem_actionPerformed(ActionEvent e)
3146 if (alignPanel.overviewPanel != null)
3151 JInternalFrame frame = new JInternalFrame();
3152 OverviewPanel overview = new OverviewPanel(alignPanel);
3153 frame.setContentPane(overview);
3154 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3155 "label.overview_params", new String[]
3156 { this.getTitle() }), frame.getWidth(), frame.getHeight());
3158 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3159 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3162 public void internalFrameClosed(
3163 javax.swing.event.InternalFrameEvent evt)
3165 alignPanel.setOverviewPanel(null);
3169 alignPanel.setOverviewPanel(overview);
3173 public void textColour_actionPerformed(ActionEvent e)
3175 new TextColourChooser().chooseColour(alignPanel, null);
3185 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3197 public void clustalColour_actionPerformed(ActionEvent e)
3199 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3200 viewport.getHiddenRepSequences()));
3210 public void zappoColour_actionPerformed(ActionEvent e)
3212 changeColour(new ZappoColourScheme());
3222 public void taylorColour_actionPerformed(ActionEvent e)
3224 changeColour(new TaylorColourScheme());
3234 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3236 changeColour(new HydrophobicColourScheme());
3246 public void helixColour_actionPerformed(ActionEvent e)
3248 changeColour(new HelixColourScheme());
3258 public void strandColour_actionPerformed(ActionEvent e)
3260 changeColour(new StrandColourScheme());
3270 public void turnColour_actionPerformed(ActionEvent e)
3272 changeColour(new TurnColourScheme());
3282 public void buriedColour_actionPerformed(ActionEvent e)
3284 changeColour(new BuriedColourScheme());
3294 public void nucleotideColour_actionPerformed(ActionEvent e)
3296 changeColour(new NucleotideColourScheme());
3300 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3302 changeColour(new PurinePyrimidineColourScheme());
3306 * public void covariationColour_actionPerformed(ActionEvent e) {
3308 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3312 public void annotationColour_actionPerformed(ActionEvent e)
3314 new AnnotationColourChooser(viewport, alignPanel);
3318 public void rnahelicesColour_actionPerformed(ActionEvent e)
3320 new RNAHelicesColourChooser(viewport, alignPanel);
3330 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3332 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3341 public void changeColour(ColourSchemeI cs)
3343 // TODO: compare with applet and pull up to model method
3348 if (viewport.getAbovePIDThreshold())
3350 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3352 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3356 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3359 if (viewport.getConservationSelected())
3362 Alignment al = (Alignment) viewport.getAlignment();
3363 Conservation c = new Conservation("All",
3364 ResidueProperties.propHash, 3, al.getSequences(), 0,
3368 c.verdict(false, viewport.getConsPercGaps());
3370 cs.setConservation(c);
3372 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3377 cs.setConservation(null);
3380 cs.setConsensus(viewport.getSequenceConsensusHash());
3383 viewport.setGlobalColourScheme(cs);
3385 if (viewport.getColourAppliesToAllGroups())
3388 for (SequenceGroup sg : viewport.getAlignment().getGroups())
3396 if (cs instanceof ClustalxColourScheme)
3398 sg.cs = new ClustalxColourScheme(sg,
3399 viewport.getHiddenRepSequences());
3401 else if (cs instanceof UserColourScheme)
3403 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3409 sg.cs = cs.getClass().newInstance();
3410 } catch (Exception ex)
3415 if (viewport.getAbovePIDThreshold()
3416 || cs instanceof PIDColourScheme
3417 || cs instanceof Blosum62ColourScheme)
3419 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3421 sg.cs.setConsensus(AAFrequency.calculate(
3422 sg.getSequences(viewport.getHiddenRepSequences()),
3423 sg.getStartRes(), sg.getEndRes() + 1));
3427 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3430 if (viewport.getConservationSelected())
3432 Conservation c = new Conservation("Group",
3433 ResidueProperties.propHash, 3, sg.getSequences(viewport
3434 .getHiddenRepSequences()), sg.getStartRes(),
3435 sg.getEndRes() + 1);
3437 c.verdict(false, viewport.getConsPercGaps());
3438 sg.cs.setConservation(c);
3442 sg.cs.setConservation(null);
3447 if (alignPanel.getOverviewPanel() != null)
3449 alignPanel.getOverviewPanel().updateOverviewImage();
3452 alignPanel.paintAlignment(true);
3462 protected void modifyPID_actionPerformed(ActionEvent e)
3464 if (viewport.getAbovePIDThreshold()
3465 && viewport.getGlobalColourScheme() != null)
3467 SliderPanel.setPIDSliderSource(alignPanel,
3468 viewport.getGlobalColourScheme(), "Background");
3469 SliderPanel.showPIDSlider();
3480 protected void modifyConservation_actionPerformed(ActionEvent e)
3482 if (viewport.getConservationSelected()
3483 && viewport.getGlobalColourScheme() != null)
3485 SliderPanel.setConservationSlider(alignPanel,
3486 viewport.getGlobalColourScheme(), "Background");
3487 SliderPanel.showConservationSlider();
3498 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3500 viewport.setConservationSelected(conservationMenuItem.isSelected());
3502 viewport.setAbovePIDThreshold(false);
3503 abovePIDThreshold.setSelected(false);
3505 changeColour(viewport.getGlobalColourScheme());
3507 modifyConservation_actionPerformed(null);
3517 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3519 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3521 conservationMenuItem.setSelected(false);
3522 viewport.setConservationSelected(false);
3524 changeColour(viewport.getGlobalColourScheme());
3526 modifyPID_actionPerformed(null);
3536 public void userDefinedColour_actionPerformed(ActionEvent e)
3538 if (e.getActionCommand().equals(
3539 MessageManager.getString("action.user_defined")))
3541 new UserDefinedColours(alignPanel, null);
3545 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3546 .getUserColourSchemes().get(e.getActionCommand());
3552 public void updateUserColourMenu()
3555 Component[] menuItems = colourMenu.getMenuComponents();
3556 int i, iSize = menuItems.length;
3557 for (i = 0; i < iSize; i++)
3559 if (menuItems[i].getName() != null
3560 && menuItems[i].getName().equals("USER_DEFINED"))
3562 colourMenu.remove(menuItems[i]);
3566 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3568 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3569 .getUserColourSchemes().keys();
3571 while (userColours.hasMoreElements())
3573 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3574 userColours.nextElement().toString());
3575 radioItem.setName("USER_DEFINED");
3576 radioItem.addMouseListener(new MouseAdapter()
3579 public void mousePressed(MouseEvent evt)
3581 if (evt.isControlDown()
3582 || SwingUtilities.isRightMouseButton(evt))
3584 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3586 int option = JOptionPane.showInternalConfirmDialog(
3587 jalview.gui.Desktop.desktop,
3589 .getString("label.remove_from_default_list"),
3591 .getString("label.remove_user_defined_colour"),
3592 JOptionPane.YES_NO_OPTION);
3593 if (option == JOptionPane.YES_OPTION)
3595 jalview.gui.UserDefinedColours
3596 .removeColourFromDefaults(radioItem.getText());
3597 colourMenu.remove(radioItem);
3601 radioItem.addActionListener(new ActionListener()
3604 public void actionPerformed(ActionEvent evt)
3606 userDefinedColour_actionPerformed(evt);
3613 radioItem.addActionListener(new ActionListener()
3616 public void actionPerformed(ActionEvent evt)
3618 userDefinedColour_actionPerformed(evt);
3622 colourMenu.insert(radioItem, 15);
3623 colours.add(radioItem);
3635 public void PIDColour_actionPerformed(ActionEvent e)
3637 changeColour(new PIDColourScheme());
3647 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3649 changeColour(new Blosum62ColourScheme());
3659 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3661 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3662 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3663 .getAlignment().getSequenceAt(0), null);
3664 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3665 viewport.getAlignment()));
3666 alignPanel.paintAlignment(true);
3676 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3678 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3679 AlignmentSorter.sortByID(viewport.getAlignment());
3680 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3681 viewport.getAlignment()));
3682 alignPanel.paintAlignment(true);
3692 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3694 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3695 AlignmentSorter.sortByLength(viewport.getAlignment());
3696 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3697 viewport.getAlignment()));
3698 alignPanel.paintAlignment(true);
3708 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3710 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3711 AlignmentSorter.sortByGroup(viewport.getAlignment());
3712 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3713 viewport.getAlignment()));
3715 alignPanel.paintAlignment(true);
3725 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3727 new RedundancyPanel(alignPanel, this);
3737 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3739 if ((viewport.getSelectionGroup() == null)
3740 || (viewport.getSelectionGroup().getSize() < 2))
3742 JOptionPane.showInternalMessageDialog(this, MessageManager
3743 .getString("label.you_must_select_least_two_sequences"),
3744 MessageManager.getString("label.invalid_selection"),
3745 JOptionPane.WARNING_MESSAGE);
3749 JInternalFrame frame = new JInternalFrame();
3750 frame.setContentPane(new PairwiseAlignPanel(viewport));
3751 Desktop.addInternalFrame(frame,
3752 MessageManager.getString("action.pairwise_alignment"), 600,
3764 public void PCAMenuItem_actionPerformed(ActionEvent e)
3766 if (((viewport.getSelectionGroup() != null)
3767 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3768 .getSelectionGroup().getSize() > 0))
3769 || (viewport.getAlignment().getHeight() < 4))
3772 .showInternalMessageDialog(
3775 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3777 .getString("label.sequence_selection_insufficient"),
3778 JOptionPane.WARNING_MESSAGE);
3783 new PCAPanel(alignPanel);
3787 public void autoCalculate_actionPerformed(ActionEvent e)
3789 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3790 if (viewport.autoCalculateConsensus)
3792 viewport.firePropertyChange("alignment", null, viewport
3793 .getAlignment().getSequences());
3798 public void sortByTreeOption_actionPerformed(ActionEvent e)
3800 viewport.sortByTree = sortByTree.isSelected();
3804 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3806 viewport.followSelection = listenToViewSelections.isSelected();
3816 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3818 NewTreePanel("AV", "PID", "Average distance tree using PID");
3828 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3830 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3840 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3842 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3852 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3854 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3867 void NewTreePanel(String type, String pwType, String title)
3871 if (viewport.getSelectionGroup() != null
3872 && viewport.getSelectionGroup().getSize() > 0)
3874 if (viewport.getSelectionGroup().getSize() < 3)
3880 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3882 .getString("label.not_enough_sequences"),
3883 JOptionPane.WARNING_MESSAGE);
3887 SequenceGroup sg = viewport.getSelectionGroup();
3889 /* Decide if the selection is a column region */
3890 for (SequenceI _s : sg.getSequences())
3892 if (_s.getLength() < sg.getEndRes())
3898 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3900 .getString("label.sequences_selection_not_aligned"),
3901 JOptionPane.WARNING_MESSAGE);
3907 title = title + " on region";
3908 tp = new TreePanel(alignPanel, type, pwType);
3912 // are the visible sequences aligned?
3913 if (!viewport.getAlignment().isAligned(false))
3919 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3921 .getString("label.sequences_not_aligned"),
3922 JOptionPane.WARNING_MESSAGE);
3927 if (viewport.getAlignment().getHeight() < 2)
3932 tp = new TreePanel(alignPanel, type, pwType);
3937 if (viewport.viewName != null)
3939 title += viewport.viewName + " of ";
3942 title += this.title;
3944 Desktop.addInternalFrame(tp, title, 600, 500);
3955 public void addSortByOrderMenuItem(String title,
3956 final AlignmentOrder order)
3958 final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new String[]{title}));
3960 item.addActionListener(new java.awt.event.ActionListener()
3963 public void actionPerformed(ActionEvent e)
3965 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3967 // TODO: JBPNote - have to map order entries to curent SequenceI
3969 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3971 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3974 alignPanel.paintAlignment(true);
3980 * Add a new sort by annotation score menu item
3983 * the menu to add the option to
3985 * the label used to retrieve scores for each sequence on the
3988 public void addSortByAnnotScoreMenuItem(JMenu sort,
3989 final String scoreLabel)
3991 final JMenuItem item = new JMenuItem(scoreLabel);
3993 item.addActionListener(new java.awt.event.ActionListener()
3996 public void actionPerformed(ActionEvent e)
3998 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3999 AlignmentSorter.sortByAnnotationScore(scoreLabel,
4000 viewport.getAlignment());// ,viewport.getSelectionGroup());
4001 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4002 viewport.getAlignment()));
4003 alignPanel.paintAlignment(true);
4009 * last hash for alignment's annotation array - used to minimise cost of
4012 protected int _annotationScoreVectorHash;
4015 * search the alignment and rebuild the sort by annotation score submenu the
4016 * last alignment annotation vector hash is stored to minimize cost of
4017 * rebuilding in subsequence calls.
4021 public void buildSortByAnnotationScoresMenu()
4023 if (viewport.getAlignment().getAlignmentAnnotation() == null)
4028 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4030 sortByAnnotScore.removeAll();
4031 // almost certainly a quicker way to do this - but we keep it simple
4032 Hashtable scoreSorts = new Hashtable();
4033 AlignmentAnnotation aann[];
4034 for (SequenceI sqa : viewport.getAlignment().getSequences())
4036 aann = sqa.getAnnotation();
4037 for (int i = 0; aann != null && i < aann.length; i++)
4039 if (aann[i].hasScore() && aann[i].sequenceRef != null)
4041 scoreSorts.put(aann[i].label, aann[i].label);
4045 Enumeration labels = scoreSorts.keys();
4046 while (labels.hasMoreElements())
4048 addSortByAnnotScoreMenuItem(sortByAnnotScore,
4049 (String) labels.nextElement());
4051 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4054 _annotationScoreVectorHash = viewport.getAlignment()
4055 .getAlignmentAnnotation().hashCode();
4060 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4061 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4062 * call. Listeners are added to remove the menu item when the treePanel is
4063 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4067 * Displayed tree window.
4069 * SortBy menu item title.
4072 public void buildTreeMenu()
4074 calculateTree.removeAll();
4075 // build the calculate menu
4077 for (final String type : new String[]
4080 String treecalcnm = MessageManager.getString("label.tree_calc_"
4081 + type.toLowerCase());
4082 for (final Object pwtype : ResidueProperties.scoreMatrices.keySet())
4084 JMenuItem tm = new JMenuItem();
4085 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4086 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4088 String smn = MessageManager.getStringOrReturn(
4089 "label.score_model_", sm.getName());
4090 final String title = MessageManager.formatMessage(
4091 "label.treecalc_title", treecalcnm, smn);
4092 tm.setText(title);//
4093 tm.addActionListener(new java.awt.event.ActionListener()
4096 public void actionPerformed(ActionEvent e)
4098 NewTreePanel(type, (String) pwtype, title);
4101 calculateTree.add(tm);
4106 sortByTreeMenu.removeAll();
4108 Vector comps = (Vector) PaintRefresher.components.get(viewport
4109 .getSequenceSetId());
4110 Vector treePanels = new Vector();
4111 int i, iSize = comps.size();
4112 for (i = 0; i < iSize; i++)
4114 if (comps.elementAt(i) instanceof TreePanel)
4116 treePanels.add(comps.elementAt(i));
4120 iSize = treePanels.size();
4124 sortByTreeMenu.setVisible(false);
4128 sortByTreeMenu.setVisible(true);
4130 for (i = 0; i < treePanels.size(); i++)
4132 final TreePanel tp = (TreePanel) treePanels.elementAt(i);
4133 final JMenuItem item = new JMenuItem(tp.getTitle());
4134 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
4135 item.addActionListener(new java.awt.event.ActionListener()
4138 public void actionPerformed(ActionEvent e)
4140 tp.sortByTree_actionPerformed(null);
4141 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4146 sortByTreeMenu.add(item);
4150 public boolean sortBy(AlignmentOrder alorder, String undoname)
4152 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4153 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4154 if (undoname != null)
4156 addHistoryItem(new OrderCommand(undoname, oldOrder,
4157 viewport.getAlignment()));
4159 alignPanel.paintAlignment(true);
4164 * Work out whether the whole set of sequences or just the selected set will
4165 * be submitted for multiple alignment.
4168 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4170 // Now, check we have enough sequences
4171 AlignmentView msa = null;
4173 if ((viewport.getSelectionGroup() != null)
4174 && (viewport.getSelectionGroup().getSize() > 1))
4176 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4177 // some common interface!
4179 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4180 * SequenceI[sz = seqs.getSize(false)];
4182 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4183 * seqs.getSequenceAt(i); }
4185 msa = viewport.getAlignmentView(true);
4190 * Vector seqs = viewport.getAlignment().getSequences();
4192 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
4194 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
4195 * seqs.elementAt(i); } }
4197 msa = viewport.getAlignmentView(false);
4203 * Decides what is submitted to a secondary structure prediction service: the
4204 * first sequence in the alignment, or in the current selection, or, if the
4205 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4206 * region or the whole alignment. (where the first sequence in the set is the
4207 * one that the prediction will be for).
4209 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4211 AlignmentView seqs = null;
4213 if ((viewport.getSelectionGroup() != null)
4214 && (viewport.getSelectionGroup().getSize() > 0))
4216 seqs = viewport.getAlignmentView(true);
4220 seqs = viewport.getAlignmentView(false);
4222 // limit sequences - JBPNote in future - could spawn multiple prediction
4224 // TODO: viewport.getAlignment().isAligned is a global state - the local
4225 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4226 if (!viewport.getAlignment().isAligned(false))
4228 seqs.setSequences(new SeqCigar[]
4229 { seqs.getSequences()[0] });
4230 // TODO: if seqs.getSequences().length>1 then should really have warned
4244 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
4246 // Pick the tree file
4247 JalviewFileChooser chooser = new JalviewFileChooser(
4248 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4249 chooser.setFileView(new JalviewFileView());
4250 chooser.setDialogTitle(MessageManager
4251 .getString("label.select_newick_like_tree_file"));
4252 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4254 int value = chooser.showOpenDialog(null);
4256 if (value == JalviewFileChooser.APPROVE_OPTION)
4258 String choice = chooser.getSelectedFile().getPath();
4259 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4260 jalview.io.NewickFile fin = null;
4263 fin = new jalview.io.NewickFile(choice, "File");
4264 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4265 } catch (Exception ex)
4272 .getString("label.problem_reading_tree_file"),
4273 JOptionPane.WARNING_MESSAGE);
4274 ex.printStackTrace();
4276 if (fin != null && fin.hasWarningMessage())
4278 JOptionPane.showMessageDialog(Desktop.desktop, fin
4279 .getWarningMessage(), MessageManager
4280 .getString("label.possible_problem_with_tree_file"),
4281 JOptionPane.WARNING_MESSAGE);
4287 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4289 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4292 public TreePanel ShowNewickTree(NewickFile nf, String title)
4294 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4297 public TreePanel ShowNewickTree(NewickFile nf, String title,
4298 AlignmentView input)
4300 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4303 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4304 int h, int x, int y)
4306 return ShowNewickTree(nf, title, null, w, h, x, y);
4310 * Add a treeviewer for the tree extracted from a newick file object to the
4311 * current alignment view
4318 * Associated alignment input data (or null)
4327 * @return TreePanel handle
4329 public TreePanel ShowNewickTree(NewickFile nf, String title,
4330 AlignmentView input, int w, int h, int x, int y)
4332 TreePanel tp = null;
4338 if (nf.getTree() != null)
4340 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4346 tp.setLocation(x, y);
4349 Desktop.addInternalFrame(tp, title, w, h);
4351 } catch (Exception ex)
4353 ex.printStackTrace();
4359 private boolean buildingMenu = false;
4362 * Generates menu items and listener event actions for web service clients
4365 public void BuildWebServiceMenu()
4367 while (buildingMenu)
4371 System.err.println("Waiting for building menu to finish.");
4373 } catch (Exception e)
4378 final AlignFrame me = this;
4379 buildingMenu = true;
4380 new Thread(new Runnable()
4385 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4388 System.err.println("Building ws menu again "
4389 + Thread.currentThread());
4390 // TODO: add support for context dependent disabling of services based
4392 // alignment and current selection
4393 // TODO: add additional serviceHandle parameter to specify abstract
4395 // class independently of AbstractName
4396 // TODO: add in rediscovery GUI function to restart discoverer
4397 // TODO: group services by location as well as function and/or
4399 // object broker mechanism.
4400 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4401 final IProgressIndicator af = me;
4402 final JMenu msawsmenu = new JMenu("Alignment");
4403 final JMenu secstrmenu = new JMenu(
4404 "Secondary Structure Prediction");
4405 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4406 final JMenu analymenu = new JMenu("Analysis");
4407 final JMenu dismenu = new JMenu("Protein Disorder");
4408 // final JMenu msawsmenu = new
4409 // JMenu(MessageManager.getString("label.alignment"));
4410 // final JMenu secstrmenu = new
4411 // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
4412 // final JMenu seqsrchmenu = new
4413 // JMenu(MessageManager.getString("label.sequence_database_search"));
4414 // final JMenu analymenu = new
4415 // JMenu(MessageManager.getString("label.analysis"));
4416 // final JMenu dismenu = new
4417 // JMenu(MessageManager.getString("label.protein_disorder"));
4418 // JAL-940 - only show secondary structure prediction services from
4419 // the legacy server
4420 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4422 Discoverer.services != null && (Discoverer.services.size() > 0))
4424 // TODO: refactor to allow list of AbstractName/Handler bindings to
4426 // stored or retrieved from elsewhere
4427 // No MSAWS used any more:
4428 // Vector msaws = null; // (Vector)
4429 // Discoverer.services.get("MsaWS");
4430 Vector secstrpr = (Vector) Discoverer.services
4432 if (secstrpr != null)
4434 // Add any secondary structure prediction services
4435 for (int i = 0, j = secstrpr.size(); i < j; i++)
4437 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4439 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4440 .getServiceClient(sh);
4441 int p = secstrmenu.getItemCount();
4442 impl.attachWSMenuEntry(secstrmenu, me);
4443 int q = secstrmenu.getItemCount();
4444 for (int litm = p; litm < q; litm++)
4446 legacyItems.add(secstrmenu.getItem(litm));
4452 // Add all submenus in the order they should appear on the web
4454 wsmenu.add(msawsmenu);
4455 wsmenu.add(secstrmenu);
4456 wsmenu.add(dismenu);
4457 wsmenu.add(analymenu);
4458 // No search services yet
4459 // wsmenu.add(seqsrchmenu);
4461 javax.swing.SwingUtilities.invokeLater(new Runnable()
4468 webService.removeAll();
4469 // first, add discovered services onto the webservices menu
4470 if (wsmenu.size() > 0)
4472 for (int i = 0, j = wsmenu.size(); i < j; i++)
4474 webService.add(wsmenu.get(i));
4479 webService.add(me.webServiceNoServices);
4481 // TODO: move into separate menu builder class.
4482 boolean new_sspred = false;
4483 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4485 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4486 if (jws2servs != null)
4488 if (jws2servs.hasServices())
4490 jws2servs.attachWSMenuEntry(webService, me);
4491 for (Jws2Instance sv : jws2servs.getServices())
4493 if (sv.description.toLowerCase().contains("jpred"))
4495 for (JMenuItem jmi : legacyItems)
4497 jmi.setVisible(false);
4503 if (jws2servs.isRunning())
4505 JMenuItem tm = new JMenuItem(
4506 "Still discovering JABA Services");
4507 tm.setEnabled(false);
4512 build_urlServiceMenu(me.webService);
4513 build_fetchdbmenu(webService);
4514 for (JMenu item : wsmenu)
4516 if (item.getItemCount() == 0)
4518 item.setEnabled(false);
4522 item.setEnabled(true);
4525 } catch (Exception e)
4528 .debug("Exception during web service menu building process.",
4534 } catch (Exception e)
4539 buildingMenu = false;
4546 * construct any groupURL type service menu entries.
4550 private void build_urlServiceMenu(JMenu webService)
4552 // TODO: remove this code when 2.7 is released
4553 // DEBUG - alignmentView
4555 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4556 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4558 * @Override public void actionPerformed(ActionEvent e) {
4559 * jalview.datamodel.AlignmentView
4560 * .testSelectionViews(af.viewport.getAlignment(),
4561 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4563 * }); webService.add(testAlView);
4565 // TODO: refactor to RestClient discoverer and merge menu entries for
4566 // rest-style services with other types of analysis/calculation service
4567 // SHmmr test client - still being implemented.
4568 // DEBUG - alignmentView
4570 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4573 client.attachWSMenuEntry(
4574 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4580 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4581 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4582 * getProperty("LAST_DIRECTORY"));
4584 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4585 * to Vamsas file"); chooser.setToolTipText("Export");
4587 * int value = chooser.showSaveDialog(this);
4589 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4590 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4591 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4592 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4595 * prototype of an automatically enabled/disabled analysis function
4598 protected void setShowProductsEnabled()
4600 SequenceI[] selection = viewport.getSequenceSelection();
4601 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4602 viewport.getAlignment().getDataset()))
4604 showProducts.setEnabled(true);
4609 showProducts.setEnabled(false);
4614 * search selection for sequence xRef products and build the show products
4619 * @return true if showProducts menu should be enabled.
4621 public boolean canShowProducts(SequenceI[] selection,
4622 boolean isRegionSelection, Alignment dataset)
4624 boolean showp = false;
4627 showProducts.removeAll();
4628 final boolean dna = viewport.getAlignment().isNucleotide();
4629 final Alignment ds = dataset;
4630 String[] ptypes = (selection == null || selection.length == 0) ? null
4631 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4633 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4634 // selection, dataset, true);
4635 final SequenceI[] sel = selection;
4636 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4639 final boolean isRegSel = isRegionSelection;
4640 final AlignFrame af = this;
4641 final String source = ptypes[t];
4642 JMenuItem xtype = new JMenuItem(ptypes[t]);
4643 xtype.addActionListener(new ActionListener()
4647 public void actionPerformed(ActionEvent e)
4649 // TODO: new thread for this call with vis-delay
4650 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4651 isRegSel, dna, source);
4655 showProducts.add(xtype);
4657 showProducts.setVisible(showp);
4658 showProducts.setEnabled(showp);
4659 } catch (Exception e)
4661 jalview.bin.Cache.log
4662 .warn("canTranslate threw an exception - please report to help@jalview.org",
4669 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4670 boolean isRegSel, boolean dna, String source)
4672 final boolean fisRegSel = isRegSel;
4673 final boolean fdna = dna;
4674 final String fsrc = source;
4675 final AlignFrame ths = this;
4676 final SequenceI[] fsel = sel;
4677 Runnable foo = new Runnable()
4683 final long sttime = System.currentTimeMillis();
4684 ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{fsrc}), sttime);
4687 Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4691 Alignment prods = CrossRef
4692 .findXrefSequences(fsel, fdna, fsrc, ds);
4695 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4696 for (int s = 0; s < sprods.length; s++)
4698 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4699 if (ds.getSequences() == null
4700 || !ds.getSequences().contains(
4701 sprods[s].getDatasetSequence()))
4703 ds.addSequence(sprods[s].getDatasetSequence());
4705 sprods[s].updatePDBIds();
4707 Alignment al = new Alignment(sprods);
4708 AlignedCodonFrame[] cf = prods.getCodonFrames();
4710 for (int s = 0; cf != null && s < cf.length; s++)
4712 al.addCodonFrame(cf[s]);
4715 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4717 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4718 + " for " + ((fisRegSel) ? "selected region of " : "")
4720 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4725 System.err.println("No Sequences generated for xRef type "
4728 } catch (Exception e)
4730 jalview.bin.Cache.log.error(
4731 "Exception when finding crossreferences", e);
4732 } catch (OutOfMemoryError e)
4734 new OOMWarning("whilst fetching crossreferences", e);
4737 jalview.bin.Cache.log.error("Error when finding crossreferences",
4740 ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{fsrc}),
4745 Thread frunner = new Thread(foo);
4749 public boolean canShowTranslationProducts(SequenceI[] selection,
4750 AlignmentI alignment)
4755 return (jalview.analysis.Dna.canTranslate(selection,
4756 viewport.getViewAsVisibleContigs(true)));
4757 } catch (Exception e)
4759 jalview.bin.Cache.log
4760 .warn("canTranslate threw an exception - please report to help@jalview.org",
4767 public void showProducts_actionPerformed(ActionEvent e)
4769 // /////////////////////////////
4770 // Collect Data to be translated/transferred
4772 SequenceI[] selection = viewport.getSequenceSelection();
4773 AlignmentI al = null;
4776 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4777 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4778 viewport.getAlignment().getDataset());
4779 } catch (Exception ex)
4782 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4790 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4791 MessageManager.getString("label.translation_failed"),
4792 JOptionPane.WARNING_MESSAGE);
4796 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4797 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4798 "label.translation_of_params", new String[]
4799 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4804 public void showTranslation_actionPerformed(ActionEvent e)
4806 // /////////////////////////////
4807 // Collect Data to be translated/transferred
4809 SequenceI[] selection = viewport.getSequenceSelection();
4810 String[] seqstring = viewport.getViewAsString(true);
4811 AlignmentI al = null;
4814 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4815 viewport.getViewAsVisibleContigs(true), viewport
4816 .getGapCharacter(), viewport.getAlignment()
4817 .getAlignmentAnnotation(), viewport.getAlignment()
4818 .getWidth(), viewport.getAlignment().getDataset());
4819 } catch (Exception ex)
4822 jalview.bin.Cache.log.error(
4823 "Exception during translation. Please report this !", ex);
4828 .getString("label.error_when_translating_sequences_submit_bug_report"),
4830 .getString("label.implementation_error")
4832 .getString("translation_failed"),
4833 JOptionPane.ERROR_MESSAGE);
4842 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4843 MessageManager.getString("label.translation_failed"),
4844 JOptionPane.WARNING_MESSAGE);
4848 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4849 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4850 "label.translation_of_params", new String[]
4851 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4856 * Try to load a features file onto the alignment.
4859 * contents or path to retrieve file
4861 * access mode of file (see jalview.io.AlignFile)
4862 * @return true if features file was parsed corectly.
4864 public boolean parseFeaturesFile(String file, String type)
4866 boolean featuresFile = false;
4869 featuresFile = new FeaturesFile(file, type).parse(viewport
4870 .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4871 .getFeatureRenderer().featureColours, false,
4872 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4873 } catch (Exception ex)
4875 ex.printStackTrace();
4880 viewport.showSequenceFeatures = true;
4881 showSeqFeatures.setSelected(true);
4882 if (alignPanel.seqPanel.seqCanvas.fr != null)
4884 // update the min/max ranges where necessary
4885 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4887 if (featureSettings != null)
4889 featureSettings.setTableData();
4891 alignPanel.paintAlignment(true);
4894 return featuresFile;
4898 public void dragEnter(DropTargetDragEvent evt)
4903 public void dragExit(DropTargetEvent evt)
4908 public void dragOver(DropTargetDragEvent evt)
4913 public void dropActionChanged(DropTargetDragEvent evt)
4918 public void drop(DropTargetDropEvent evt)
4920 Transferable t = evt.getTransferable();
4921 java.util.List files = null;
4925 DataFlavor uriListFlavor = new DataFlavor(
4926 "text/uri-list;class=java.lang.String");
4927 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4929 // Works on Windows and MacOSX
4930 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4931 files = (java.util.List) t
4932 .getTransferData(DataFlavor.javaFileListFlavor);
4934 else if (t.isDataFlavorSupported(uriListFlavor))
4936 // This is used by Unix drag system
4937 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4938 String data = (String) t.getTransferData(uriListFlavor);
4939 files = new java.util.ArrayList(1);
4940 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4941 data, "\r\n"); st.hasMoreTokens();)
4943 String s = st.nextToken();
4944 if (s.startsWith("#"))
4946 // the line is a comment (as per the RFC 2483)
4950 java.net.URI uri = new java.net.URI(s);
4951 // check to see if we can handle this kind of URI
4952 if (uri.getScheme().toLowerCase().startsWith("http"))
4954 files.add(uri.toString());
4958 // otherwise preserve old behaviour: catch all for file objects
4959 java.io.File file = new java.io.File(uri);
4960 files.add(file.toString());
4964 } catch (Exception e)
4966 e.printStackTrace();
4972 // check to see if any of these files have names matching sequences in
4974 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4975 .getAlignment().getSequencesArray());
4977 * Object[] { String,SequenceI}
4979 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4980 ArrayList<String> filesnotmatched = new ArrayList<String>();
4981 for (int i = 0; i < files.size(); i++)
4983 String file = files.get(i).toString();
4985 String protocol = FormatAdapter.checkProtocol(file);
4986 if (protocol == jalview.io.FormatAdapter.FILE)
4988 File fl = new File(file);
4989 pdbfn = fl.getName();
4991 else if (protocol == jalview.io.FormatAdapter.URL)
4993 URL url = new URL(file);
4994 pdbfn = url.getFile();
4996 if (pdbfn.length() > 0)
4998 // attempt to find a match in the alignment
4999 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
5000 int l = 0, c = pdbfn.indexOf(".");
5001 while (mtch == null && c != -1)
5006 } while ((c = pdbfn.indexOf(".", l)) > l);
5009 pdbfn = pdbfn.substring(0, l);
5011 mtch = idm.findAllIdMatches(pdbfn);
5018 type = new IdentifyFile().Identify(file, protocol);
5019 } catch (Exception ex)
5025 if (type.equalsIgnoreCase("PDB"))
5027 filesmatched.add(new Object[]
5028 { file, protocol, mtch });
5033 // File wasn't named like one of the sequences or wasn't a PDB file.
5034 filesnotmatched.add(file);
5038 if (filesmatched.size() > 0)
5040 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
5046 "label.automatically_associate_pdb_files_with_sequences_same_name",
5053 .getString("label.automatically_associate_pdb_files_by_name"),
5054 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
5057 for (Object[] fm : filesmatched)
5059 // try and associate
5060 // TODO: may want to set a standard ID naming formalism for
5061 // associating PDB files which have no IDs.
5062 for (SequenceI toassoc : (SequenceI[]) fm[2])
5064 PDBEntry pe = new AssociatePdbFileWithSeq()
5065 .associatePdbWithSeq((String) fm[0],
5066 (String) fm[1], toassoc, false,
5070 System.err.println("Associated file : "
5071 + ((String) fm[0]) + " with "
5072 + toassoc.getDisplayId(true));
5076 alignPanel.paintAlignment(true);
5080 if (filesnotmatched.size() > 0)
5083 && (Cache.getDefault(
5084 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5087 "<html>"+MessageManager
5089 "label.ignore_unmatched_dropped_files_info",
5094 .toString() })+"</html>",
5096 .getString("label.ignore_unmatched_dropped_files"),
5097 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5101 for (String fn : filesnotmatched)
5103 loadJalviewDataFile(fn, null, null, null);
5107 } catch (Exception ex)
5109 ex.printStackTrace();
5115 * Attempt to load a "dropped" file or URL string: First by testing whether
5116 * it's and Annotation file, then a JNet file, and finally a features file. If
5117 * all are false then the user may have dropped an alignment file onto this
5121 * either a filename or a URL string.
5123 public void loadJalviewDataFile(String file, String protocol,
5124 String format, SequenceI assocSeq)
5128 if (protocol == null)
5130 protocol = jalview.io.FormatAdapter.checkProtocol(file);
5132 // if the file isn't identified, or not positively identified as some
5133 // other filetype (PFAM is default unidentified alignment file type) then
5134 // try to parse as annotation.
5135 boolean isAnnotation = (format == null || format
5136 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5137 .readAnnotationFile(viewport.getAlignment(), file, protocol)
5142 // first see if its a T-COFFEE score file
5143 TCoffeeScoreFile tcf = null;
5146 tcf = new TCoffeeScoreFile(file, protocol);
5149 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5151 tcoffeeColour.setEnabled(true);
5152 tcoffeeColour.setSelected(true);
5153 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5154 isAnnotation = true;
5156 .setText(MessageManager
5157 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5161 // some problem - if no warning its probable that the ID matching
5162 // process didn't work
5166 tcf.getWarningMessage() == null ? MessageManager
5167 .getString("label.check_file_matches_sequence_ids_alignment")
5168 : tcf.getWarningMessage(),
5170 .getString("label.problem_reading_tcoffee_score_file"),
5171 JOptionPane.WARNING_MESSAGE);
5178 } catch (Exception x)
5181 .debug("Exception when processing data source as T-COFFEE score file",
5187 // try to see if its a JNet 'concise' style annotation file *before*
5189 // try to parse it as a features file
5192 format = new IdentifyFile().Identify(file, protocol);
5194 if (format.equalsIgnoreCase("JnetFile"))
5196 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5198 new JnetAnnotationMaker().add_annotation(predictions,
5199 viewport.getAlignment(), 0, false);
5200 isAnnotation = true;
5205 * if (format.equalsIgnoreCase("PDB")) {
5207 * String pdbfn = ""; // try to match up filename with sequence id
5208 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5209 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5210 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5211 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5212 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5213 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5214 * // attempt to find a match in the alignment SequenceI mtch =
5215 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5216 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5217 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5218 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5219 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5220 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5221 * { System.err.println("Associated file : " + file + " with " +
5222 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5223 * TODO: maybe need to load as normal otherwise return; } }
5225 // try to parse it as a features file
5226 boolean isGroupsFile = parseFeaturesFile(file, protocol);
5227 // if it wasn't a features file then we just treat it as a general
5228 // alignment file to load into the current view.
5231 new FileLoader().LoadFile(viewport, file, protocol, format);
5235 alignPanel.paintAlignment(true);
5243 alignPanel.adjustAnnotationHeight();
5244 viewport.updateSequenceIdColours();
5245 buildSortByAnnotationScoresMenu();
5246 alignPanel.paintAlignment(true);
5248 } catch (Exception ex)
5250 ex.printStackTrace();
5251 } catch (OutOfMemoryError oom)
5256 } catch (Exception x)
5262 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5263 : "using " + protocol + " from " + file)
5265 + (format != null ? "(parsing as '" + format
5266 + "' file)" : ""), oom, Desktop.desktop);
5271 public void tabSelectionChanged(int index)
5275 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
5276 viewport = alignPanel.av;
5277 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5278 setMenusFromViewport(viewport);
5283 public void tabbedPane_mousePressed(MouseEvent e)
5285 if (SwingUtilities.isRightMouseButton(e))
5287 String reply = JOptionPane.showInternalInputDialog(this,
5288 MessageManager.getString("label.enter_view_name"),
5289 MessageManager.getString("label.enter_view_name"),
5290 JOptionPane.QUESTION_MESSAGE);
5294 viewport.viewName = reply;
5295 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5300 public AlignViewport getCurrentView()
5306 * Open the dialog for regex description parsing.
5309 protected void extractScores_actionPerformed(ActionEvent e)
5311 ParseProperties pp = new jalview.analysis.ParseProperties(
5312 viewport.getAlignment());
5313 // TODO: verify regex and introduce GUI dialog for version 2.5
5314 // if (pp.getScoresFromDescription("col", "score column ",
5315 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5317 if (pp.getScoresFromDescription("description column",
5318 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5320 buildSortByAnnotationScoresMenu();
5328 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5332 protected void showDbRefs_actionPerformed(ActionEvent e)
5334 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
5340 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5344 protected void showNpFeats_actionPerformed(ActionEvent e)
5346 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
5350 * find the viewport amongst the tabs in this alignment frame and close that
5355 public boolean closeView(AlignViewport av)
5359 this.closeMenuItem_actionPerformed(false);
5362 Component[] comp = tabbedPane.getComponents();
5363 for (int i = 0; comp != null && i < comp.length; i++)
5365 if (comp[i] instanceof AlignmentPanel)
5367 if (((AlignmentPanel) comp[i]).av == av)
5370 closeView((AlignmentPanel) comp[i]);
5378 protected void build_fetchdbmenu(JMenu webService)
5380 // Temporary hack - DBRef Fetcher always top level ws entry.
5381 // TODO We probably want to store a sequence database checklist in
5382 // preferences and have checkboxes.. rather than individual sources selected
5384 final JMenu rfetch = new JMenu(
5385 MessageManager.getString("action.fetch_db_references"));
5386 rfetch.setToolTipText(MessageManager
5387 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5388 webService.add(rfetch);
5390 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5391 MessageManager.getString("option.trim_retrieved_seqs"));
5392 trimrs.setToolTipText(MessageManager
5393 .getString("label.trim_retrieved_sequences"));
5394 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5395 trimrs.addActionListener(new ActionListener()
5398 public void actionPerformed(ActionEvent e)
5400 trimrs.setSelected(trimrs.isSelected());
5401 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5402 Boolean.valueOf(trimrs.isSelected()).toString());
5406 JMenuItem fetchr = new JMenuItem(
5407 MessageManager.getString("label.standard_databases"));
5408 fetchr.setToolTipText(MessageManager
5409 .getString("label.fetch_embl_uniprot"));
5410 fetchr.addActionListener(new ActionListener()
5414 public void actionPerformed(ActionEvent e)
5416 new Thread(new Runnable()
5422 new jalview.ws.DBRefFetcher(alignPanel.av
5423 .getSequenceSelection(), alignPanel.alignFrame)
5424 .fetchDBRefs(false);
5432 final AlignFrame me = this;
5433 new Thread(new Runnable()
5438 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5439 .getSequenceFetcherSingleton(me);
5440 javax.swing.SwingUtilities.invokeLater(new Runnable()
5445 String[] dbclasses = sf.getOrderedSupportedSources();
5446 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5447 // jalview.util.QuickSort.sort(otherdb, otherdb);
5448 List<DbSourceProxy> otherdb;
5449 JMenu dfetch = new JMenu();
5450 JMenu ifetch = new JMenu();
5451 JMenuItem fetchr = null;
5452 int comp = 0, icomp = 0, mcomp = 15;
5453 String mname = null;
5455 for (String dbclass : dbclasses)
5457 otherdb = sf.getSourceProxy(dbclass);
5458 // add a single entry for this class, or submenu allowing 'fetch
5460 if (otherdb == null || otherdb.size() < 1)
5464 // List<DbSourceProxy> dbs=otherdb;
5465 // otherdb=new ArrayList<DbSourceProxy>();
5466 // for (DbSourceProxy db:dbs)
5468 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5472 mname = "From " + dbclass;
5474 if (otherdb.size() == 1)
5476 final DbSourceProxy[] dassource = otherdb
5477 .toArray(new DbSourceProxy[0]);
5478 DbSourceProxy src = otherdb.get(0);
5479 fetchr = new JMenuItem(src.getDbSource());
5480 fetchr.addActionListener(new ActionListener()
5484 public void actionPerformed(ActionEvent e)
5486 new Thread(new Runnable()
5492 new jalview.ws.DBRefFetcher(alignPanel.av
5493 .getSequenceSelection(),
5494 alignPanel.alignFrame, dassource)
5495 .fetchDBRefs(false);
5501 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{src.getDbName()})));
5507 final DbSourceProxy[] dassource = otherdb
5508 .toArray(new DbSourceProxy[0]);
5510 DbSourceProxy src = otherdb.get(0);
5511 fetchr = new JMenuItem(MessageManager.formatMessage(
5512 "label.fetch_all_param", new String[]
5513 { src.getDbSource() }));
5514 fetchr.addActionListener(new ActionListener()
5517 public void actionPerformed(ActionEvent e)
5519 new Thread(new Runnable()
5525 new jalview.ws.DBRefFetcher(alignPanel.av
5526 .getSequenceSelection(),
5527 alignPanel.alignFrame, dassource)
5528 .fetchDBRefs(false);
5534 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new String[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
5537 // and then build the rest of the individual menus
5538 ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new String[]{src.getDbSource()}));
5540 String imname = null;
5542 for (DbSourceProxy sproxy : otherdb)
5544 String dbname = sproxy.getDbName();
5545 String sname = dbname.length() > 5 ? dbname.substring(0,
5546 5) + "..." : dbname;
5547 String msname = dbname.length() > 10 ? dbname.substring(
5548 0, 10) + "..." : dbname;
5551 imname = MessageManager.formatMessage("label.from_msname", new String[]{sname});
5553 fetchr = new JMenuItem(msname);
5554 final DbSourceProxy[] dassrc =
5556 fetchr.addActionListener(new ActionListener()
5560 public void actionPerformed(ActionEvent e)
5562 new Thread(new Runnable()
5568 new jalview.ws.DBRefFetcher(alignPanel.av
5569 .getSequenceSelection(),
5570 alignPanel.alignFrame, dassrc)
5571 .fetchDBRefs(false);
5577 fetchr.setToolTipText("<html>"
5578 + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname}));
5581 if (++icomp >= mcomp || i == (otherdb.size()))
5583 ifetch.setText(MessageManager.formatMessage(
5584 "label.source_to_target", imname, sname));
5586 ifetch = new JMenu();
5594 if (comp >= mcomp || dbi >= (dbclasses.length))
5596 dfetch.setText(MessageManager.formatMessage(
5597 "label.source_to_target", mname, dbclass));
5599 dfetch = new JMenu();
5612 * Left justify the whole alignment.
5615 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5617 AlignmentI al = viewport.getAlignment();
5619 viewport.firePropertyChange("alignment", null, al);
5623 * Right justify the whole alignment.
5626 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5628 AlignmentI al = viewport.getAlignment();
5630 viewport.firePropertyChange("alignment", null, al);
5633 public void setShowSeqFeatures(boolean b)
5635 showSeqFeatures.setSelected(true);
5636 viewport.setShowSequenceFeatures(true);
5643 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5644 * awt.event.ActionEvent)
5647 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5649 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5650 alignPanel.paintAlignment(true);
5657 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5661 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5663 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5664 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5672 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5673 * .event.ActionEvent)
5676 protected void showGroupConservation_actionPerformed(ActionEvent e)
5678 viewport.setShowGroupConservation(showGroupConservation.getState());
5679 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5686 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5687 * .event.ActionEvent)
5690 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5692 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5693 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5700 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5701 * .event.ActionEvent)
5704 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5706 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5707 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5711 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5713 showSequenceLogo.setState(true);
5714 viewport.setShowSequenceLogo(true);
5715 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5716 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5720 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5722 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5729 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5730 * .event.ActionEvent)
5733 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5735 if (avc.makeGroupsFromSelection())
5737 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5738 alignPanel.updateAnnotation();
5739 alignPanel.paintAlignment(true);
5744 protected void createGroup_actionPerformed(ActionEvent e)
5746 if (avc.createGroup())
5748 alignPanel.alignmentChanged();
5753 protected void unGroup_actionPerformed(ActionEvent e)
5757 alignPanel.alignmentChanged();
5762 * make the given alignmentPanel the currently selected tab
5764 * @param alignmentPanel
5766 public void setDisplayedView(AlignmentPanel alignmentPanel)
5768 if (!viewport.getSequenceSetId().equals(
5769 alignmentPanel.av.getSequenceSetId()))
5771 throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
5773 if (tabbedPane != null
5774 & alignPanels.indexOf(alignmentPanel) != tabbedPane
5775 .getSelectedIndex())
5777 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5782 * Action on selection of menu options to Show or Hide annotations.
5785 * @param forSequences
5786 * update sequence-related annotations
5787 * @param forAlignment
5788 * update non-sequence-related annotations
5791 protected void setAnnotationsVisibility(boolean visible,
5792 boolean forSequences, boolean forAlignment)
5794 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5795 .getAlignmentAnnotation())
5797 boolean apply = (aa.sequenceRef == null && forAlignment)
5798 || (aa.sequenceRef != null && forSequences);
5801 aa.visible = visible;
5804 alignPanel.validateAnnotationDimensions(false);
5805 alignPanel.alignmentChanged();
5809 * Store selected annotation sort order for the view and repaint.
5812 protected void sortAnnotations_actionPerformed()
5814 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5816 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5817 alignPanel.paintAlignment(true);
5821 class PrintThread extends Thread
5825 public PrintThread(AlignmentPanel ap)
5830 static PageFormat pf;
5835 PrinterJob printJob = PrinterJob.getPrinterJob();
5839 printJob.setPrintable(ap, pf);
5843 printJob.setPrintable(ap);
5846 if (printJob.printDialog())
5851 } catch (Exception PrintException)
5853 PrintException.printStackTrace();