2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AAFrequency;
24 import jalview.analysis.AlignmentSorter;
25 import jalview.analysis.AlignmentUtils;
26 import jalview.analysis.Conservation;
27 import jalview.analysis.CrossRef;
28 import jalview.analysis.NJTree;
29 import jalview.analysis.ParseProperties;
30 import jalview.analysis.SequenceIdMatcher;
31 import jalview.api.AlignViewControllerGuiI;
32 import jalview.api.AlignViewControllerI;
33 import jalview.api.analysis.ScoreModelI;
34 import jalview.bin.Cache;
35 import jalview.commands.CommandI;
36 import jalview.commands.EditCommand;
37 import jalview.commands.OrderCommand;
38 import jalview.commands.RemoveGapColCommand;
39 import jalview.commands.RemoveGapsCommand;
40 import jalview.commands.SlideSequencesCommand;
41 import jalview.commands.TrimRegionCommand;
42 import jalview.datamodel.AlignedCodonFrame;
43 import jalview.datamodel.Alignment;
44 import jalview.datamodel.AlignmentAnnotation;
45 import jalview.datamodel.AlignmentI;
46 import jalview.datamodel.AlignmentOrder;
47 import jalview.datamodel.AlignmentView;
48 import jalview.datamodel.ColumnSelection;
49 import jalview.datamodel.PDBEntry;
50 import jalview.datamodel.SeqCigar;
51 import jalview.datamodel.Sequence;
52 import jalview.datamodel.SequenceGroup;
53 import jalview.datamodel.SequenceI;
54 import jalview.io.AlignmentProperties;
55 import jalview.io.AnnotationFile;
56 import jalview.io.FeaturesFile;
57 import jalview.io.FileLoader;
58 import jalview.io.FormatAdapter;
59 import jalview.io.HTMLOutput;
60 import jalview.io.IdentifyFile;
61 import jalview.io.JalviewFileChooser;
62 import jalview.io.JalviewFileView;
63 import jalview.io.JnetAnnotationMaker;
64 import jalview.io.NewickFile;
65 import jalview.io.TCoffeeScoreFile;
66 import jalview.jbgui.GAlignFrame;
67 import jalview.schemes.Blosum62ColourScheme;
68 import jalview.schemes.BuriedColourScheme;
69 import jalview.schemes.ClustalxColourScheme;
70 import jalview.schemes.ColourSchemeI;
71 import jalview.schemes.ColourSchemeProperty;
72 import jalview.schemes.HelixColourScheme;
73 import jalview.schemes.HydrophobicColourScheme;
74 import jalview.schemes.NucleotideColourScheme;
75 import jalview.schemes.PIDColourScheme;
76 import jalview.schemes.PurinePyrimidineColourScheme;
77 import jalview.schemes.RNAHelicesColourChooser;
78 import jalview.schemes.ResidueProperties;
79 import jalview.schemes.StrandColourScheme;
80 import jalview.schemes.TCoffeeColourScheme;
81 import jalview.schemes.TaylorColourScheme;
82 import jalview.schemes.TurnColourScheme;
83 import jalview.schemes.UserColourScheme;
84 import jalview.schemes.ZappoColourScheme;
85 import jalview.util.MessageManager;
86 import jalview.ws.jws1.Discoverer;
87 import jalview.ws.jws2.Jws2Discoverer;
88 import jalview.ws.jws2.jabaws2.Jws2Instance;
89 import jalview.ws.seqfetcher.DbSourceProxy;
91 import java.awt.BorderLayout;
92 import java.awt.Component;
93 import java.awt.GridLayout;
94 import java.awt.Rectangle;
95 import java.awt.Toolkit;
96 import java.awt.datatransfer.Clipboard;
97 import java.awt.datatransfer.DataFlavor;
98 import java.awt.datatransfer.StringSelection;
99 import java.awt.datatransfer.Transferable;
100 import java.awt.dnd.DnDConstants;
101 import java.awt.dnd.DropTargetDragEvent;
102 import java.awt.dnd.DropTargetDropEvent;
103 import java.awt.dnd.DropTargetEvent;
104 import java.awt.dnd.DropTargetListener;
105 import java.awt.event.ActionEvent;
106 import java.awt.event.ActionListener;
107 import java.awt.event.KeyAdapter;
108 import java.awt.event.KeyEvent;
109 import java.awt.event.MouseAdapter;
110 import java.awt.event.MouseEvent;
111 import java.awt.print.PageFormat;
112 import java.awt.print.PrinterJob;
113 import java.beans.PropertyChangeEvent;
116 import java.util.ArrayList;
117 import java.util.Enumeration;
118 import java.util.Hashtable;
119 import java.util.List;
120 import java.util.Vector;
122 import javax.swing.JButton;
123 import javax.swing.JCheckBoxMenuItem;
124 import javax.swing.JEditorPane;
125 import javax.swing.JInternalFrame;
126 import javax.swing.JLabel;
127 import javax.swing.JLayeredPane;
128 import javax.swing.JMenu;
129 import javax.swing.JMenuItem;
130 import javax.swing.JOptionPane;
131 import javax.swing.JPanel;
132 import javax.swing.JProgressBar;
133 import javax.swing.JRadioButtonMenuItem;
134 import javax.swing.JScrollPane;
135 import javax.swing.SwingUtilities;
141 * @version $Revision$
143 public class AlignFrame extends GAlignFrame implements DropTargetListener,
144 IProgressIndicator, AlignViewControllerGuiI
148 public static final int DEFAULT_WIDTH = 700;
151 public static final int DEFAULT_HEIGHT = 500;
153 public AlignmentPanel alignPanel;
155 AlignViewport viewport;
157 public AlignViewControllerI avc;
159 Vector alignPanels = new Vector();
162 * Last format used to load or save alignments in this window
164 String currentFileFormat = null;
167 * Current filename for this alignment
169 String fileName = null;
172 * Creates a new AlignFrame object with specific width and height.
178 public AlignFrame(AlignmentI al, int width, int height)
180 this(al, null, width, height);
184 * Creates a new AlignFrame object with specific width, height and
190 * @param sequenceSetId
192 public AlignFrame(AlignmentI al, int width, int height,
193 String sequenceSetId)
195 this(al, null, width, height, sequenceSetId);
199 * Creates a new AlignFrame object with specific width, height and
205 * @param sequenceSetId
208 public AlignFrame(AlignmentI al, int width, int height,
209 String sequenceSetId, String viewId)
211 this(al, null, width, height, sequenceSetId, viewId);
215 * new alignment window with hidden columns
219 * @param hiddenColumns
220 * ColumnSelection or null
222 * Width of alignment frame
226 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
227 int width, int height)
229 this(al, hiddenColumns, width, height, null);
233 * Create alignment frame for al with hiddenColumns, a specific width and
234 * height, and specific sequenceId
237 * @param hiddenColumns
240 * @param sequenceSetId
243 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
244 int width, int height, String sequenceSetId)
246 this(al, hiddenColumns, width, height, sequenceSetId, null);
250 * Create alignment frame for al with hiddenColumns, a specific width and
251 * height, and specific sequenceId
254 * @param hiddenColumns
257 * @param sequenceSetId
262 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
263 int width, int height, String sequenceSetId, String viewId)
265 setSize(width, height);
267 if (al.getDataset() == null)
272 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
274 alignPanel = new AlignmentPanel(this, viewport);
277 addAlignmentPanel(alignPanel, true);
282 * Make a new AlignFrame from exisiting alignmentPanels
289 public AlignFrame(AlignmentPanel ap)
293 addAlignmentPanel(ap, false);
298 * initalise the alignframe from the underlying viewport data and the
303 avc = new jalview.controller.AlignViewController(this, viewport,
305 if (viewport.getAlignmentConservationAnnotation() == null)
307 BLOSUM62Colour.setEnabled(false);
308 conservationMenuItem.setEnabled(false);
309 modifyConservation.setEnabled(false);
310 // PIDColour.setEnabled(false);
311 // abovePIDThreshold.setEnabled(false);
312 // modifyPID.setEnabled(false);
315 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
318 if (sortby.equals("Id"))
320 sortIDMenuItem_actionPerformed(null);
322 else if (sortby.equals("Pairwise Identity"))
324 sortPairwiseMenuItem_actionPerformed(null);
327 if (Desktop.desktop != null)
329 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
330 addServiceListeners();
331 setGUINucleotide(viewport.getAlignment().isNucleotide());
334 setMenusFromViewport(viewport);
335 buildSortByAnnotationScoresMenu();
338 if (viewport.wrapAlignment)
340 wrapMenuItem_actionPerformed(null);
343 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
345 this.overviewMenuItem_actionPerformed(null);
353 * Change the filename and format for the alignment, and enable the 'reload'
354 * button functionality.
361 public void setFileName(String file, String format)
364 currentFileFormat = format;
365 reload.setEnabled(true);
368 void addKeyListener()
370 addKeyListener(new KeyAdapter()
373 public void keyPressed(KeyEvent evt)
375 if (viewport.cursorMode
376 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
377 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
378 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
379 && Character.isDigit(evt.getKeyChar()))
380 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
382 switch (evt.getKeyCode())
385 case 27: // escape key
386 deselectAllSequenceMenuItem_actionPerformed(null);
390 case KeyEvent.VK_DOWN:
391 if (evt.isAltDown() || !viewport.cursorMode)
392 moveSelectedSequences(false);
393 if (viewport.cursorMode)
394 alignPanel.seqPanel.moveCursor(0, 1);
398 if (evt.isAltDown() || !viewport.cursorMode)
399 moveSelectedSequences(true);
400 if (viewport.cursorMode)
401 alignPanel.seqPanel.moveCursor(0, -1);
405 case KeyEvent.VK_LEFT:
406 if (evt.isAltDown() || !viewport.cursorMode)
407 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
409 alignPanel.seqPanel.moveCursor(-1, 0);
413 case KeyEvent.VK_RIGHT:
414 if (evt.isAltDown() || !viewport.cursorMode)
415 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
417 alignPanel.seqPanel.moveCursor(1, 0);
420 case KeyEvent.VK_SPACE:
421 if (viewport.cursorMode)
423 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
424 || evt.isShiftDown() || evt.isAltDown());
428 // case KeyEvent.VK_A:
429 // if (viewport.cursorMode)
431 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
432 // //System.out.println("A");
436 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
437 * System.out.println("closing bracket"); } break;
439 case KeyEvent.VK_DELETE:
440 case KeyEvent.VK_BACK_SPACE:
441 if (!viewport.cursorMode)
443 cut_actionPerformed(null);
447 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
448 || evt.isShiftDown() || evt.isAltDown());
454 if (viewport.cursorMode)
456 alignPanel.seqPanel.setCursorRow();
460 if (viewport.cursorMode && !evt.isControlDown())
462 alignPanel.seqPanel.setCursorColumn();
466 if (viewport.cursorMode)
468 alignPanel.seqPanel.setCursorPosition();
472 case KeyEvent.VK_ENTER:
473 case KeyEvent.VK_COMMA:
474 if (viewport.cursorMode)
476 alignPanel.seqPanel.setCursorRowAndColumn();
481 if (viewport.cursorMode)
483 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
487 if (viewport.cursorMode)
489 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
494 viewport.cursorMode = !viewport.cursorMode;
495 statusBar.setText(MessageManager.formatMessage(
496 "label.keyboard_editing_mode", new String[]
497 { (viewport.cursorMode ? "on" : "off") }));
498 if (viewport.cursorMode)
500 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
501 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
503 alignPanel.seqPanel.seqCanvas.repaint();
509 Help.showHelpWindow();
510 } catch (Exception ex)
512 ex.printStackTrace();
517 boolean toggleSeqs = !evt.isControlDown();
518 boolean toggleCols = !evt.isShiftDown();
519 toggleHiddenRegions(toggleSeqs, toggleCols);
522 case KeyEvent.VK_PAGE_UP:
523 if (viewport.wrapAlignment)
525 alignPanel.scrollUp(true);
529 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
530 - viewport.endSeq + viewport.startSeq);
533 case KeyEvent.VK_PAGE_DOWN:
534 if (viewport.wrapAlignment)
536 alignPanel.scrollUp(false);
540 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
541 + viewport.endSeq - viewport.startSeq);
548 public void keyReleased(KeyEvent evt)
550 switch (evt.getKeyCode())
552 case KeyEvent.VK_LEFT:
553 if (evt.isAltDown() || !viewport.cursorMode)
554 viewport.firePropertyChange("alignment", null, viewport
555 .getAlignment().getSequences());
558 case KeyEvent.VK_RIGHT:
559 if (evt.isAltDown() || !viewport.cursorMode)
560 viewport.firePropertyChange("alignment", null, viewport
561 .getAlignment().getSequences());
568 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
570 ap.alignFrame = this;
571 avc = new jalview.controller.AlignViewController(this, viewport,
574 alignPanels.addElement(ap);
576 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
578 int aSize = alignPanels.size();
580 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
582 if (aSize == 1 && ap.av.viewName == null)
584 this.getContentPane().add(ap, BorderLayout.CENTER);
590 setInitialTabVisible();
593 expandViews.setEnabled(true);
594 gatherViews.setEnabled(true);
595 tabbedPane.addTab(ap.av.viewName, ap);
597 ap.setVisible(false);
602 if (ap.av.isPadGaps())
604 ap.av.getAlignment().padGaps();
606 ap.av.updateConservation(ap);
607 ap.av.updateConsensus(ap);
608 ap.av.updateStrucConsensus(ap);
612 public void setInitialTabVisible()
614 expandViews.setEnabled(true);
615 gatherViews.setEnabled(true);
616 tabbedPane.setVisible(true);
617 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
618 tabbedPane.addTab(first.av.viewName, first);
619 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
622 public AlignViewport getViewport()
627 /* Set up intrinsic listeners for dynamically generated GUI bits. */
628 private void addServiceListeners()
630 final java.beans.PropertyChangeListener thisListener;
631 Desktop.instance.addJalviewPropertyChangeListener("services",
632 thisListener = new java.beans.PropertyChangeListener()
635 public void propertyChange(PropertyChangeEvent evt)
637 // // System.out.println("Discoverer property change.");
638 // if (evt.getPropertyName().equals("services"))
640 SwingUtilities.invokeLater(new Runnable()
647 .println("Rebuild WS Menu for service change");
648 BuildWebServiceMenu();
655 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
658 public void internalFrameClosed(
659 javax.swing.event.InternalFrameEvent evt)
661 System.out.println("deregistering discoverer listener");
662 Desktop.instance.removeJalviewPropertyChangeListener("services",
664 closeMenuItem_actionPerformed(true);
667 // Finally, build the menu once to get current service state
668 new Thread(new Runnable()
673 BuildWebServiceMenu();
678 public void setGUINucleotide(boolean nucleotide)
680 showTranslation.setVisible(nucleotide);
681 conservationMenuItem.setEnabled(!nucleotide);
682 modifyConservation.setEnabled(!nucleotide);
683 showGroupConservation.setEnabled(!nucleotide);
684 rnahelicesColour.setEnabled(nucleotide);
685 purinePyrimidineColour.setEnabled(nucleotide);
686 // Remember AlignFrame always starts as protein
690 // calculateMenu.remove(calculateMenu.getItemCount() - 2);
695 * set up menus for the currently viewport. This may be called after any
696 * operation that affects the data in the current view (selection changed,
697 * etc) to update the menus to reflect the new state.
699 public void setMenusForViewport()
701 setMenusFromViewport(viewport);
705 * Need to call this method when tabs are selected for multiple views, or when
706 * loading from Jalview2XML.java
711 void setMenusFromViewport(AlignViewport av)
713 padGapsMenuitem.setSelected(av.isPadGaps());
714 colourTextMenuItem.setSelected(av.showColourText);
715 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
716 conservationMenuItem.setSelected(av.getConservationSelected());
717 seqLimits.setSelected(av.getShowJVSuffix());
718 idRightAlign.setSelected(av.rightAlignIds);
719 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
720 renderGapsMenuItem.setSelected(av.renderGaps);
721 wrapMenuItem.setSelected(av.wrapAlignment);
722 scaleAbove.setVisible(av.wrapAlignment);
723 scaleLeft.setVisible(av.wrapAlignment);
724 scaleRight.setVisible(av.wrapAlignment);
725 annotationPanelMenuItem.setState(av.showAnnotation);
727 * Show/hide all annotations only enabled if annotation panel is shown
729 showAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
730 hideAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
731 viewBoxesMenuItem.setSelected(av.showBoxes);
732 viewTextMenuItem.setSelected(av.showText);
733 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
734 showGroupConsensus.setSelected(av.isShowGroupConsensus());
735 showGroupConservation.setSelected(av.isShowGroupConservation());
736 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
737 showSequenceLogo.setSelected(av.isShowSequenceLogo());
738 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
740 setColourSelected(ColourSchemeProperty.getColourName(av
741 .getGlobalColourScheme()));
743 showSeqFeatures.setSelected(av.showSequenceFeatures);
744 hiddenMarkers.setState(av.showHiddenMarkers);
745 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
746 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
747 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
748 autoCalculate.setSelected(av.autoCalculateConsensus);
749 sortByTree.setSelected(av.sortByTree);
750 listenToViewSelections.setSelected(av.followSelection);
751 rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
753 .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
754 setShowProductsEnabled();
758 // methods for implementing IProgressIndicator
759 // need to refactor to a reusable stub class
760 Hashtable progressBars, progressBarHandlers;
765 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
768 public void setProgressBar(String message, long id)
770 if (progressBars == null)
772 progressBars = new Hashtable();
773 progressBarHandlers = new Hashtable();
776 JPanel progressPanel;
777 Long lId = new Long(id);
778 GridLayout layout = (GridLayout) statusPanel.getLayout();
779 if (progressBars.get(lId) != null)
781 progressPanel = (JPanel) progressBars.get(new Long(id));
782 statusPanel.remove(progressPanel);
783 progressBars.remove(lId);
784 progressPanel = null;
787 statusBar.setText(message);
789 if (progressBarHandlers.contains(lId))
791 progressBarHandlers.remove(lId);
793 layout.setRows(layout.getRows() - 1);
797 progressPanel = new JPanel(new BorderLayout(10, 5));
799 JProgressBar progressBar = new JProgressBar();
800 progressBar.setIndeterminate(true);
802 progressPanel.add(new JLabel(message), BorderLayout.WEST);
803 progressPanel.add(progressBar, BorderLayout.CENTER);
805 layout.setRows(layout.getRows() + 1);
806 statusPanel.add(progressPanel);
808 progressBars.put(lId, progressPanel);
811 // setMenusForViewport();
816 public void registerHandler(final long id,
817 final IProgressIndicatorHandler handler)
819 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
822 "call setProgressBar before registering the progress bar's handler.");
824 progressBarHandlers.put(new Long(id), handler);
825 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
826 if (handler.canCancel())
828 JButton cancel = new JButton(
829 MessageManager.getString("action.cancel"));
830 final IProgressIndicator us = this;
831 cancel.addActionListener(new ActionListener()
835 public void actionPerformed(ActionEvent e)
837 handler.cancelActivity(id);
840 + ((JLabel) progressPanel.getComponent(0))
844 progressPanel.add(cancel, BorderLayout.EAST);
850 * @return true if any progress bars are still active
853 public boolean operationInProgress()
855 if (progressBars != null && progressBars.size() > 0)
863 public void setStatus(String text)
865 statusBar.setText(text);
869 * Added so Castor Mapping file can obtain Jalview Version
871 public String getVersion()
873 return jalview.bin.Cache.getProperty("VERSION");
876 public FeatureRenderer getFeatureRenderer()
878 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
882 public void fetchSequence_actionPerformed(ActionEvent e)
884 new SequenceFetcher(this);
888 public void addFromFile_actionPerformed(ActionEvent e)
890 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
894 public void reload_actionPerformed(ActionEvent e)
896 if (fileName != null)
898 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
899 // originating file's format
900 // TODO: work out how to recover feature settings for correct view(s) when
902 if (currentFileFormat.equals("Jalview"))
904 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
905 for (int i = 0; i < frames.length; i++)
907 if (frames[i] instanceof AlignFrame && frames[i] != this
908 && ((AlignFrame) frames[i]).fileName != null
909 && ((AlignFrame) frames[i]).fileName.equals(fileName))
913 frames[i].setSelected(true);
914 Desktop.instance.closeAssociatedWindows();
915 } catch (java.beans.PropertyVetoException ex)
921 Desktop.instance.closeAssociatedWindows();
923 FileLoader loader = new FileLoader();
924 String protocol = fileName.startsWith("http:") ? "URL" : "File";
925 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
929 Rectangle bounds = this.getBounds();
931 FileLoader loader = new FileLoader();
932 String protocol = fileName.startsWith("http:") ? "URL" : "File";
933 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
934 protocol, currentFileFormat);
936 newframe.setBounds(bounds);
937 if (featureSettings != null && featureSettings.isShowing())
939 final Rectangle fspos = featureSettings.frame.getBounds();
940 // TODO: need a 'show feature settings' function that takes bounds -
941 // need to refactor Desktop.addFrame
942 newframe.featureSettings_actionPerformed(null);
943 final FeatureSettings nfs = newframe.featureSettings;
944 SwingUtilities.invokeLater(new Runnable()
949 nfs.frame.setBounds(fspos);
952 this.featureSettings.close();
953 this.featureSettings = null;
955 this.closeMenuItem_actionPerformed(true);
961 public void addFromText_actionPerformed(ActionEvent e)
963 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
967 public void addFromURL_actionPerformed(ActionEvent e)
969 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
973 public void save_actionPerformed(ActionEvent e)
976 || (currentFileFormat == null || !jalview.io.FormatAdapter
977 .isValidIOFormat(currentFileFormat, true))
978 || fileName.startsWith("http"))
980 saveAs_actionPerformed(null);
984 saveAlignment(fileName, currentFileFormat);
995 public void saveAs_actionPerformed(ActionEvent e)
997 JalviewFileChooser chooser = new JalviewFileChooser(
998 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
999 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
1000 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
1001 currentFileFormat, false);
1003 chooser.setFileView(new JalviewFileView());
1004 chooser.setDialogTitle("Save Alignment to file");
1005 chooser.setToolTipText(MessageManager.getString("action.save"));
1007 int value = chooser.showSaveDialog(this);
1009 if (value == JalviewFileChooser.APPROVE_OPTION)
1011 currentFileFormat = chooser.getSelectedFormat();
1012 if (currentFileFormat == null)
1015 .showInternalMessageDialog(
1018 .getString("label.select_file_format_before_saving"),
1020 .getString("label.file_format_not_specified"),
1021 JOptionPane.WARNING_MESSAGE);
1022 value = chooser.showSaveDialog(this);
1026 fileName = chooser.getSelectedFile().getPath();
1028 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
1031 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1032 if (currentFileFormat.indexOf(" ") > -1)
1034 currentFileFormat = currentFileFormat.substring(0,
1035 currentFileFormat.indexOf(" "));
1037 saveAlignment(fileName, currentFileFormat);
1041 public boolean saveAlignment(String file, String format)
1043 boolean success = true;
1045 if (format.equalsIgnoreCase("Jalview"))
1047 String shortName = title;
1049 if (shortName.indexOf(java.io.File.separatorChar) > -1)
1051 shortName = shortName.substring(shortName
1052 .lastIndexOf(java.io.File.separatorChar) + 1);
1055 success = new Jalview2XML().SaveAlignment(this, file, shortName);
1057 statusBar.setText(MessageManager.formatMessage(
1058 "label.successfully_saved_to_file_in_format", new String[]
1059 { fileName, format }));
1064 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1066 warningMessage("Cannot save file " + fileName + " using format "
1067 + format, "Alignment output format not supported");
1068 saveAs_actionPerformed(null);
1069 // JBPNote need to have a raise_gui flag here
1073 String[] omitHidden = null;
1075 if (viewport.hasHiddenColumns())
1077 int reply = JOptionPane
1078 .showInternalConfirmDialog(
1081 .getString("label.alignment_contains_hidden_columns"),
1083 .getString("action.save_omit_hidden_columns"),
1084 JOptionPane.YES_NO_OPTION,
1085 JOptionPane.QUESTION_MESSAGE);
1087 if (reply == JOptionPane.YES_OPTION)
1089 omitHidden = viewport.getViewAsString(false);
1092 FormatAdapter f = new FormatAdapter();
1093 String output = f.formatSequences(format,
1094 viewport.getAlignment(), // class cast exceptions will
1095 // occur in the distant future
1096 omitHidden, f.getCacheSuffixDefault(format),
1097 viewport.getColumnSelection());
1107 java.io.PrintWriter out = new java.io.PrintWriter(
1108 new java.io.FileWriter(file));
1112 this.setTitle(file);
1113 statusBar.setText(MessageManager.formatMessage(
1114 "label.successfully_saved_to_file_in_format",
1116 { fileName, format }));
1117 } catch (Exception ex)
1120 ex.printStackTrace();
1127 JOptionPane.showInternalMessageDialog(this, MessageManager
1128 .formatMessage("label.couldnt_save_file", new String[]
1129 { fileName }), MessageManager
1130 .getString("label.error_saving_file"),
1131 JOptionPane.WARNING_MESSAGE);
1137 private void warningMessage(String warning, String title)
1139 if (new jalview.util.Platform().isHeadless())
1141 System.err.println("Warning: " + title + "\nWarning: " + warning);
1146 JOptionPane.showInternalMessageDialog(this, warning, title,
1147 JOptionPane.WARNING_MESSAGE);
1159 protected void outputText_actionPerformed(ActionEvent e)
1161 String[] omitHidden = null;
1163 if (viewport.hasHiddenColumns())
1165 int reply = JOptionPane
1166 .showInternalConfirmDialog(
1169 .getString("label.alignment_contains_hidden_columns"),
1171 .getString("action.save_omit_hidden_columns"),
1172 JOptionPane.YES_NO_OPTION,
1173 JOptionPane.QUESTION_MESSAGE);
1175 if (reply == JOptionPane.YES_OPTION)
1177 omitHidden = viewport.getViewAsString(false);
1181 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1182 cap.setForInput(null);
1186 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1187 viewport.getAlignment(), omitHidden,
1188 viewport.getColumnSelection()));
1189 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1190 "label.alignment_output_command", new String[]
1191 { e.getActionCommand() }), 600, 500);
1192 } catch (OutOfMemoryError oom)
1194 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1207 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1209 new HTMLOutput(alignPanel,
1210 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1211 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1214 public void createImageMap(File file, String image)
1216 alignPanel.makePNGImageMap(file, image);
1226 public void createPNG(File f)
1228 alignPanel.makePNG(f);
1238 public void createEPS(File f)
1240 alignPanel.makeEPS(f);
1244 public void pageSetup_actionPerformed(ActionEvent e)
1246 PrinterJob printJob = PrinterJob.getPrinterJob();
1247 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1257 public void printMenuItem_actionPerformed(ActionEvent e)
1259 // Putting in a thread avoids Swing painting problems
1260 PrintThread thread = new PrintThread(alignPanel);
1265 public void exportFeatures_actionPerformed(ActionEvent e)
1267 new AnnotationExporter().exportFeatures(alignPanel);
1271 public void exportAnnotations_actionPerformed(ActionEvent e)
1273 new AnnotationExporter().exportAnnotations(alignPanel,
1274 viewport.showAnnotation ? viewport.getAlignment()
1275 .getAlignmentAnnotation() : null, viewport
1276 .getAlignment().getGroups(), ((Alignment) viewport
1277 .getAlignment()).alignmentProperties);
1281 public void associatedData_actionPerformed(ActionEvent e)
1283 // Pick the tree file
1284 JalviewFileChooser chooser = new JalviewFileChooser(
1285 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1286 chooser.setFileView(new JalviewFileView());
1287 chooser.setDialogTitle(MessageManager
1288 .getString("label.load_jalview_annotations"));
1289 chooser.setToolTipText(MessageManager
1290 .getString("label.load_jalview_annotations"));
1292 int value = chooser.showOpenDialog(null);
1294 if (value == JalviewFileChooser.APPROVE_OPTION)
1296 String choice = chooser.getSelectedFile().getPath();
1297 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1298 loadJalviewDataFile(choice, null, null, null);
1304 * Close the current view or all views in the alignment frame. If the frame
1305 * only contains one view then the alignment will be removed from memory.
1307 * @param closeAllTabs
1310 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1312 if (alignPanels != null && alignPanels.size() < 2)
1314 closeAllTabs = true;
1319 if (alignPanels != null)
1323 if (this.isClosed())
1325 // really close all the windows - otherwise wait till
1326 // setClosed(true) is called
1327 for (int i = 0; i < alignPanels.size(); i++)
1329 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1336 closeView(alignPanel);
1342 this.setClosed(true);
1344 } catch (Exception ex)
1346 ex.printStackTrace();
1351 * close alignPanel2 and shuffle tabs appropriately.
1353 * @param alignPanel2
1355 public void closeView(AlignmentPanel alignPanel2)
1357 int index = tabbedPane.getSelectedIndex();
1358 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1359 alignPanels.removeElement(alignPanel2);
1361 // if (viewport == alignPanel2.av)
1365 alignPanel2.closePanel();
1368 tabbedPane.removeTabAt(closedindex);
1369 tabbedPane.validate();
1371 if (index > closedindex || index == tabbedPane.getTabCount())
1373 // modify currently selected tab index if necessary.
1377 this.tabSelectionChanged(index);
1383 void updateEditMenuBar()
1386 if (viewport.historyList.size() > 0)
1388 undoMenuItem.setEnabled(true);
1389 CommandI command = (CommandI) viewport.historyList.peek();
1390 undoMenuItem.setText(MessageManager.formatMessage(
1391 "label.undo_command", new String[]
1392 { command.getDescription() }));
1396 undoMenuItem.setEnabled(false);
1397 undoMenuItem.setText(MessageManager.getString("action.undo"));
1400 if (viewport.redoList.size() > 0)
1402 redoMenuItem.setEnabled(true);
1404 CommandI command = (CommandI) viewport.redoList.peek();
1405 redoMenuItem.setText(MessageManager.formatMessage(
1406 "label.redo_command", new String[]
1407 { command.getDescription() }));
1411 redoMenuItem.setEnabled(false);
1412 redoMenuItem.setText(MessageManager.getString("action.redo"));
1416 public void addHistoryItem(CommandI command)
1418 if (command.getSize() > 0)
1420 viewport.historyList.push(command);
1421 viewport.redoList.clear();
1422 updateEditMenuBar();
1423 viewport.updateHiddenColumns();
1424 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1425 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1426 // viewport.getColumnSelection()
1427 // .getHiddenColumns().size() > 0);
1433 * @return alignment objects for all views
1435 AlignmentI[] getViewAlignments()
1437 if (alignPanels != null)
1439 Enumeration e = alignPanels.elements();
1440 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1441 for (int i = 0; e.hasMoreElements(); i++)
1443 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1447 if (viewport != null)
1449 return new AlignmentI[]
1450 { viewport.getAlignment() };
1462 protected void undoMenuItem_actionPerformed(ActionEvent e)
1464 if (viewport.historyList.empty())
1466 CommandI command = (CommandI) viewport.historyList.pop();
1467 viewport.redoList.push(command);
1468 command.undoCommand(getViewAlignments());
1470 AlignViewport originalSource = getOriginatingSource(command);
1471 updateEditMenuBar();
1473 if (originalSource != null)
1475 if (originalSource != viewport)
1478 .warn("Implementation worry: mismatch of viewport origin for undo");
1480 originalSource.updateHiddenColumns();
1481 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1483 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1484 // viewport.getColumnSelection()
1485 // .getHiddenColumns().size() > 0);
1486 originalSource.firePropertyChange("alignment", null, originalSource
1487 .getAlignment().getSequences());
1498 protected void redoMenuItem_actionPerformed(ActionEvent e)
1500 if (viewport.redoList.size() < 1)
1505 CommandI command = (CommandI) viewport.redoList.pop();
1506 viewport.historyList.push(command);
1507 command.doCommand(getViewAlignments());
1509 AlignViewport originalSource = getOriginatingSource(command);
1510 updateEditMenuBar();
1512 if (originalSource != null)
1515 if (originalSource != viewport)
1518 .warn("Implementation worry: mismatch of viewport origin for redo");
1520 originalSource.updateHiddenColumns();
1521 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1523 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1524 // viewport.getColumnSelection()
1525 // .getHiddenColumns().size() > 0);
1526 originalSource.firePropertyChange("alignment", null, originalSource
1527 .getAlignment().getSequences());
1531 AlignViewport getOriginatingSource(CommandI command)
1533 AlignViewport originalSource = null;
1534 // For sequence removal and addition, we need to fire
1535 // the property change event FROM the viewport where the
1536 // original alignment was altered
1537 AlignmentI al = null;
1538 if (command instanceof EditCommand)
1540 EditCommand editCommand = (EditCommand) command;
1541 al = editCommand.getAlignment();
1542 Vector comps = (Vector) PaintRefresher.components.get(viewport
1543 .getSequenceSetId());
1545 for (int i = 0; i < comps.size(); i++)
1547 if (comps.elementAt(i) instanceof AlignmentPanel)
1549 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1551 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1558 if (originalSource == null)
1560 // The original view is closed, we must validate
1561 // the current view against the closed view first
1564 PaintRefresher.validateSequences(al, viewport.getAlignment());
1567 originalSource = viewport;
1570 return originalSource;
1579 public void moveSelectedSequences(boolean up)
1581 SequenceGroup sg = viewport.getSelectionGroup();
1587 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1588 viewport.getHiddenRepSequences(), up);
1589 alignPanel.paintAlignment(true);
1592 synchronized void slideSequences(boolean right, int size)
1594 List<SequenceI> sg = new Vector();
1595 if (viewport.cursorMode)
1597 sg.add(viewport.getAlignment().getSequenceAt(
1598 alignPanel.seqPanel.seqCanvas.cursorY));
1600 else if (viewport.getSelectionGroup() != null
1601 && viewport.getSelectionGroup().getSize() != viewport
1602 .getAlignment().getHeight())
1604 sg = viewport.getSelectionGroup().getSequences(
1605 viewport.getHiddenRepSequences());
1613 Vector invertGroup = new Vector();
1615 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1617 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1618 invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1621 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1623 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1624 for (int i = 0; i < invertGroup.size(); i++)
1625 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1627 SlideSequencesCommand ssc;
1629 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1630 size, viewport.getGapCharacter());
1632 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1633 size, viewport.getGapCharacter());
1635 int groupAdjustment = 0;
1636 if (ssc.getGapsInsertedBegin() && right)
1638 if (viewport.cursorMode)
1639 alignPanel.seqPanel.moveCursor(size, 0);
1641 groupAdjustment = size;
1643 else if (!ssc.getGapsInsertedBegin() && !right)
1645 if (viewport.cursorMode)
1646 alignPanel.seqPanel.moveCursor(-size, 0);
1648 groupAdjustment = -size;
1651 if (groupAdjustment != 0)
1653 viewport.getSelectionGroup().setStartRes(
1654 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1655 viewport.getSelectionGroup().setEndRes(
1656 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1659 boolean appendHistoryItem = false;
1660 if (viewport.historyList != null && viewport.historyList.size() > 0
1661 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1663 appendHistoryItem = ssc
1664 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1668 if (!appendHistoryItem)
1669 addHistoryItem(ssc);
1681 protected void copy_actionPerformed(ActionEvent e)
1684 if (viewport.getSelectionGroup() == null)
1688 // TODO: preserve the ordering of displayed alignment annotation in any
1689 // internal paste (particularly sequence associated annotation)
1690 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1691 String[] omitHidden = null;
1693 if (viewport.hasHiddenColumns())
1695 omitHidden = viewport.getViewAsString(true);
1698 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1701 StringSelection ss = new StringSelection(output);
1705 jalview.gui.Desktop.internalCopy = true;
1706 // Its really worth setting the clipboard contents
1707 // to empty before setting the large StringSelection!!
1708 Toolkit.getDefaultToolkit().getSystemClipboard()
1709 .setContents(new StringSelection(""), null);
1711 Toolkit.getDefaultToolkit().getSystemClipboard()
1712 .setContents(ss, Desktop.instance);
1713 } catch (OutOfMemoryError er)
1715 new OOMWarning("copying region", er);
1719 Vector hiddenColumns = null;
1720 if (viewport.hasHiddenColumns())
1722 hiddenColumns = new Vector();
1723 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1724 .getSelectionGroup().getEndRes();
1725 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1728 int[] region = (int[]) viewport.getColumnSelection()
1729 .getHiddenColumns().elementAt(i);
1730 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1732 hiddenColumns.addElement(new int[]
1733 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1738 Desktop.jalviewClipboard = new Object[]
1739 { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1740 statusBar.setText(MessageManager.formatMessage(
1741 "label.copied_sequences_to_clipboard", new String[]
1742 { Integer.valueOf(seqs.length).toString() }));
1752 protected void pasteNew_actionPerformed(ActionEvent e)
1764 protected void pasteThis_actionPerformed(ActionEvent e)
1770 * Paste contents of Jalview clipboard
1772 * @param newAlignment
1773 * true to paste to a new alignment, otherwise add to this.
1775 void paste(boolean newAlignment)
1777 boolean externalPaste = true;
1780 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1781 Transferable contents = c.getContents(this);
1783 if (contents == null)
1791 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1792 if (str.length() < 1)
1797 format = new IdentifyFile().Identify(str, "Paste");
1799 } catch (OutOfMemoryError er)
1801 new OOMWarning("Out of memory pasting sequences!!", er);
1805 SequenceI[] sequences;
1806 boolean annotationAdded = false;
1807 AlignmentI alignment = null;
1809 if (Desktop.jalviewClipboard != null)
1811 // The clipboard was filled from within Jalview, we must use the
1813 // And dataset from the copied alignment
1814 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1815 // be doubly sure that we create *new* sequence objects.
1816 sequences = new SequenceI[newseq.length];
1817 for (int i = 0; i < newseq.length; i++)
1819 sequences[i] = new Sequence(newseq[i]);
1821 alignment = new Alignment(sequences);
1822 externalPaste = false;
1826 // parse the clipboard as an alignment.
1827 alignment = new FormatAdapter().readFile(str, "Paste", format);
1828 sequences = alignment.getSequencesArray();
1832 ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
1838 if (Desktop.jalviewClipboard != null)
1840 // dataset is inherited
1841 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1845 // new dataset is constructed
1846 alignment.setDataset(null);
1848 alwidth = alignment.getWidth() + 1;
1852 AlignmentI pastedal = alignment; // preserve pasted alignment object
1853 // Add pasted sequences and dataset into existing alignment.
1854 alignment = viewport.getAlignment();
1855 alwidth = alignment.getWidth() + 1;
1856 // decide if we need to import sequences from an existing dataset
1857 boolean importDs = Desktop.jalviewClipboard != null
1858 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1859 // importDs==true instructs us to copy over new dataset sequences from
1860 // an existing alignment
1861 Vector newDs = (importDs) ? new Vector() : null; // used to create
1862 // minimum dataset set
1864 for (int i = 0; i < sequences.length; i++)
1868 newDs.addElement(null);
1870 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1872 if (importDs && ds != null)
1874 if (!newDs.contains(ds))
1876 newDs.setElementAt(ds, i);
1877 ds = new Sequence(ds);
1878 // update with new dataset sequence
1879 sequences[i].setDatasetSequence(ds);
1883 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1888 // copy and derive new dataset sequence
1889 sequences[i] = sequences[i].deriveSequence();
1890 alignment.getDataset().addSequence(
1891 sequences[i].getDatasetSequence());
1892 // TODO: avoid creation of duplicate dataset sequences with a
1893 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1895 alignment.addSequence(sequences[i]); // merges dataset
1899 newDs.clear(); // tidy up
1901 if (alignment.getAlignmentAnnotation() != null)
1903 for (AlignmentAnnotation alan : alignment
1904 .getAlignmentAnnotation())
1906 if (alan.graphGroup > fgroup)
1908 fgroup = alan.graphGroup;
1912 if (pastedal.getAlignmentAnnotation() != null)
1914 // Add any annotation attached to alignment.
1915 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1916 for (int i = 0; i < alann.length; i++)
1918 annotationAdded = true;
1919 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1921 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1922 if (newann.graphGroup > -1)
1924 if (newGraphGroups.size() <= newann.graphGroup
1925 || newGraphGroups.get(newann.graphGroup) == null)
1927 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1929 newGraphGroups.add(q, null);
1931 newGraphGroups.set(newann.graphGroup, new Integer(
1934 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1938 newann.padAnnotation(alwidth);
1939 alignment.addAnnotation(newann);
1949 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1950 sequences, 0, alignment.getWidth(), alignment));
1952 // Add any annotations attached to sequences
1953 for (int i = 0; i < sequences.length; i++)
1955 if (sequences[i].getAnnotation() != null)
1957 AlignmentAnnotation newann;
1958 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1960 annotationAdded = true;
1961 newann = sequences[i].getAnnotation()[a];
1962 newann.adjustForAlignment();
1963 newann.padAnnotation(alwidth);
1964 if (newann.graphGroup > -1)
1966 if (newann.graphGroup > -1)
1968 if (newGraphGroups.size() <= newann.graphGroup
1969 || newGraphGroups.get(newann.graphGroup) == null)
1971 for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
1973 newGraphGroups.add(q, null);
1975 newGraphGroups.set(newann.graphGroup, new Integer(
1978 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
1982 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1987 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1994 // propagate alignment changed.
1995 viewport.setEndSeq(alignment.getHeight());
1996 if (annotationAdded)
1998 // Duplicate sequence annotation in all views.
1999 AlignmentI[] alview = this.getViewAlignments();
2000 for (int i = 0; i < sequences.length; i++)
2002 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2005 for (int avnum = 0; avnum < alview.length; avnum++)
2007 if (alview[avnum] != alignment)
2009 // duplicate in a view other than the one with input focus
2010 int avwidth = alview[avnum].getWidth() + 1;
2011 // this relies on sann being preserved after we
2012 // modify the sequence's annotation array for each duplication
2013 for (int a = 0; a < sann.length; a++)
2015 AlignmentAnnotation newann = new AlignmentAnnotation(
2017 sequences[i].addAlignmentAnnotation(newann);
2018 newann.padAnnotation(avwidth);
2019 alview[avnum].addAnnotation(newann); // annotation was
2020 // duplicated earlier
2021 // TODO JAL-1145 graphGroups are not updated for sequence
2022 // annotation added to several views. This may cause
2024 alview[avnum].setAnnotationIndex(newann, a);
2029 buildSortByAnnotationScoresMenu();
2031 viewport.firePropertyChange("alignment", null,
2032 alignment.getSequences());
2033 if (alignPanels != null)
2035 for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
2037 ap.validateAnnotationDimensions(false);
2042 alignPanel.validateAnnotationDimensions(false);
2048 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2050 String newtitle = new String("Copied sequences");
2052 if (Desktop.jalviewClipboard != null
2053 && Desktop.jalviewClipboard[2] != null)
2055 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2056 for (int i = 0; i < hc.size(); i++)
2058 int[] region = (int[]) hc.elementAt(i);
2059 af.viewport.hideColumns(region[0], region[1]);
2063 // >>>This is a fix for the moment, until a better solution is
2065 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2067 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2069 // TODO: maintain provenance of an alignment, rather than just make the
2070 // title a concatenation of operations.
2073 if (title.startsWith("Copied sequences"))
2079 newtitle = newtitle.concat("- from " + title);
2084 newtitle = new String("Pasted sequences");
2087 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2092 } catch (Exception ex)
2094 ex.printStackTrace();
2095 System.out.println("Exception whilst pasting: " + ex);
2096 // could be anything being pasted in here
2102 protected void expand_newalign(ActionEvent e)
2106 AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2107 .getAlignment(), -1);
2108 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2110 String newtitle = new String("Flanking alignment");
2112 if (Desktop.jalviewClipboard != null
2113 && Desktop.jalviewClipboard[2] != null)
2115 Vector hc = (Vector) Desktop.jalviewClipboard[2];
2116 for (int i = 0; i < hc.size(); i++)
2118 int[] region = (int[]) hc.elementAt(i);
2119 af.viewport.hideColumns(region[0], region[1]);
2123 // >>>This is a fix for the moment, until a better solution is
2125 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
2127 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
2129 // TODO: maintain provenance of an alignment, rather than just make the
2130 // title a concatenation of operations.
2132 if (title.startsWith("Copied sequences"))
2138 newtitle = newtitle.concat("- from " + title);
2142 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2144 } catch (Exception ex)
2146 ex.printStackTrace();
2147 System.out.println("Exception whilst pasting: " + ex);
2148 // could be anything being pasted in here
2149 } catch (OutOfMemoryError oom)
2151 new OOMWarning("Viewing flanking region of alignment", oom);
2162 protected void cut_actionPerformed(ActionEvent e)
2164 copy_actionPerformed(null);
2165 delete_actionPerformed(null);
2175 protected void delete_actionPerformed(ActionEvent evt)
2178 SequenceGroup sg = viewport.getSelectionGroup();
2184 List<SequenceI> seqs = new ArrayList<SequenceI>(sg.getSize());
2186 for (int i = 0; i < sg.getSize(); i++)
2188 seq = sg.getSequenceAt(i);
2192 // If the cut affects all sequences, warn, remove highlighted columns
2193 if (sg.getSize() == viewport.getAlignment().getHeight())
2195 int confirm = JOptionPane.showConfirmDialog(this,
2196 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2197 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2198 JOptionPane.OK_CANCEL_OPTION);
2200 if (confirm == JOptionPane.CANCEL_OPTION
2201 || confirm == JOptionPane.CLOSED_OPTION)
2205 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2206 sg.getEndRes() + 1);
2209 SequenceI[] cut = new SequenceI[seqs.size()];
2210 for (int i = 0; i < seqs.size(); i++)
2212 cut[i] = seqs.get(i);
2216 * //ADD HISTORY ITEM
2218 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
2219 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2220 viewport.getAlignment()));
2222 viewport.setSelectionGroup(null);
2223 viewport.sendSelection();
2224 viewport.getAlignment().deleteGroup(sg);
2226 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2228 if (viewport.getAlignment().getHeight() < 1)
2232 this.setClosed(true);
2233 } catch (Exception ex)
2246 protected void deleteGroups_actionPerformed(ActionEvent e)
2248 if (avc.deleteGroups())
2250 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2251 alignPanel.updateAnnotation();
2252 alignPanel.paintAlignment(true);
2263 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2265 SequenceGroup sg = new SequenceGroup();
2267 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2269 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2272 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2273 viewport.setSelectionGroup(sg);
2274 viewport.sendSelection();
2275 alignPanel.paintAlignment(true);
2276 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2286 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2288 if (viewport.cursorMode)
2290 alignPanel.seqPanel.keyboardNo1 = null;
2291 alignPanel.seqPanel.keyboardNo2 = null;
2293 viewport.setSelectionGroup(null);
2294 viewport.getColumnSelection().clear();
2295 viewport.setSelectionGroup(null);
2296 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2297 alignPanel.idPanel.idCanvas.searchResults = null;
2298 alignPanel.paintAlignment(true);
2299 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2300 viewport.sendSelection();
2310 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2312 SequenceGroup sg = viewport.getSelectionGroup();
2316 selectAllSequenceMenuItem_actionPerformed(null);
2321 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2323 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2326 alignPanel.paintAlignment(true);
2327 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2328 viewport.sendSelection();
2332 public void invertColSel_actionPerformed(ActionEvent e)
2334 viewport.invertColumnSelection();
2335 alignPanel.paintAlignment(true);
2336 viewport.sendSelection();
2346 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2348 trimAlignment(true);
2358 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2360 trimAlignment(false);
2363 void trimAlignment(boolean trimLeft)
2365 ColumnSelection colSel = viewport.getColumnSelection();
2368 if (colSel.size() > 0)
2372 column = colSel.getMin();
2376 column = colSel.getMax();
2380 if (viewport.getSelectionGroup() != null)
2382 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2383 viewport.getHiddenRepSequences());
2387 seqs = viewport.getAlignment().getSequencesArray();
2390 TrimRegionCommand trimRegion;
2393 trimRegion = new TrimRegionCommand("Remove Left",
2394 TrimRegionCommand.TRIM_LEFT, seqs, column,
2395 viewport.getAlignment(), viewport.getColumnSelection(),
2396 viewport.getSelectionGroup());
2397 viewport.setStartRes(0);
2401 trimRegion = new TrimRegionCommand("Remove Right",
2402 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2403 viewport.getAlignment(), viewport.getColumnSelection(),
2404 viewport.getSelectionGroup());
2407 statusBar.setText(MessageManager.formatMessage(
2408 "label.removed_columns", new String[]
2409 { Integer.valueOf(trimRegion.getSize()).toString() }));
2411 addHistoryItem(trimRegion);
2413 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2415 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2416 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2418 viewport.getAlignment().deleteGroup(sg);
2422 viewport.firePropertyChange("alignment", null, viewport
2423 .getAlignment().getSequences());
2434 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2436 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2439 if (viewport.getSelectionGroup() != null)
2441 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2442 viewport.getHiddenRepSequences());
2443 start = viewport.getSelectionGroup().getStartRes();
2444 end = viewport.getSelectionGroup().getEndRes();
2448 seqs = viewport.getAlignment().getSequencesArray();
2451 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2452 "Remove Gapped Columns", seqs, start, end,
2453 viewport.getAlignment());
2455 addHistoryItem(removeGapCols);
2457 statusBar.setText(MessageManager.formatMessage(
2458 "label.removed_empty_columns", new String[]
2459 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2461 // This is to maintain viewport position on first residue
2462 // of first sequence
2463 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2464 int startRes = seq.findPosition(viewport.startRes);
2465 // ShiftList shifts;
2466 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2467 // edit.alColumnChanges=shifts.getInverse();
2468 // if (viewport.hasHiddenColumns)
2469 // viewport.getColumnSelection().compensateForEdits(shifts);
2470 viewport.setStartRes(seq.findIndex(startRes) - 1);
2471 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2483 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2485 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2488 if (viewport.getSelectionGroup() != null)
2490 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2491 viewport.getHiddenRepSequences());
2492 start = viewport.getSelectionGroup().getStartRes();
2493 end = viewport.getSelectionGroup().getEndRes();
2497 seqs = viewport.getAlignment().getSequencesArray();
2500 // This is to maintain viewport position on first residue
2501 // of first sequence
2502 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2503 int startRes = seq.findPosition(viewport.startRes);
2505 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2506 viewport.getAlignment()));
2508 viewport.setStartRes(seq.findIndex(startRes) - 1);
2510 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2522 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2524 viewport.setPadGaps(padGapsMenuitem.isSelected());
2525 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2531 // if (justifySeqs>0)
2533 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2546 public void findMenuItem_actionPerformed(ActionEvent e)
2552 public void newView_actionPerformed(ActionEvent e)
2559 * @param copyAnnotation
2560 * if true then duplicate all annnotation, groups and settings
2561 * @return new alignment panel, already displayed.
2563 public AlignmentPanel newView(boolean copyAnnotation)
2565 return newView(null, copyAnnotation);
2571 * title of newly created view
2572 * @return new alignment panel, already displayed.
2574 public AlignmentPanel newView(String viewTitle)
2576 return newView(viewTitle, true);
2582 * title of newly created view
2583 * @param copyAnnotation
2584 * if true then duplicate all annnotation, groups and settings
2585 * @return new alignment panel, already displayed.
2587 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2589 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2591 if (!copyAnnotation)
2593 // just remove all the current annotation except for the automatic stuff
2594 newap.av.getAlignment().deleteAllGroups();
2595 for (AlignmentAnnotation alan : newap.av.getAlignment()
2596 .getAlignmentAnnotation())
2598 if (!alan.autoCalculated)
2600 newap.av.getAlignment().deleteAnnotation(alan);
2606 newap.av.gatherViewsHere = false;
2608 if (viewport.viewName == null)
2610 viewport.viewName = "Original";
2613 newap.av.historyList = viewport.historyList;
2614 newap.av.redoList = viewport.redoList;
2616 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2617 // make sure the new view has a unique name - this is essential for Jalview
2619 boolean addFirstIndex = false;
2620 if (viewTitle == null || viewTitle.trim().length() == 0)
2623 addFirstIndex = true;
2627 index = 1;// we count from 1 if given a specific name
2629 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2630 Vector comps = (Vector) PaintRefresher.components.get(viewport
2631 .getSequenceSetId());
2632 Vector existingNames = new Vector();
2633 for (int i = 0; i < comps.size(); i++)
2635 if (comps.elementAt(i) instanceof AlignmentPanel)
2637 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2638 if (!existingNames.contains(ap.av.viewName))
2640 existingNames.addElement(ap.av.viewName);
2645 while (existingNames.contains(newViewName))
2647 newViewName = viewTitle + " " + (++index);
2650 newap.av.viewName = newViewName;
2652 addAlignmentPanel(newap, true);
2653 newap.alignmentChanged();
2655 if (alignPanels.size() == 2)
2657 viewport.gatherViewsHere = true;
2659 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2664 public void expandViews_actionPerformed(ActionEvent e)
2666 Desktop.instance.explodeViews(this);
2670 public void gatherViews_actionPerformed(ActionEvent e)
2672 Desktop.instance.gatherViews(this);
2682 public void font_actionPerformed(ActionEvent e)
2684 new FontChooser(alignPanel);
2694 protected void seqLimit_actionPerformed(ActionEvent e)
2696 viewport.setShowJVSuffix(seqLimits.isSelected());
2698 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2699 .calculateIdWidth());
2700 alignPanel.paintAlignment(true);
2704 public void idRightAlign_actionPerformed(ActionEvent e)
2706 viewport.rightAlignIds = idRightAlign.isSelected();
2707 alignPanel.paintAlignment(true);
2711 public void centreColumnLabels_actionPerformed(ActionEvent e)
2713 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2714 alignPanel.paintAlignment(true);
2720 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2723 protected void followHighlight_actionPerformed()
2725 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2727 alignPanel.scrollToPosition(
2728 alignPanel.seqPanel.seqCanvas.searchResults, false);
2739 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2741 viewport.setColourText(colourTextMenuItem.isSelected());
2742 alignPanel.paintAlignment(true);
2752 public void wrapMenuItem_actionPerformed(ActionEvent e)
2754 scaleAbove.setVisible(wrapMenuItem.isSelected());
2755 scaleLeft.setVisible(wrapMenuItem.isSelected());
2756 scaleRight.setVisible(wrapMenuItem.isSelected());
2757 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2758 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2762 public void showAllSeqs_actionPerformed(ActionEvent e)
2764 viewport.showAllHiddenSeqs();
2768 public void showAllColumns_actionPerformed(ActionEvent e)
2770 viewport.showAllHiddenColumns();
2775 public void hideSelSequences_actionPerformed(ActionEvent e)
2777 viewport.hideAllSelectedSeqs();
2778 alignPanel.paintAlignment(true);
2782 * called by key handler and the hide all/show all menu items
2787 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2790 boolean hide = false;
2791 SequenceGroup sg = viewport.getSelectionGroup();
2792 if (!toggleSeqs && !toggleCols)
2794 // Hide everything by the current selection - this is a hack - we do the
2795 // invert and then hide
2796 // first check that there will be visible columns after the invert.
2797 if ((viewport.getColumnSelection() != null
2798 && viewport.getColumnSelection().getSelected() != null && viewport
2799 .getColumnSelection().getSelected().size() > 0)
2800 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2803 // now invert the sequence set, if required - empty selection implies
2804 // that no hiding is required.
2807 invertSequenceMenuItem_actionPerformed(null);
2808 sg = viewport.getSelectionGroup();
2812 viewport.expandColSelection(sg, true);
2813 // finally invert the column selection and get the new sequence
2815 invertColSel_actionPerformed(null);
2822 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2824 hideSelSequences_actionPerformed(null);
2827 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2830 showAllSeqs_actionPerformed(null);
2836 if (viewport.getColumnSelection().getSelected().size() > 0)
2838 hideSelColumns_actionPerformed(null);
2841 viewport.setSelectionGroup(sg);
2846 showAllColumns_actionPerformed(null);
2855 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2856 * event.ActionEvent)
2859 public void hideAllButSelection_actionPerformed(ActionEvent e)
2861 toggleHiddenRegions(false, false);
2868 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2872 public void hideAllSelection_actionPerformed(ActionEvent e)
2874 SequenceGroup sg = viewport.getSelectionGroup();
2875 viewport.expandColSelection(sg, false);
2876 viewport.hideAllSelectedSeqs();
2877 viewport.hideSelectedColumns();
2878 alignPanel.paintAlignment(true);
2885 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2889 public void showAllhidden_actionPerformed(ActionEvent e)
2891 viewport.showAllHiddenColumns();
2892 viewport.showAllHiddenSeqs();
2893 alignPanel.paintAlignment(true);
2897 public void hideSelColumns_actionPerformed(ActionEvent e)
2899 viewport.hideSelectedColumns();
2900 alignPanel.paintAlignment(true);
2904 public void hiddenMarkers_actionPerformed(ActionEvent e)
2906 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2917 protected void scaleAbove_actionPerformed(ActionEvent e)
2919 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2920 alignPanel.paintAlignment(true);
2930 protected void scaleLeft_actionPerformed(ActionEvent e)
2932 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2933 alignPanel.paintAlignment(true);
2943 protected void scaleRight_actionPerformed(ActionEvent e)
2945 viewport.setScaleRightWrapped(scaleRight.isSelected());
2946 alignPanel.paintAlignment(true);
2956 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2958 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2959 alignPanel.paintAlignment(true);
2969 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2971 viewport.setShowText(viewTextMenuItem.isSelected());
2972 alignPanel.paintAlignment(true);
2982 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2984 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2985 alignPanel.paintAlignment(true);
2988 public FeatureSettings featureSettings;
2991 public void featureSettings_actionPerformed(ActionEvent e)
2993 if (featureSettings != null)
2995 featureSettings.close();
2996 featureSettings = null;
2998 if (!showSeqFeatures.isSelected())
3000 // make sure features are actually displayed
3001 showSeqFeatures.setSelected(true);
3002 showSeqFeatures_actionPerformed(null);
3004 featureSettings = new FeatureSettings(this);
3008 * Set or clear 'Show Sequence Features'
3014 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3016 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3017 alignPanel.paintAlignment(true);
3018 if (alignPanel.getOverviewPanel() != null)
3020 alignPanel.getOverviewPanel().updateOverviewImage();
3025 * Set or clear 'Show Sequence Features'
3031 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
3033 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
3035 if (viewport.getShowSequenceFeaturesHeight())
3037 // ensure we're actually displaying features
3038 viewport.setShowSequenceFeatures(true);
3039 showSeqFeatures.setSelected(true);
3041 alignPanel.paintAlignment(true);
3042 if (alignPanel.getOverviewPanel() != null)
3044 alignPanel.getOverviewPanel().updateOverviewImage();
3049 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3050 * the annotations panel as a whole.
3052 * The options to show/hide all annotations should be enabled when the panel
3053 * is shown, and disabled when the panel is hidden.
3058 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3060 final boolean setVisible = annotationPanelMenuItem.isSelected();
3061 viewport.setShowAnnotation(setVisible);
3062 alignPanel.setAnnotationVisible(setVisible);
3063 this.showAllAnnotations.setEnabled(setVisible);
3064 this.hideAllAnnotations.setEnabled(setVisible);
3068 public void alignmentProperties()
3070 JEditorPane editPane = new JEditorPane("text/html", "");
3071 editPane.setEditable(false);
3072 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3074 editPane.setText(MessageManager.formatMessage("label.html_content",
3076 { contents.toString() }));
3077 JInternalFrame frame = new JInternalFrame();
3078 frame.getContentPane().add(new JScrollPane(editPane));
3080 Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage(
3081 "label.alignment_properties", new String[]
3082 { getTitle() }), 500, 400);
3092 public void overviewMenuItem_actionPerformed(ActionEvent e)
3094 if (alignPanel.overviewPanel != null)
3099 JInternalFrame frame = new JInternalFrame();
3100 OverviewPanel overview = new OverviewPanel(alignPanel);
3101 frame.setContentPane(overview);
3102 Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3103 "label.overview_params", new String[]
3104 { this.getTitle() }), frame.getWidth(), frame.getHeight());
3106 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3107 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3110 public void internalFrameClosed(
3111 javax.swing.event.InternalFrameEvent evt)
3113 alignPanel.setOverviewPanel(null);
3117 alignPanel.setOverviewPanel(overview);
3121 public void textColour_actionPerformed(ActionEvent e)
3123 new TextColourChooser().chooseColour(alignPanel, null);
3133 protected void noColourmenuItem_actionPerformed(ActionEvent e)
3145 public void clustalColour_actionPerformed(ActionEvent e)
3147 changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3148 viewport.getHiddenRepSequences()));
3158 public void zappoColour_actionPerformed(ActionEvent e)
3160 changeColour(new ZappoColourScheme());
3170 public void taylorColour_actionPerformed(ActionEvent e)
3172 changeColour(new TaylorColourScheme());
3182 public void hydrophobicityColour_actionPerformed(ActionEvent e)
3184 changeColour(new HydrophobicColourScheme());
3194 public void helixColour_actionPerformed(ActionEvent e)
3196 changeColour(new HelixColourScheme());
3206 public void strandColour_actionPerformed(ActionEvent e)
3208 changeColour(new StrandColourScheme());
3218 public void turnColour_actionPerformed(ActionEvent e)
3220 changeColour(new TurnColourScheme());
3230 public void buriedColour_actionPerformed(ActionEvent e)
3232 changeColour(new BuriedColourScheme());
3242 public void nucleotideColour_actionPerformed(ActionEvent e)
3244 changeColour(new NucleotideColourScheme());
3248 public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3250 changeColour(new PurinePyrimidineColourScheme());
3254 * public void covariationColour_actionPerformed(ActionEvent e) {
3256 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3260 public void annotationColour_actionPerformed(ActionEvent e)
3262 new AnnotationColourChooser(viewport, alignPanel);
3266 public void rnahelicesColour_actionPerformed(ActionEvent e)
3268 new RNAHelicesColourChooser(viewport, alignPanel);
3278 protected void applyToAllGroups_actionPerformed(ActionEvent e)
3280 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3289 public void changeColour(ColourSchemeI cs)
3291 // TODO: compare with applet and pull up to model method
3296 if (viewport.getAbovePIDThreshold())
3298 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3300 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3304 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3307 if (viewport.getConservationSelected())
3310 Alignment al = (Alignment) viewport.getAlignment();
3311 Conservation c = new Conservation("All",
3312 ResidueProperties.propHash, 3, al.getSequences(), 0,
3316 c.verdict(false, viewport.getConsPercGaps());
3318 cs.setConservation(c);
3320 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3325 cs.setConservation(null);
3328 cs.setConsensus(viewport.getSequenceConsensusHash());
3331 viewport.setGlobalColourScheme(cs);
3333 if (viewport.getColourAppliesToAllGroups())
3336 for (SequenceGroup sg : viewport.getAlignment().getGroups())
3344 if (cs instanceof ClustalxColourScheme)
3346 sg.cs = new ClustalxColourScheme(sg,
3347 viewport.getHiddenRepSequences());
3349 else if (cs instanceof UserColourScheme)
3351 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3357 sg.cs = cs.getClass().newInstance();
3358 } catch (Exception ex)
3363 if (viewport.getAbovePIDThreshold()
3364 || cs instanceof PIDColourScheme
3365 || cs instanceof Blosum62ColourScheme)
3367 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3369 sg.cs.setConsensus(AAFrequency.calculate(
3370 sg.getSequences(viewport.getHiddenRepSequences()),
3371 sg.getStartRes(), sg.getEndRes() + 1));
3375 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3378 if (viewport.getConservationSelected())
3380 Conservation c = new Conservation("Group",
3381 ResidueProperties.propHash, 3, sg.getSequences(viewport
3382 .getHiddenRepSequences()), sg.getStartRes(),
3383 sg.getEndRes() + 1);
3385 c.verdict(false, viewport.getConsPercGaps());
3386 sg.cs.setConservation(c);
3390 sg.cs.setConservation(null);
3395 if (alignPanel.getOverviewPanel() != null)
3397 alignPanel.getOverviewPanel().updateOverviewImage();
3400 alignPanel.paintAlignment(true);
3410 protected void modifyPID_actionPerformed(ActionEvent e)
3412 if (viewport.getAbovePIDThreshold()
3413 && viewport.getGlobalColourScheme() != null)
3415 SliderPanel.setPIDSliderSource(alignPanel,
3416 viewport.getGlobalColourScheme(), "Background");
3417 SliderPanel.showPIDSlider();
3428 protected void modifyConservation_actionPerformed(ActionEvent e)
3430 if (viewport.getConservationSelected()
3431 && viewport.getGlobalColourScheme() != null)
3433 SliderPanel.setConservationSlider(alignPanel,
3434 viewport.getGlobalColourScheme(), "Background");
3435 SliderPanel.showConservationSlider();
3446 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3448 viewport.setConservationSelected(conservationMenuItem.isSelected());
3450 viewport.setAbovePIDThreshold(false);
3451 abovePIDThreshold.setSelected(false);
3453 changeColour(viewport.getGlobalColourScheme());
3455 modifyConservation_actionPerformed(null);
3465 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3467 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3469 conservationMenuItem.setSelected(false);
3470 viewport.setConservationSelected(false);
3472 changeColour(viewport.getGlobalColourScheme());
3474 modifyPID_actionPerformed(null);
3484 public void userDefinedColour_actionPerformed(ActionEvent e)
3486 if (e.getActionCommand().equals(
3487 MessageManager.getString("action.user_defined")))
3489 new UserDefinedColours(alignPanel, null);
3493 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3494 .getUserColourSchemes().get(e.getActionCommand());
3500 public void updateUserColourMenu()
3503 Component[] menuItems = colourMenu.getMenuComponents();
3504 int i, iSize = menuItems.length;
3505 for (i = 0; i < iSize; i++)
3507 if (menuItems[i].getName() != null
3508 && menuItems[i].getName().equals("USER_DEFINED"))
3510 colourMenu.remove(menuItems[i]);
3514 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3516 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3517 .getUserColourSchemes().keys();
3519 while (userColours.hasMoreElements())
3521 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3522 userColours.nextElement().toString());
3523 radioItem.setName("USER_DEFINED");
3524 radioItem.addMouseListener(new MouseAdapter()
3527 public void mousePressed(MouseEvent evt)
3529 if (evt.isControlDown()
3530 || SwingUtilities.isRightMouseButton(evt))
3532 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3534 int option = JOptionPane.showInternalConfirmDialog(
3535 jalview.gui.Desktop.desktop,
3537 .getString("label.remove_from_default_list"),
3539 .getString("label.remove_user_defined_colour"),
3540 JOptionPane.YES_NO_OPTION);
3541 if (option == JOptionPane.YES_OPTION)
3543 jalview.gui.UserDefinedColours
3544 .removeColourFromDefaults(radioItem.getText());
3545 colourMenu.remove(radioItem);
3549 radioItem.addActionListener(new ActionListener()
3552 public void actionPerformed(ActionEvent evt)
3554 userDefinedColour_actionPerformed(evt);
3561 radioItem.addActionListener(new ActionListener()
3564 public void actionPerformed(ActionEvent evt)
3566 userDefinedColour_actionPerformed(evt);
3570 colourMenu.insert(radioItem, 15);
3571 colours.add(radioItem);
3583 public void PIDColour_actionPerformed(ActionEvent e)
3585 changeColour(new PIDColourScheme());
3595 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3597 changeColour(new Blosum62ColourScheme());
3607 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3609 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3610 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3611 .getAlignment().getSequenceAt(0), null);
3612 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3613 viewport.getAlignment()));
3614 alignPanel.paintAlignment(true);
3624 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3626 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3627 AlignmentSorter.sortByID(viewport.getAlignment());
3628 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3629 viewport.getAlignment()));
3630 alignPanel.paintAlignment(true);
3640 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3642 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3643 AlignmentSorter.sortByLength(viewport.getAlignment());
3644 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3645 viewport.getAlignment()));
3646 alignPanel.paintAlignment(true);
3656 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3658 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3659 AlignmentSorter.sortByGroup(viewport.getAlignment());
3660 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3661 viewport.getAlignment()));
3663 alignPanel.paintAlignment(true);
3673 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3675 new RedundancyPanel(alignPanel, this);
3685 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3687 if ((viewport.getSelectionGroup() == null)
3688 || (viewport.getSelectionGroup().getSize() < 2))
3690 JOptionPane.showInternalMessageDialog(this, MessageManager
3691 .getString("label.you_must_select_least_two_sequences"),
3692 MessageManager.getString("label.invalid_selection"),
3693 JOptionPane.WARNING_MESSAGE);
3697 JInternalFrame frame = new JInternalFrame();
3698 frame.setContentPane(new PairwiseAlignPanel(viewport));
3699 Desktop.addInternalFrame(frame,
3700 MessageManager.getString("action.pairwise_alignment"), 600,
3712 public void PCAMenuItem_actionPerformed(ActionEvent e)
3714 if (((viewport.getSelectionGroup() != null)
3715 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3716 .getSelectionGroup().getSize() > 0))
3717 || (viewport.getAlignment().getHeight() < 4))
3720 .showInternalMessageDialog(
3723 .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3725 .getString("label.sequence_selection_insufficient"),
3726 JOptionPane.WARNING_MESSAGE);
3731 new PCAPanel(alignPanel);
3735 public void autoCalculate_actionPerformed(ActionEvent e)
3737 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3738 if (viewport.autoCalculateConsensus)
3740 viewport.firePropertyChange("alignment", null, viewport
3741 .getAlignment().getSequences());
3746 public void sortByTreeOption_actionPerformed(ActionEvent e)
3748 viewport.sortByTree = sortByTree.isSelected();
3752 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3754 viewport.followSelection = listenToViewSelections.isSelected();
3764 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3766 NewTreePanel("AV", "PID", "Average distance tree using PID");
3776 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3778 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3788 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3790 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3800 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3802 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3815 void NewTreePanel(String type, String pwType, String title)
3819 if (viewport.getSelectionGroup() != null
3820 && viewport.getSelectionGroup().getSize() > 0)
3822 if (viewport.getSelectionGroup().getSize() < 3)
3828 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3830 .getString("label.not_enough_sequences"),
3831 JOptionPane.WARNING_MESSAGE);
3835 SequenceGroup sg = viewport.getSelectionGroup();
3837 /* Decide if the selection is a column region */
3838 for (SequenceI _s : sg.getSequences())
3840 if (_s.getLength() < sg.getEndRes())
3846 .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3848 .getString("label.sequences_selection_not_aligned"),
3849 JOptionPane.WARNING_MESSAGE);
3855 title = title + " on region";
3856 tp = new TreePanel(alignPanel, type, pwType);
3860 // are the visible sequences aligned?
3861 if (!viewport.getAlignment().isAligned(false))
3867 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3869 .getString("label.sequences_not_aligned"),
3870 JOptionPane.WARNING_MESSAGE);
3875 if (viewport.getAlignment().getHeight() < 2)
3880 tp = new TreePanel(alignPanel, type, pwType);
3885 if (viewport.viewName != null)
3887 title += viewport.viewName + " of ";
3890 title += this.title;
3892 Desktop.addInternalFrame(tp, title, 600, 500);
3903 public void addSortByOrderMenuItem(String title,
3904 final AlignmentOrder order)
3906 final JMenuItem item = new JMenuItem("by " + title);
3908 item.addActionListener(new java.awt.event.ActionListener()
3911 public void actionPerformed(ActionEvent e)
3913 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3915 // TODO: JBPNote - have to map order entries to curent SequenceI
3917 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3919 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3922 alignPanel.paintAlignment(true);
3928 * Add a new sort by annotation score menu item
3931 * the menu to add the option to
3933 * the label used to retrieve scores for each sequence on the
3936 public void addSortByAnnotScoreMenuItem(JMenu sort,
3937 final String scoreLabel)
3939 final JMenuItem item = new JMenuItem(scoreLabel);
3941 item.addActionListener(new java.awt.event.ActionListener()
3944 public void actionPerformed(ActionEvent e)
3946 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3947 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3948 viewport.getAlignment());// ,viewport.getSelectionGroup());
3949 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3950 viewport.getAlignment()));
3951 alignPanel.paintAlignment(true);
3957 * last hash for alignment's annotation array - used to minimise cost of
3960 protected int _annotationScoreVectorHash;
3963 * search the alignment and rebuild the sort by annotation score submenu the
3964 * last alignment annotation vector hash is stored to minimize cost of
3965 * rebuilding in subsequence calls.
3969 public void buildSortByAnnotationScoresMenu()
3971 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3976 if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3978 sortByAnnotScore.removeAll();
3979 // almost certainly a quicker way to do this - but we keep it simple
3980 Hashtable scoreSorts = new Hashtable();
3981 AlignmentAnnotation aann[];
3982 for (SequenceI sqa : viewport.getAlignment().getSequences())
3984 aann = sqa.getAnnotation();
3985 for (int i = 0; aann != null && i < aann.length; i++)
3987 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3989 scoreSorts.put(aann[i].label, aann[i].label);
3993 Enumeration labels = scoreSorts.keys();
3994 while (labels.hasMoreElements())
3996 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3997 (String) labels.nextElement());
3999 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4002 _annotationScoreVectorHash = viewport.getAlignment()
4003 .getAlignmentAnnotation().hashCode();
4008 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4009 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4010 * call. Listeners are added to remove the menu item when the treePanel is
4011 * closed, and adjust the tree leaf to sequence mapping when the alignment is
4015 * Displayed tree window.
4017 * SortBy menu item title.
4020 public void buildTreeMenu()
4022 calculateTree.removeAll();
4023 // build the calculate menu
4025 for (final String type : new String[]
4028 String treecalcnm = MessageManager.getString("label.tree_calc_"
4029 + type.toLowerCase());
4030 for (final Object pwtype : ResidueProperties.scoreMatrices.keySet())
4032 JMenuItem tm = new JMenuItem();
4033 ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4034 if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
4036 String smn = MessageManager.getStringOrReturn(
4037 "label.score_model_", sm.getName());
4038 final String title = MessageManager.formatMessage(
4039 "label.treecalc_title", treecalcnm, smn);
4040 tm.setText(title);//
4041 tm.addActionListener(new java.awt.event.ActionListener()
4044 public void actionPerformed(ActionEvent e)
4046 NewTreePanel(type, (String) pwtype, title);
4049 calculateTree.add(tm);
4054 sortByTreeMenu.removeAll();
4056 Vector comps = (Vector) PaintRefresher.components.get(viewport
4057 .getSequenceSetId());
4058 Vector treePanels = new Vector();
4059 int i, iSize = comps.size();
4060 for (i = 0; i < iSize; i++)
4062 if (comps.elementAt(i) instanceof TreePanel)
4064 treePanels.add(comps.elementAt(i));
4068 iSize = treePanels.size();
4072 sortByTreeMenu.setVisible(false);
4076 sortByTreeMenu.setVisible(true);
4078 for (i = 0; i < treePanels.size(); i++)
4080 final TreePanel tp = (TreePanel) treePanels.elementAt(i);
4081 final JMenuItem item = new JMenuItem(tp.getTitle());
4082 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
4083 item.addActionListener(new java.awt.event.ActionListener()
4086 public void actionPerformed(ActionEvent e)
4088 tp.sortByTree_actionPerformed(null);
4089 addHistoryItem(tp.sortAlignmentIn(alignPanel));
4094 sortByTreeMenu.add(item);
4098 public boolean sortBy(AlignmentOrder alorder, String undoname)
4100 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4101 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4102 if (undoname != null)
4104 addHistoryItem(new OrderCommand(undoname, oldOrder,
4105 viewport.getAlignment()));
4107 alignPanel.paintAlignment(true);
4112 * Work out whether the whole set of sequences or just the selected set will
4113 * be submitted for multiple alignment.
4116 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4118 // Now, check we have enough sequences
4119 AlignmentView msa = null;
4121 if ((viewport.getSelectionGroup() != null)
4122 && (viewport.getSelectionGroup().getSize() > 1))
4124 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4125 // some common interface!
4127 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4128 * SequenceI[sz = seqs.getSize(false)];
4130 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4131 * seqs.getSequenceAt(i); }
4133 msa = viewport.getAlignmentView(true);
4138 * Vector seqs = viewport.getAlignment().getSequences();
4140 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
4142 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
4143 * seqs.elementAt(i); } }
4145 msa = viewport.getAlignmentView(false);
4151 * Decides what is submitted to a secondary structure prediction service: the
4152 * first sequence in the alignment, or in the current selection, or, if the
4153 * alignment is 'aligned' (ie padded with gaps), then the currently selected
4154 * region or the whole alignment. (where the first sequence in the set is the
4155 * one that the prediction will be for).
4157 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4159 AlignmentView seqs = null;
4161 if ((viewport.getSelectionGroup() != null)
4162 && (viewport.getSelectionGroup().getSize() > 0))
4164 seqs = viewport.getAlignmentView(true);
4168 seqs = viewport.getAlignmentView(false);
4170 // limit sequences - JBPNote in future - could spawn multiple prediction
4172 // TODO: viewport.getAlignment().isAligned is a global state - the local
4173 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4174 if (!viewport.getAlignment().isAligned(false))
4176 seqs.setSequences(new SeqCigar[]
4177 { seqs.getSequences()[0] });
4178 // TODO: if seqs.getSequences().length>1 then should really have warned
4192 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
4194 // Pick the tree file
4195 JalviewFileChooser chooser = new JalviewFileChooser(
4196 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4197 chooser.setFileView(new JalviewFileView());
4198 chooser.setDialogTitle(MessageManager
4199 .getString("label.select_newick_like_tree_file"));
4200 chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4202 int value = chooser.showOpenDialog(null);
4204 if (value == JalviewFileChooser.APPROVE_OPTION)
4206 String choice = chooser.getSelectedFile().getPath();
4207 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4208 jalview.io.NewickFile fin = null;
4211 fin = new jalview.io.NewickFile(choice, "File");
4212 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4213 } catch (Exception ex)
4220 .getString("label.problem_reading_tree_file"),
4221 JOptionPane.WARNING_MESSAGE);
4222 ex.printStackTrace();
4224 if (fin != null && fin.hasWarningMessage())
4226 JOptionPane.showMessageDialog(Desktop.desktop, fin
4227 .getWarningMessage(), MessageManager
4228 .getString("label.possible_problem_with_tree_file"),
4229 JOptionPane.WARNING_MESSAGE);
4235 protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4237 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4240 public TreePanel ShowNewickTree(NewickFile nf, String title)
4242 return ShowNewickTree(nf, title, 600, 500, 4, 5);
4245 public TreePanel ShowNewickTree(NewickFile nf, String title,
4246 AlignmentView input)
4248 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4251 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4252 int h, int x, int y)
4254 return ShowNewickTree(nf, title, null, w, h, x, y);
4258 * Add a treeviewer for the tree extracted from a newick file object to the
4259 * current alignment view
4266 * Associated alignment input data (or null)
4275 * @return TreePanel handle
4277 public TreePanel ShowNewickTree(NewickFile nf, String title,
4278 AlignmentView input, int w, int h, int x, int y)
4280 TreePanel tp = null;
4286 if (nf.getTree() != null)
4288 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4294 tp.setLocation(x, y);
4297 Desktop.addInternalFrame(tp, title, w, h);
4299 } catch (Exception ex)
4301 ex.printStackTrace();
4307 private boolean buildingMenu = false;
4310 * Generates menu items and listener event actions for web service clients
4313 public void BuildWebServiceMenu()
4315 while (buildingMenu)
4319 System.err.println("Waiting for building menu to finish.");
4321 } catch (Exception e)
4326 final AlignFrame me = this;
4327 buildingMenu = true;
4328 new Thread(new Runnable()
4333 final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4336 System.err.println("Building ws menu again "
4337 + Thread.currentThread());
4338 // TODO: add support for context dependent disabling of services based
4340 // alignment and current selection
4341 // TODO: add additional serviceHandle parameter to specify abstract
4343 // class independently of AbstractName
4344 // TODO: add in rediscovery GUI function to restart discoverer
4345 // TODO: group services by location as well as function and/or
4347 // object broker mechanism.
4348 final Vector<JMenu> wsmenu = new Vector<JMenu>();
4349 final IProgressIndicator af = me;
4350 final JMenu msawsmenu = new JMenu("Alignment");
4351 final JMenu secstrmenu = new JMenu(
4352 "Secondary Structure Prediction");
4353 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4354 final JMenu analymenu = new JMenu("Analysis");
4355 final JMenu dismenu = new JMenu("Protein Disorder");
4356 // JAL-940 - only show secondary structure prediction services from
4357 // the legacy server
4358 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4360 Discoverer.services != null && (Discoverer.services.size() > 0))
4362 // TODO: refactor to allow list of AbstractName/Handler bindings to
4364 // stored or retrieved from elsewhere
4365 // No MSAWS used any more:
4366 // Vector msaws = null; // (Vector)
4367 // Discoverer.services.get("MsaWS");
4368 Vector secstrpr = (Vector) Discoverer.services
4370 if (secstrpr != null)
4372 // Add any secondary structure prediction services
4373 for (int i = 0, j = secstrpr.size(); i < j; i++)
4375 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4377 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4378 .getServiceClient(sh);
4379 int p = secstrmenu.getItemCount();
4380 impl.attachWSMenuEntry(secstrmenu, me);
4381 int q = secstrmenu.getItemCount();
4382 for (int litm = p; litm < q; litm++)
4384 legacyItems.add(secstrmenu.getItem(litm));
4390 // Add all submenus in the order they should appear on the web
4392 wsmenu.add(msawsmenu);
4393 wsmenu.add(secstrmenu);
4394 wsmenu.add(dismenu);
4395 wsmenu.add(analymenu);
4396 // No search services yet
4397 // wsmenu.add(seqsrchmenu);
4399 javax.swing.SwingUtilities.invokeLater(new Runnable()
4406 webService.removeAll();
4407 // first, add discovered services onto the webservices menu
4408 if (wsmenu.size() > 0)
4410 for (int i = 0, j = wsmenu.size(); i < j; i++)
4412 webService.add(wsmenu.get(i));
4417 webService.add(me.webServiceNoServices);
4419 // TODO: move into separate menu builder class.
4420 boolean new_sspred = false;
4421 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4423 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4424 if (jws2servs != null)
4426 if (jws2servs.hasServices())
4428 jws2servs.attachWSMenuEntry(webService, me);
4429 for (Jws2Instance sv : jws2servs.getServices())
4431 if (sv.description.toLowerCase().contains("jpred"))
4433 for (JMenuItem jmi : legacyItems)
4435 jmi.setVisible(false);
4441 if (jws2servs.isRunning())
4443 JMenuItem tm = new JMenuItem(
4444 "Still discovering JABA Services");
4445 tm.setEnabled(false);
4450 build_urlServiceMenu(me.webService);
4451 build_fetchdbmenu(webService);
4452 for (JMenu item : wsmenu)
4454 if (item.getItemCount() == 0)
4456 item.setEnabled(false);
4460 item.setEnabled(true);
4463 } catch (Exception e)
4466 .debug("Exception during web service menu building process.",
4472 } catch (Exception e)
4477 buildingMenu = false;
4484 * construct any groupURL type service menu entries.
4488 private void build_urlServiceMenu(JMenu webService)
4490 // TODO: remove this code when 2.7 is released
4491 // DEBUG - alignmentView
4493 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4494 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4496 * @Override public void actionPerformed(ActionEvent e) {
4497 * jalview.datamodel.AlignmentView
4498 * .testSelectionViews(af.viewport.getAlignment(),
4499 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4501 * }); webService.add(testAlView);
4503 // TODO: refactor to RestClient discoverer and merge menu entries for
4504 // rest-style services with other types of analysis/calculation service
4505 // SHmmr test client - still being implemented.
4506 // DEBUG - alignmentView
4508 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4511 client.attachWSMenuEntry(
4512 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4518 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4519 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4520 * getProperty("LAST_DIRECTORY"));
4522 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4523 * to Vamsas file"); chooser.setToolTipText("Export");
4525 * int value = chooser.showSaveDialog(this);
4527 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4528 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4529 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4530 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4533 * prototype of an automatically enabled/disabled analysis function
4536 protected void setShowProductsEnabled()
4538 SequenceI[] selection = viewport.getSequenceSelection();
4539 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4540 viewport.getAlignment().getDataset()))
4542 showProducts.setEnabled(true);
4547 showProducts.setEnabled(false);
4552 * search selection for sequence xRef products and build the show products
4557 * @return true if showProducts menu should be enabled.
4559 public boolean canShowProducts(SequenceI[] selection,
4560 boolean isRegionSelection, Alignment dataset)
4562 boolean showp = false;
4565 showProducts.removeAll();
4566 final boolean dna = viewport.getAlignment().isNucleotide();
4567 final Alignment ds = dataset;
4568 String[] ptypes = (selection == null || selection.length == 0) ? null
4569 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4571 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4572 // selection, dataset, true);
4573 final SequenceI[] sel = selection;
4574 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4577 final boolean isRegSel = isRegionSelection;
4578 final AlignFrame af = this;
4579 final String source = ptypes[t];
4580 JMenuItem xtype = new JMenuItem(ptypes[t]);
4581 xtype.addActionListener(new ActionListener()
4585 public void actionPerformed(ActionEvent e)
4587 // TODO: new thread for this call with vis-delay
4588 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4589 isRegSel, dna, source);
4593 showProducts.add(xtype);
4595 showProducts.setVisible(showp);
4596 showProducts.setEnabled(showp);
4597 } catch (Exception e)
4599 jalview.bin.Cache.log
4600 .warn("canTranslate threw an exception - please report to help@jalview.org",
4607 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4608 boolean isRegSel, boolean dna, String source)
4610 final boolean fisRegSel = isRegSel;
4611 final boolean fdna = dna;
4612 final String fsrc = source;
4613 final AlignFrame ths = this;
4614 final SequenceI[] fsel = sel;
4615 Runnable foo = new Runnable()
4621 final long sttime = System.currentTimeMillis();
4622 ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4625 Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4629 Alignment prods = CrossRef
4630 .findXrefSequences(fsel, fdna, fsrc, ds);
4633 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4634 for (int s = 0; s < sprods.length; s++)
4636 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4637 if (ds.getSequences() == null
4638 || !ds.getSequences().contains(
4639 sprods[s].getDatasetSequence()))
4640 ds.addSequence(sprods[s].getDatasetSequence());
4641 sprods[s].updatePDBIds();
4643 Alignment al = new Alignment(sprods);
4644 AlignedCodonFrame[] cf = prods.getCodonFrames();
4646 for (int s = 0; cf != null && s < cf.length; s++)
4648 al.addCodonFrame(cf[s]);
4651 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4653 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4654 + " for " + ((fisRegSel) ? "selected region of " : "")
4656 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4661 System.err.println("No Sequences generated for xRef type "
4664 } catch (Exception e)
4666 jalview.bin.Cache.log.error(
4667 "Exception when finding crossreferences", e);
4668 } catch (OutOfMemoryError e)
4670 new OOMWarning("whilst fetching crossreferences", e);
4673 jalview.bin.Cache.log.error("Error when finding crossreferences",
4676 ths.setProgressBar("Finished searching for sequences from " + fsrc,
4681 Thread frunner = new Thread(foo);
4685 public boolean canShowTranslationProducts(SequenceI[] selection,
4686 AlignmentI alignment)
4691 return (jalview.analysis.Dna.canTranslate(selection,
4692 viewport.getViewAsVisibleContigs(true)));
4693 } catch (Exception e)
4695 jalview.bin.Cache.log
4696 .warn("canTranslate threw an exception - please report to help@jalview.org",
4703 public void showProducts_actionPerformed(ActionEvent e)
4705 // /////////////////////////////
4706 // Collect Data to be translated/transferred
4708 SequenceI[] selection = viewport.getSequenceSelection();
4709 AlignmentI al = null;
4712 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4713 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4714 viewport.getAlignment().getDataset());
4715 } catch (Exception ex)
4718 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4726 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4727 MessageManager.getString("label.translation_failed"),
4728 JOptionPane.WARNING_MESSAGE);
4732 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4733 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4734 "label.translation_of_params", new String[]
4735 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4740 public void showTranslation_actionPerformed(ActionEvent e)
4742 // /////////////////////////////
4743 // Collect Data to be translated/transferred
4745 SequenceI[] selection = viewport.getSequenceSelection();
4746 String[] seqstring = viewport.getViewAsString(true);
4747 AlignmentI al = null;
4750 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4751 viewport.getViewAsVisibleContigs(true), viewport
4752 .getGapCharacter(), viewport.getAlignment()
4753 .getAlignmentAnnotation(), viewport.getAlignment()
4754 .getWidth(), viewport.getAlignment().getDataset());
4755 } catch (Exception ex)
4758 jalview.bin.Cache.log.error(
4759 "Exception during translation. Please report this !", ex);
4764 .getString("label.error_when_translating_sequences_submit_bug_report"),
4766 .getString("label.implementation_error")
4768 .getString("translation_failed"),
4769 JOptionPane.ERROR_MESSAGE);
4778 .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
4779 MessageManager.getString("label.translation_failed"),
4780 JOptionPane.WARNING_MESSAGE);
4784 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4785 Desktop.addInternalFrame(af, MessageManager.formatMessage(
4786 "label.translation_of_params", new String[]
4787 { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
4792 * Try to load a features file onto the alignment.
4795 * contents or path to retrieve file
4797 * access mode of file (see jalview.io.AlignFile)
4798 * @return true if features file was parsed corectly.
4800 public boolean parseFeaturesFile(String file, String type)
4802 boolean featuresFile = false;
4805 featuresFile = new FeaturesFile(file, type).parse(viewport
4806 .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4807 .getFeatureRenderer().featureColours, false,
4808 jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4809 } catch (Exception ex)
4811 ex.printStackTrace();
4816 viewport.showSequenceFeatures = true;
4817 showSeqFeatures.setSelected(true);
4818 if (alignPanel.seqPanel.seqCanvas.fr != null)
4820 // update the min/max ranges where necessary
4821 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4823 if (featureSettings != null)
4825 featureSettings.setTableData();
4827 alignPanel.paintAlignment(true);
4830 return featuresFile;
4834 public void dragEnter(DropTargetDragEvent evt)
4839 public void dragExit(DropTargetEvent evt)
4844 public void dragOver(DropTargetDragEvent evt)
4849 public void dropActionChanged(DropTargetDragEvent evt)
4854 public void drop(DropTargetDropEvent evt)
4856 Transferable t = evt.getTransferable();
4857 java.util.List files = null;
4861 DataFlavor uriListFlavor = new DataFlavor(
4862 "text/uri-list;class=java.lang.String");
4863 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4865 // Works on Windows and MacOSX
4866 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4867 files = (java.util.List) t
4868 .getTransferData(DataFlavor.javaFileListFlavor);
4870 else if (t.isDataFlavorSupported(uriListFlavor))
4872 // This is used by Unix drag system
4873 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4874 String data = (String) t.getTransferData(uriListFlavor);
4875 files = new java.util.ArrayList(1);
4876 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4877 data, "\r\n"); st.hasMoreTokens();)
4879 String s = st.nextToken();
4880 if (s.startsWith("#"))
4882 // the line is a comment (as per the RFC 2483)
4886 java.net.URI uri = new java.net.URI(s);
4887 // check to see if we can handle this kind of URI
4888 if (uri.getScheme().toLowerCase().startsWith("http"))
4890 files.add(uri.toString());
4894 // otherwise preserve old behaviour: catch all for file objects
4895 java.io.File file = new java.io.File(uri);
4896 files.add(file.toString());
4900 } catch (Exception e)
4902 e.printStackTrace();
4908 // check to see if any of these files have names matching sequences in
4910 SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4911 .getAlignment().getSequencesArray());
4913 * Object[] { String,SequenceI}
4915 ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4916 ArrayList<String> filesnotmatched = new ArrayList<String>();
4917 for (int i = 0; i < files.size(); i++)
4919 String file = files.get(i).toString();
4921 String protocol = FormatAdapter.checkProtocol(file);
4922 if (protocol == jalview.io.FormatAdapter.FILE)
4924 File fl = new File(file);
4925 pdbfn = fl.getName();
4927 else if (protocol == jalview.io.FormatAdapter.URL)
4929 URL url = new URL(file);
4930 pdbfn = url.getFile();
4932 if (pdbfn.length() > 0)
4934 // attempt to find a match in the alignment
4935 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4936 int l = 0, c = pdbfn.indexOf(".");
4937 while (mtch == null && c != -1)
4942 } while ((c = pdbfn.indexOf(".", l)) > l);
4945 pdbfn = pdbfn.substring(0, l);
4947 mtch = idm.findAllIdMatches(pdbfn);
4954 type = new IdentifyFile().Identify(file, protocol);
4955 } catch (Exception ex)
4961 if (type.equalsIgnoreCase("PDB"))
4963 filesmatched.add(new Object[]
4964 { file, protocol, mtch });
4969 // File wasn't named like one of the sequences or wasn't a PDB file.
4970 filesnotmatched.add(file);
4974 if (filesmatched.size() > 0)
4976 if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4982 "label.automatically_associate_pdb_files_with_sequences_same_name",
4989 .getString("label.automatically_associate_pdb_files_by_name"),
4990 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4993 for (Object[] fm : filesmatched)
4995 // try and associate
4996 // TODO: may want to set a standard ID naming formalism for
4997 // associating PDB files which have no IDs.
4998 for (SequenceI toassoc : (SequenceI[]) fm[2])
5000 PDBEntry pe = new AssociatePdbFileWithSeq()
5001 .associatePdbWithSeq((String) fm[0],
5002 (String) fm[1], toassoc, false);
5005 System.err.println("Associated file : "
5006 + ((String) fm[0]) + " with "
5007 + toassoc.getDisplayId(true));
5011 alignPanel.paintAlignment(true);
5015 if (filesnotmatched.size() > 0)
5018 && (Cache.getDefault(
5019 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
5024 "label.ignore_unmatched_dropped_files_info",
5031 .getString("label.ignore_unmatched_dropped_files"),
5032 JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
5036 for (String fn : filesnotmatched)
5038 loadJalviewDataFile(fn, null, null, null);
5042 } catch (Exception ex)
5044 ex.printStackTrace();
5050 * Attempt to load a "dropped" file or URL string: First by testing whether
5051 * it's and Annotation file, then a JNet file, and finally a features file. If
5052 * all are false then the user may have dropped an alignment file onto this
5056 * either a filename or a URL string.
5058 public void loadJalviewDataFile(String file, String protocol,
5059 String format, SequenceI assocSeq)
5063 if (protocol == null)
5065 protocol = jalview.io.FormatAdapter.checkProtocol(file);
5067 // if the file isn't identified, or not positively identified as some
5068 // other filetype (PFAM is default unidentified alignment file type) then
5069 // try to parse as annotation.
5070 boolean isAnnotation = (format == null || format
5071 .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
5072 .readAnnotationFile(viewport.getAlignment(), file, protocol)
5077 // first see if its a T-COFFEE score file
5078 TCoffeeScoreFile tcf = null;
5081 tcf = new TCoffeeScoreFile(file, protocol);
5084 if (tcf.annotateAlignment(viewport.getAlignment(), true))
5086 tcoffeeColour.setEnabled(true);
5087 tcoffeeColour.setSelected(true);
5088 changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5089 isAnnotation = true;
5091 .setText(MessageManager
5092 .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5096 // some problem - if no warning its probable that the ID matching
5097 // process didn't work
5101 tcf.getWarningMessage() == null ? MessageManager
5102 .getString("label.check_file_matches_sequence_ids_alignment")
5103 : tcf.getWarningMessage(),
5105 .getString("label.problem_reading_tcoffee_score_file"),
5106 JOptionPane.WARNING_MESSAGE);
5113 } catch (Exception x)
5116 .debug("Exception when processing data source as T-COFFEE score file",
5122 // try to see if its a JNet 'concise' style annotation file *before*
5124 // try to parse it as a features file
5127 format = new IdentifyFile().Identify(file, protocol);
5129 if (format.equalsIgnoreCase("JnetFile"))
5131 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
5133 new JnetAnnotationMaker().add_annotation(predictions,
5134 viewport.getAlignment(), 0, false);
5135 isAnnotation = true;
5140 * if (format.equalsIgnoreCase("PDB")) {
5142 * String pdbfn = ""; // try to match up filename with sequence id
5143 * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
5144 * new File(file); pdbfn = fl.getName(); } else if (protocol ==
5145 * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
5146 * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
5147 * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
5148 * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
5149 * // attempt to find a match in the alignment SequenceI mtch =
5150 * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
5151 * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
5152 * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
5153 * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
5154 * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
5155 * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
5156 * { System.err.println("Associated file : " + file + " with " +
5157 * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
5158 * TODO: maybe need to load as normal otherwise return; } }
5160 // try to parse it as a features file
5161 boolean isGroupsFile = parseFeaturesFile(file, protocol);
5162 // if it wasn't a features file then we just treat it as a general
5163 // alignment file to load into the current view.
5166 new FileLoader().LoadFile(viewport, file, protocol, format);
5170 alignPanel.paintAlignment(true);
5178 alignPanel.adjustAnnotationHeight();
5179 viewport.updateSequenceIdColours();
5180 buildSortByAnnotationScoresMenu();
5181 alignPanel.paintAlignment(true);
5183 } catch (Exception ex)
5185 ex.printStackTrace();
5186 } catch (OutOfMemoryError oom)
5191 } catch (Exception x)
5197 + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
5198 : "using " + protocol + " from " + file)
5200 + (format != null ? "(parsing as '" + format
5201 + "' file)" : ""), oom, Desktop.desktop);
5206 public void tabSelectionChanged(int index)
5210 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
5211 viewport = alignPanel.av;
5212 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5213 setMenusFromViewport(viewport);
5218 public void tabbedPane_mousePressed(MouseEvent e)
5220 if (SwingUtilities.isRightMouseButton(e))
5222 String reply = JOptionPane.showInternalInputDialog(this,
5223 MessageManager.getString("label.enter_view_name"),
5224 MessageManager.getString("label.enter_view_name"),
5225 JOptionPane.QUESTION_MESSAGE);
5229 viewport.viewName = reply;
5230 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5235 public AlignViewport getCurrentView()
5241 * Open the dialog for regex description parsing.
5244 protected void extractScores_actionPerformed(ActionEvent e)
5246 ParseProperties pp = new jalview.analysis.ParseProperties(
5247 viewport.getAlignment());
5248 // TODO: verify regex and introduce GUI dialog for version 2.5
5249 // if (pp.getScoresFromDescription("col", "score column ",
5250 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5252 if (pp.getScoresFromDescription("description column",
5253 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5255 buildSortByAnnotationScoresMenu();
5263 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5267 protected void showDbRefs_actionPerformed(ActionEvent e)
5269 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
5275 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5279 protected void showNpFeats_actionPerformed(ActionEvent e)
5281 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
5285 * find the viewport amongst the tabs in this alignment frame and close that
5290 public boolean closeView(AlignViewport av)
5294 this.closeMenuItem_actionPerformed(false);
5297 Component[] comp = tabbedPane.getComponents();
5298 for (int i = 0; comp != null && i < comp.length; i++)
5300 if (comp[i] instanceof AlignmentPanel)
5302 if (((AlignmentPanel) comp[i]).av == av)
5305 closeView((AlignmentPanel) comp[i]);
5313 protected void build_fetchdbmenu(JMenu webService)
5315 // Temporary hack - DBRef Fetcher always top level ws entry.
5316 // TODO We probably want to store a sequence database checklist in
5317 // preferences and have checkboxes.. rather than individual sources selected
5319 final JMenu rfetch = new JMenu(
5320 MessageManager.getString("action.fetch_db_references"));
5321 rfetch.setToolTipText(MessageManager
5322 .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5323 webService.add(rfetch);
5325 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5326 MessageManager.getString("option.trim_retrieved_seqs"));
5327 trimrs.setToolTipText(MessageManager
5328 .getString("label.trim_retrieved_sequences"));
5329 trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5330 trimrs.addActionListener(new ActionListener()
5333 public void actionPerformed(ActionEvent e)
5335 trimrs.setSelected(trimrs.isSelected());
5336 Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5337 Boolean.valueOf(trimrs.isSelected()).toString());
5341 JMenuItem fetchr = new JMenuItem(
5342 MessageManager.getString("label.standard_databases"));
5343 fetchr.setToolTipText(MessageManager
5344 .getString("label.fetch_embl_uniprot"));
5345 fetchr.addActionListener(new ActionListener()
5349 public void actionPerformed(ActionEvent e)
5351 new Thread(new Runnable()
5357 new jalview.ws.DBRefFetcher(alignPanel.av
5358 .getSequenceSelection(), alignPanel.alignFrame)
5359 .fetchDBRefs(false);
5367 final AlignFrame me = this;
5368 new Thread(new Runnable()
5373 final jalview.ws.SequenceFetcher sf = SequenceFetcher
5374 .getSequenceFetcherSingleton(me);
5375 javax.swing.SwingUtilities.invokeLater(new Runnable()
5380 String[] dbclasses = sf.getOrderedSupportedSources();
5381 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5382 // jalview.util.QuickSort.sort(otherdb, otherdb);
5383 List<DbSourceProxy> otherdb;
5384 JMenu dfetch = new JMenu();
5385 JMenu ifetch = new JMenu();
5386 JMenuItem fetchr = null;
5387 int comp = 0, icomp = 0, mcomp = 15;
5388 String mname = null;
5390 for (String dbclass : dbclasses)
5392 otherdb = sf.getSourceProxy(dbclass);
5393 // add a single entry for this class, or submenu allowing 'fetch
5395 if (otherdb == null || otherdb.size() < 1)
5399 // List<DbSourceProxy> dbs=otherdb;
5400 // otherdb=new ArrayList<DbSourceProxy>();
5401 // for (DbSourceProxy db:dbs)
5403 // if (!db.isA(DBRefSource.ALIGNMENTDB)
5407 mname = "From " + dbclass;
5409 if (otherdb.size() == 1)
5411 final DbSourceProxy[] dassource = otherdb
5412 .toArray(new DbSourceProxy[0]);
5413 DbSourceProxy src = otherdb.get(0);
5414 fetchr = new JMenuItem(src.getDbSource());
5415 fetchr.addActionListener(new ActionListener()
5419 public void actionPerformed(ActionEvent e)
5421 new Thread(new Runnable()
5427 new jalview.ws.DBRefFetcher(alignPanel.av
5428 .getSequenceSelection(),
5429 alignPanel.alignFrame, dassource)
5430 .fetchDBRefs(false);
5436 fetchr.setToolTipText("<html>"
5437 + JvSwingUtils.wrapTooltip("Retrieve from "
5438 + src.getDbName()) + "<html>");
5444 final DbSourceProxy[] dassource = otherdb
5445 .toArray(new DbSourceProxy[0]);
5447 DbSourceProxy src = otherdb.get(0);
5448 fetchr = new JMenuItem(MessageManager.formatMessage(
5449 "label.fetch_all_param", new String[]
5450 { src.getDbSource() }));
5451 fetchr.addActionListener(new ActionListener()
5454 public void actionPerformed(ActionEvent e)
5456 new Thread(new Runnable()
5462 new jalview.ws.DBRefFetcher(alignPanel.av
5463 .getSequenceSelection(),
5464 alignPanel.alignFrame, dassource)
5465 .fetchDBRefs(false);
5471 fetchr.setToolTipText("<html>"
5472 + JvSwingUtils.wrapTooltip("Retrieve from all "
5473 + otherdb.size() + " sources in "
5474 + src.getDbSource() + "<br>First is :"
5475 + src.getDbName()) + "<html>");
5478 // and then build the rest of the individual menus
5479 ifetch = new JMenu("Sources from " + src.getDbSource());
5481 String imname = null;
5483 for (DbSourceProxy sproxy : otherdb)
5485 String dbname = sproxy.getDbName();
5486 String sname = dbname.length() > 5 ? dbname.substring(0,
5487 5) + "..." : dbname;
5488 String msname = dbname.length() > 10 ? dbname.substring(
5489 0, 10) + "..." : dbname;
5492 imname = "from '" + sname + "'";
5494 fetchr = new JMenuItem(msname);
5495 final DbSourceProxy[] dassrc =
5497 fetchr.addActionListener(new ActionListener()
5501 public void actionPerformed(ActionEvent e)
5503 new Thread(new Runnable()
5509 new jalview.ws.DBRefFetcher(alignPanel.av
5510 .getSequenceSelection(),
5511 alignPanel.alignFrame, dassrc)
5512 .fetchDBRefs(false);
5518 fetchr.setToolTipText("<html>"
5519 + JvSwingUtils.wrapTooltip("Retrieve from "
5520 + dbname) + "</html>");
5523 if (++icomp >= mcomp || i == (otherdb.size()))
5525 ifetch.setText(MessageManager.formatMessage(
5526 "label.source_to_target", imname, sname));
5528 ifetch = new JMenu();
5536 if (comp >= mcomp || dbi >= (dbclasses.length))
5538 dfetch.setText(MessageManager.formatMessage(
5539 "label.source_to_target", mname, dbclass));
5541 dfetch = new JMenu();
5554 * Left justify the whole alignment.
5557 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5559 AlignmentI al = viewport.getAlignment();
5561 viewport.firePropertyChange("alignment", null, al);
5565 * Right justify the whole alignment.
5568 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5570 AlignmentI al = viewport.getAlignment();
5572 viewport.firePropertyChange("alignment", null, al);
5575 public void setShowSeqFeatures(boolean b)
5577 showSeqFeatures.setSelected(true);
5578 viewport.setShowSequenceFeatures(true);
5585 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5586 * awt.event.ActionEvent)
5589 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5591 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5592 alignPanel.paintAlignment(true);
5599 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5603 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5605 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5606 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5614 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5615 * .event.ActionEvent)
5618 protected void showGroupConservation_actionPerformed(ActionEvent e)
5620 viewport.setShowGroupConservation(showGroupConservation.getState());
5621 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5628 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5629 * .event.ActionEvent)
5632 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5634 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5635 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5642 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5643 * .event.ActionEvent)
5646 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5648 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5649 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5653 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5655 showSequenceLogo.setState(true);
5656 viewport.setShowSequenceLogo(true);
5657 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5658 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5662 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5664 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5671 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5672 * .event.ActionEvent)
5675 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5677 if (avc.makeGroupsFromSelection())
5679 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5680 alignPanel.updateAnnotation();
5681 alignPanel.paintAlignment(true);
5686 protected void createGroup_actionPerformed(ActionEvent e)
5688 if (avc.createGroup())
5690 alignPanel.alignmentChanged();
5695 protected void unGroup_actionPerformed(ActionEvent e)
5699 alignPanel.alignmentChanged();
5704 * make the given alignmentPanel the currently selected tab
5706 * @param alignmentPanel
5708 public void setDisplayedView(AlignmentPanel alignmentPanel)
5710 if (!viewport.getSequenceSetId().equals(
5711 alignmentPanel.av.getSequenceSetId()))
5714 "Implementation error: cannot show a view from another alignment in an AlignFrame.");
5716 if (tabbedPane != null
5717 & alignPanels.indexOf(alignmentPanel) != tabbedPane
5718 .getSelectedIndex())
5720 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5725 * Action on selection of menu option to Show or Hide all annotations.
5730 protected void setAllAnnotationsVisibility(boolean visible)
5732 for (AlignmentAnnotation aa : alignPanel.getAlignment()
5733 .getAlignmentAnnotation())
5735 aa.visible = visible;
5737 this.alignPanel.paintAlignment(true);
5741 class PrintThread extends Thread
5745 public PrintThread(AlignmentPanel ap)
5750 static PageFormat pf;
5755 PrinterJob printJob = PrinterJob.getPrinterJob();
5759 printJob.setPrintable(ap, pf);
5763 printJob.setPrintable(ap);
5766 if (printJob.printDialog())
5771 } catch (Exception PrintException)
5773 PrintException.printStackTrace();