2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
3 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
26 import java.awt.datatransfer.*;
27 import java.awt.dnd.*;
28 import java.awt.event.*;
29 import java.awt.print.*;
31 import javax.swing.event.MenuEvent;
33 import jalview.analysis.*;
34 import jalview.commands.*;
35 import jalview.datamodel.*;
37 import jalview.jbgui.*;
38 import jalview.schemes.*;
47 public class AlignFrame extends GAlignFrame implements DropTargetListener,
52 public static final int DEFAULT_WIDTH = 700;
55 public static final int DEFAULT_HEIGHT = 500;
57 public AlignmentPanel alignPanel;
59 AlignViewport viewport;
61 Vector alignPanels = new Vector();
64 * Last format used to load or save alignments in this window
66 String currentFileFormat = null;
69 * Current filename for this alignment
71 String fileName = null;
74 * Creates a new AlignFrame object with specific width and height.
80 public AlignFrame(AlignmentI al, int width, int height)
82 this(al, null, width, height);
86 * Creates a new AlignFrame object with specific width, height and
92 * @param sequenceSetId
94 public AlignFrame(AlignmentI al, int width, int height,
97 this(al, null, width, height, sequenceSetId);
101 * Creates a new AlignFrame object with specific width, height and
107 * @param sequenceSetId
110 public AlignFrame(AlignmentI al, int width, int height,
111 String sequenceSetId, String viewId)
113 this(al, null, width, height, sequenceSetId, viewId);
117 * new alignment window with hidden columns
121 * @param hiddenColumns
122 * ColumnSelection or null
124 * Width of alignment frame
128 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
129 int width, int height)
131 this(al, hiddenColumns, width, height, null);
135 * Create alignment frame for al with hiddenColumns, a specific width and
136 * height, and specific sequenceId
139 * @param hiddenColumns
142 * @param sequenceSetId
145 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
146 int width, int height, String sequenceSetId)
148 this(al, hiddenColumns, width, height, sequenceSetId, null);
152 * Create alignment frame for al with hiddenColumns, a specific width and
153 * height, and specific sequenceId
156 * @param hiddenColumns
159 * @param sequenceSetId
164 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
165 int width, int height, String sequenceSetId, String viewId)
167 setSize(width, height);
168 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
170 alignPanel = new AlignmentPanel(this, viewport);
172 if (al.getDataset() == null)
177 addAlignmentPanel(alignPanel, true);
182 * Make a new AlignFrame from exisiting alignmentPanels
189 public AlignFrame(AlignmentPanel ap)
193 addAlignmentPanel(ap, false);
198 * initalise the alignframe from the underlying viewport data and the
203 if (viewport.conservation == null)
205 BLOSUM62Colour.setEnabled(false);
206 conservationMenuItem.setEnabled(false);
207 modifyConservation.setEnabled(false);
208 // PIDColour.setEnabled(false);
209 // abovePIDThreshold.setEnabled(false);
210 // modifyPID.setEnabled(false);
213 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
216 if (sortby.equals("Id"))
218 sortIDMenuItem_actionPerformed(null);
220 else if (sortby.equals("Pairwise Identity"))
222 sortPairwiseMenuItem_actionPerformed(null);
225 if (Desktop.desktop != null)
227 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
228 addServiceListeners();
229 setGUINucleotide(viewport.alignment.isNucleotide());
232 setMenusFromViewport(viewport);
233 buildSortByAnnotationScoresMenu();
234 if (viewport.wrapAlignment)
236 wrapMenuItem_actionPerformed(null);
239 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
241 this.overviewMenuItem_actionPerformed(null);
249 * Change the filename and format for the alignment, and enable the 'reload'
250 * button functionality.
257 public void setFileName(String file, String format)
260 currentFileFormat = format;
261 reload.setEnabled(true);
264 void addKeyListener()
266 addKeyListener(new KeyAdapter()
268 public void keyPressed(KeyEvent evt)
270 if (viewport.cursorMode
271 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
272 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
273 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
274 && Character.isDigit(evt.getKeyChar()))
275 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
277 switch (evt.getKeyCode())
280 case 27: // escape key
281 deselectAllSequenceMenuItem_actionPerformed(null);
285 case KeyEvent.VK_DOWN:
286 if (evt.isAltDown() || !viewport.cursorMode)
287 moveSelectedSequences(false);
288 if (viewport.cursorMode)
289 alignPanel.seqPanel.moveCursor(0, 1);
293 if (evt.isAltDown() || !viewport.cursorMode)
294 moveSelectedSequences(true);
295 if (viewport.cursorMode)
296 alignPanel.seqPanel.moveCursor(0, -1);
300 case KeyEvent.VK_LEFT:
301 if (evt.isAltDown() || !viewport.cursorMode)
302 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
304 alignPanel.seqPanel.moveCursor(-1, 0);
308 case KeyEvent.VK_RIGHT:
309 if (evt.isAltDown() || !viewport.cursorMode)
310 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
312 alignPanel.seqPanel.moveCursor(1, 0);
315 case KeyEvent.VK_SPACE:
316 if (viewport.cursorMode)
318 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
319 || evt.isShiftDown() || evt.isAltDown());
323 case KeyEvent.VK_DELETE:
324 case KeyEvent.VK_BACK_SPACE:
325 if (!viewport.cursorMode)
327 cut_actionPerformed(null);
331 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
332 || evt.isShiftDown() || evt.isAltDown());
338 if (viewport.cursorMode)
340 alignPanel.seqPanel.setCursorRow();
344 if (viewport.cursorMode && !evt.isControlDown())
346 alignPanel.seqPanel.setCursorColumn();
350 if (viewport.cursorMode)
352 alignPanel.seqPanel.setCursorPosition();
356 case KeyEvent.VK_ENTER:
357 case KeyEvent.VK_COMMA:
358 if (viewport.cursorMode)
360 alignPanel.seqPanel.setCursorRowAndColumn();
365 if (viewport.cursorMode)
367 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
371 if (viewport.cursorMode)
373 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
378 viewport.cursorMode = !viewport.cursorMode;
379 statusBar.setText("Keyboard editing mode is "
380 + (viewport.cursorMode ? "on" : "off"));
381 if (viewport.cursorMode)
383 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
384 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
386 alignPanel.seqPanel.seqCanvas.repaint();
392 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
393 java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
395 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
397 javax.help.HelpBroker hb = hs.createHelpBroker();
398 hb.setCurrentID("home");
399 hb.setDisplayed(true);
400 } catch (Exception ex)
402 ex.printStackTrace();
407 boolean toggleSeqs = !evt.isControlDown();
408 boolean toggleCols = !evt.isShiftDown();
409 toggleHiddenRegions(toggleSeqs,toggleCols);
412 case KeyEvent.VK_PAGE_UP:
413 if (viewport.wrapAlignment)
415 alignPanel.scrollUp(true);
419 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
420 - viewport.endSeq + viewport.startSeq);
423 case KeyEvent.VK_PAGE_DOWN:
424 if (viewport.wrapAlignment)
426 alignPanel.scrollUp(false);
430 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
431 + viewport.endSeq - viewport.startSeq);
437 public void keyReleased(KeyEvent evt)
439 switch (evt.getKeyCode())
441 case KeyEvent.VK_LEFT:
442 if (evt.isAltDown() || !viewport.cursorMode)
443 viewport.firePropertyChange("alignment", null, viewport
444 .getAlignment().getSequences());
447 case KeyEvent.VK_RIGHT:
448 if (evt.isAltDown() || !viewport.cursorMode)
449 viewport.firePropertyChange("alignment", null, viewport
450 .getAlignment().getSequences());
457 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
459 ap.alignFrame = this;
461 alignPanels.addElement(ap);
463 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
465 int aSize = alignPanels.size();
467 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
469 if (aSize == 1 && ap.av.viewName == null)
471 this.getContentPane().add(ap, BorderLayout.CENTER);
477 setInitialTabVisible();
480 expandViews.setEnabled(true);
481 gatherViews.setEnabled(true);
482 tabbedPane.addTab(ap.av.viewName, ap);
484 ap.setVisible(false);
491 ap.av.alignment.padGaps();
493 ap.av.updateConservation(ap);
494 ap.av.updateConsensus(ap);
498 public void setInitialTabVisible()
500 expandViews.setEnabled(true);
501 gatherViews.setEnabled(true);
502 tabbedPane.setVisible(true);
503 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
504 tabbedPane.addTab(first.av.viewName, first);
505 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
508 public AlignViewport getViewport()
513 /* Set up intrinsic listeners for dynamically generated GUI bits. */
514 private void addServiceListeners()
516 final java.beans.PropertyChangeListener thisListener;
517 // Do this once to get current state
518 BuildWebServiceMenu();
520 .addPropertyChangeListener(thisListener = new java.beans.PropertyChangeListener()
522 public void propertyChange(PropertyChangeEvent evt)
524 // System.out.println("Discoverer property change.");
525 if (evt.getPropertyName().equals("services"))
527 // System.out.println("Rebuilding web service menu");
528 BuildWebServiceMenu();
533 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
535 public void internalFrameClosed(
536 javax.swing.event.InternalFrameEvent evt)
538 // System.out.println("deregistering discoverer listener");
539 Desktop.discoverer.removePropertyChangeListener(thisListener);
540 closeMenuItem_actionPerformed(true);
545 public void setGUINucleotide(boolean nucleotide)
547 showTranslation.setVisible(nucleotide);
548 conservationMenuItem.setEnabled(!nucleotide);
549 modifyConservation.setEnabled(!nucleotide);
550 showGroupConservation.setEnabled(!nucleotide);
551 // Remember AlignFrame always starts as protein
554 calculateMenu.remove(calculateMenu.getItemCount() - 2);
559 * set up menus for the currently viewport. This may be called after any
560 * operation that affects the data in the current view (selection changed,
561 * etc) to update the menus to reflect the new state.
563 public void setMenusForViewport()
565 setMenusFromViewport(viewport);
569 * Need to call this method when tabs are selected for multiple views, or when
570 * loading from Jalview2XML.java
575 void setMenusFromViewport(AlignViewport av)
577 padGapsMenuitem.setSelected(av.padGaps);
578 colourTextMenuItem.setSelected(av.showColourText);
579 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
580 conservationMenuItem.setSelected(av.getConservationSelected());
581 seqLimits.setSelected(av.getShowJVSuffix());
582 idRightAlign.setSelected(av.rightAlignIds);
583 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
584 renderGapsMenuItem.setSelected(av.renderGaps);
585 wrapMenuItem.setSelected(av.wrapAlignment);
586 scaleAbove.setVisible(av.wrapAlignment);
587 scaleLeft.setVisible(av.wrapAlignment);
588 scaleRight.setVisible(av.wrapAlignment);
589 annotationPanelMenuItem.setState(av.showAnnotation);
590 viewBoxesMenuItem.setSelected(av.showBoxes);
591 viewTextMenuItem.setSelected(av.showText);
592 showUnconservedMenuItem.setSelected(av.showUnconserved);
593 showGroupConsensus.setSelected(av.showGroupConsensus);
594 showGroupConservation.setSelected(av.showGroupConservation);
595 showConsensusHistogram.setSelected(av.showConsensusHistogram);
596 showSequenceLogo.setSelected(av.showSequenceLogo);
597 setColourSelected(ColourSchemeProperty.getColourName(av
598 .getGlobalColourScheme()));
600 showSeqFeatures.setSelected(av.showSequenceFeatures);
601 hiddenMarkers.setState(av.showHiddenMarkers);
602 applyToAllGroups.setState(av.colourAppliesToAllGroups);
603 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
604 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
606 setShowProductsEnabled();
611 Hashtable progressBars, progressBarHandlers;
616 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
618 public void setProgressBar(String message, long id)
620 if (progressBars == null)
622 progressBars = new Hashtable();
623 progressBarHandlers = new Hashtable();
626 JPanel progressPanel;
627 Long lId=new Long(id);
628 GridLayout layout = (GridLayout) statusPanel.getLayout();
629 if (progressBars.get(lId) != null)
631 progressPanel = (JPanel) progressBars.get(new Long(id));
632 statusPanel.remove(progressPanel);
633 progressBars.remove(lId);
634 progressPanel = null;
637 statusBar.setText(message);
639 if (progressBarHandlers.contains(lId))
641 progressBarHandlers.remove(lId);
643 layout.setRows(layout.getRows() - 1);
647 progressPanel = new JPanel(new BorderLayout(10, 5));
649 JProgressBar progressBar = new JProgressBar();
650 progressBar.setIndeterminate(true);
652 progressPanel.add(new JLabel(message), BorderLayout.WEST);
653 progressPanel.add(progressBar, BorderLayout.CENTER);
655 layout.setRows(layout.getRows() + 1);
656 statusPanel.add(progressPanel);
658 progressBars.put(lId, progressPanel);
661 setMenusForViewport();
665 public void registerHandler(final long id,
666 final IProgressIndicatorHandler handler)
668 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
671 "call setProgressBar before registering the progress bar's handler.");
673 progressBarHandlers.put(new Long(id), handler);
674 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
675 if (handler.canCancel())
677 JButton cancel = new JButton("Cancel");
678 final IProgressIndicator us = this;
679 cancel.addActionListener(new ActionListener()
682 public void actionPerformed(ActionEvent e)
684 handler.cancelActivity(id);
685 us.setProgressBar("Cancelled "
686 + ((JLabel) progressPanel.getComponent(0)).getText(), id);
689 progressPanel.add(cancel, BorderLayout.EAST);
695 * @return true if any progress bars are still active
697 public boolean operationInProgress()
699 if (progressBars != null && progressBars.size() > 0)
707 * Added so Castor Mapping file can obtain Jalview Version
709 public String getVersion()
711 return jalview.bin.Cache.getProperty("VERSION");
714 public FeatureRenderer getFeatureRenderer()
716 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
719 public void fetchSequence_actionPerformed(ActionEvent e)
721 new SequenceFetcher(this);
724 public void addFromFile_actionPerformed(ActionEvent e)
726 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
729 public void reload_actionPerformed(ActionEvent e)
731 if (fileName != null)
733 // TODO: work out how to recover feature settings for correct view(s) when file is reloaded.
734 if (currentFileFormat.equals("Jalview"))
736 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
737 for (int i = 0; i < frames.length; i++)
739 if (frames[i] instanceof AlignFrame && frames[i] != this
740 && ((AlignFrame) frames[i]).fileName.equals(fileName))
744 frames[i].setSelected(true);
745 Desktop.instance.closeAssociatedWindows();
746 } catch (java.beans.PropertyVetoException ex)
752 Desktop.instance.closeAssociatedWindows();
754 FileLoader loader = new FileLoader();
755 String protocol = fileName.startsWith("http:") ? "URL" : "File";
756 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
760 Rectangle bounds = this.getBounds();
762 FileLoader loader = new FileLoader();
763 String protocol = fileName.startsWith("http:") ? "URL" : "File";
764 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
765 protocol, currentFileFormat);
767 newframe.setBounds(bounds);
768 if (featureSettings!=null && featureSettings.isShowing()) {
769 final Rectangle fspos = featureSettings.frame.getBounds();
770 // TODO: need a 'show feature settings' function that takes bounds - need to refactor Desktop.addFrame
771 newframe.featureSettings_actionPerformed(null);
772 final FeatureSettings nfs = newframe.featureSettings;
773 SwingUtilities.invokeLater(new Runnable() {
776 nfs.frame.setBounds(fspos);
779 this.featureSettings.close();
780 this.featureSettings=null;
782 this.closeMenuItem_actionPerformed(true);
787 public void addFromText_actionPerformed(ActionEvent e)
789 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
792 public void addFromURL_actionPerformed(ActionEvent e)
794 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
797 public void save_actionPerformed(ActionEvent e)
800 || (currentFileFormat == null || !jalview.io.FormatAdapter
801 .isValidIOFormat(currentFileFormat, true))
802 || fileName.startsWith("http"))
804 saveAs_actionPerformed(null);
808 saveAlignment(fileName, currentFileFormat);
818 public void saveAs_actionPerformed(ActionEvent e)
820 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
821 .getProperty("LAST_DIRECTORY"),
822 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
823 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
824 currentFileFormat, false);
826 chooser.setFileView(new JalviewFileView());
827 chooser.setDialogTitle("Save Alignment to file");
828 chooser.setToolTipText("Save");
830 int value = chooser.showSaveDialog(this);
832 if (value == JalviewFileChooser.APPROVE_OPTION)
834 currentFileFormat = chooser.getSelectedFormat();
835 if (currentFileFormat == null)
837 JOptionPane.showInternalMessageDialog(Desktop.desktop,
838 "You must select a file format before saving!",
839 "File format not specified", JOptionPane.WARNING_MESSAGE);
840 value = chooser.showSaveDialog(this);
844 fileName = chooser.getSelectedFile().getPath();
846 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
849 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
850 if (currentFileFormat.indexOf(" ") > -1)
852 currentFileFormat = currentFileFormat.substring(0,
853 currentFileFormat.indexOf(" "));
855 saveAlignment(fileName, currentFileFormat);
859 public boolean saveAlignment(String file, String format)
861 boolean success = true;
863 if (format.equalsIgnoreCase("Jalview"))
865 String shortName = title;
867 if (shortName.indexOf(java.io.File.separatorChar) > -1)
869 shortName = shortName.substring(shortName
870 .lastIndexOf(java.io.File.separatorChar) + 1);
873 success = new Jalview2XML().SaveAlignment(this, file, shortName);
875 statusBar.setText("Successfully saved to file: " + fileName + " in "
876 + format + " format.");
881 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
883 warningMessage("Cannot save file " + fileName + " using format "
884 + format, "Alignment output format not supported");
885 saveAs_actionPerformed(null);
886 // JBPNote need to have a raise_gui flag here
890 String[] omitHidden = null;
892 if (viewport.hasHiddenColumns)
894 int reply = JOptionPane
895 .showInternalConfirmDialog(
897 "The Alignment contains hidden columns."
898 + "\nDo you want to save only the visible alignment?",
899 "Save / Omit Hidden Columns",
900 JOptionPane.YES_NO_OPTION,
901 JOptionPane.QUESTION_MESSAGE);
903 if (reply == JOptionPane.YES_OPTION)
905 omitHidden = viewport.getViewAsString(false);
908 FormatAdapter f = new FormatAdapter();
909 String output = f.formatSequences(format,
910 (Alignment) viewport.alignment, // class cast exceptions will
911 // occur in the distant future
912 omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
922 java.io.PrintWriter out = new java.io.PrintWriter(
923 new java.io.FileWriter(file));
928 statusBar.setText("Successfully saved to file: " + fileName
929 + " in " + format + " format.");
930 } catch (Exception ex)
933 ex.printStackTrace();
940 JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
941 + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
947 private void warningMessage(String warning, String title)
949 if (new jalview.util.Platform().isHeadless())
951 System.err.println("Warning: " + title + "\nWarning: " + warning);
956 JOptionPane.showInternalMessageDialog(this, warning, title,
957 JOptionPane.WARNING_MESSAGE);
968 protected void outputText_actionPerformed(ActionEvent e)
970 String[] omitHidden = null;
972 if (viewport.hasHiddenColumns)
974 int reply = JOptionPane
975 .showInternalConfirmDialog(
977 "The Alignment contains hidden columns."
978 + "\nDo you want to output only the visible alignment?",
979 "Save / Omit Hidden Columns",
980 JOptionPane.YES_NO_OPTION,
981 JOptionPane.QUESTION_MESSAGE);
983 if (reply == JOptionPane.YES_OPTION)
985 omitHidden = viewport.getViewAsString(false);
989 CutAndPasteTransfer cap = new CutAndPasteTransfer();
990 cap.setForInput(null);
991 Desktop.addInternalFrame(cap, "Alignment output - "
992 + e.getActionCommand(), 600, 500);
994 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
995 viewport.alignment, omitHidden, viewport.colSel));
1004 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1006 new HTMLOutput(alignPanel, alignPanel.seqPanel.seqCanvas
1007 .getSequenceRenderer(), alignPanel.seqPanel.seqCanvas
1008 .getFeatureRenderer());
1011 public void createImageMap(File file, String image)
1013 alignPanel.makePNGImageMap(file, image);
1022 public void createPNG(File f)
1024 alignPanel.makePNG(f);
1033 public void createEPS(File f)
1035 alignPanel.makeEPS(f);
1038 public void pageSetup_actionPerformed(ActionEvent e)
1040 PrinterJob printJob = PrinterJob.getPrinterJob();
1041 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1050 public void printMenuItem_actionPerformed(ActionEvent e)
1052 // Putting in a thread avoids Swing painting problems
1053 PrintThread thread = new PrintThread(alignPanel);
1057 public void exportFeatures_actionPerformed(ActionEvent e)
1059 new AnnotationExporter().exportFeatures(alignPanel);
1062 public void exportAnnotations_actionPerformed(ActionEvent e)
1064 new AnnotationExporter().exportAnnotations(alignPanel,
1065 viewport.showAnnotation ? viewport.alignment
1066 .getAlignmentAnnotation() : null, viewport.alignment
1068 ((Alignment) viewport.alignment).alignmentProperties);
1071 public void associatedData_actionPerformed(ActionEvent e)
1073 // Pick the tree file
1074 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
1075 .getProperty("LAST_DIRECTORY"));
1076 chooser.setFileView(new JalviewFileView());
1077 chooser.setDialogTitle("Load Jalview Annotations or Features File");
1078 chooser.setToolTipText("Load Jalview Annotations / Features file");
1080 int value = chooser.showOpenDialog(null);
1082 if (value == JalviewFileChooser.APPROVE_OPTION)
1084 String choice = chooser.getSelectedFile().getPath();
1085 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1086 loadJalviewDataFile(choice);
1092 * Close the current view or all views in the alignment frame. If the frame
1093 * only contains one view then the alignment will be removed from memory.
1095 * @param closeAllTabs
1097 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1099 if (alignPanels != null && alignPanels.size() < 2)
1101 closeAllTabs = true;
1106 if (alignPanels != null)
1110 if (this.isClosed())
1112 // really close all the windows - otherwise wait till
1113 // setClosed(true) is called
1114 for (int i = 0; i < alignPanels.size(); i++)
1116 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1123 closeView(alignPanel);
1129 this.setClosed(true);
1131 } catch (Exception ex)
1133 ex.printStackTrace();
1138 * close alignPanel2 and shuffle tabs appropriately.
1140 * @param alignPanel2
1142 public void closeView(AlignmentPanel alignPanel2)
1144 int index = tabbedPane.getSelectedIndex();
1145 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1146 alignPanels.removeElement(alignPanel2);
1148 // if (viewport == alignPanel2.av)
1152 alignPanel2.closePanel();
1155 tabbedPane.removeTabAt(closedindex);
1156 tabbedPane.validate();
1158 if (index > closedindex || index == tabbedPane.getTabCount())
1160 // modify currently selected tab index if necessary.
1164 this.tabSelectionChanged(index);
1170 void updateEditMenuBar()
1173 if (viewport.historyList.size() > 0)
1175 undoMenuItem.setEnabled(true);
1176 CommandI command = (CommandI) viewport.historyList.peek();
1177 undoMenuItem.setText("Undo " + command.getDescription());
1181 undoMenuItem.setEnabled(false);
1182 undoMenuItem.setText("Undo");
1185 if (viewport.redoList.size() > 0)
1187 redoMenuItem.setEnabled(true);
1189 CommandI command = (CommandI) viewport.redoList.peek();
1190 redoMenuItem.setText("Redo " + command.getDescription());
1194 redoMenuItem.setEnabled(false);
1195 redoMenuItem.setText("Redo");
1199 public void addHistoryItem(CommandI command)
1201 if (command.getSize() > 0)
1203 viewport.historyList.push(command);
1204 viewport.redoList.clear();
1205 updateEditMenuBar();
1206 viewport.hasHiddenColumns = (viewport.colSel!=null && viewport.colSel.getHiddenColumns() != null && viewport.colSel.getHiddenColumns().size()>0);
1212 * @return alignment objects for all views
1214 AlignmentI[] getViewAlignments()
1216 if (alignPanels != null)
1218 Enumeration e = alignPanels.elements();
1219 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1220 for (int i = 0; e.hasMoreElements(); i++)
1222 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1226 if (viewport != null)
1228 return new AlignmentI[]
1229 { viewport.alignment };
1240 protected void undoMenuItem_actionPerformed(ActionEvent e)
1242 if (viewport.historyList.empty())
1244 CommandI command = (CommandI) viewport.historyList.pop();
1245 viewport.redoList.push(command);
1246 command.undoCommand(getViewAlignments());
1248 AlignViewport originalSource = getOriginatingSource(command);
1249 updateEditMenuBar();
1251 if (originalSource != null)
1253 originalSource.hasHiddenColumns = (viewport.colSel!=null && viewport.colSel.getHiddenColumns() != null && viewport.colSel.getHiddenColumns().size()>0);
1254 originalSource.firePropertyChange("alignment", null,
1255 originalSource.alignment.getSequences());
1265 protected void redoMenuItem_actionPerformed(ActionEvent e)
1267 if (viewport.redoList.size() < 1)
1272 CommandI command = (CommandI) viewport.redoList.pop();
1273 viewport.historyList.push(command);
1274 command.doCommand(getViewAlignments());
1276 AlignViewport originalSource = getOriginatingSource(command);
1277 updateEditMenuBar();
1279 if (originalSource != null)
1281 originalSource.hasHiddenColumns = (viewport.colSel!=null && viewport.colSel.getHiddenColumns() != null && viewport.colSel.getHiddenColumns().size()>0);
1282 originalSource.firePropertyChange("alignment", null,
1283 originalSource.alignment.getSequences());
1287 AlignViewport getOriginatingSource(CommandI command)
1289 AlignViewport originalSource = null;
1290 // For sequence removal and addition, we need to fire
1291 // the property change event FROM the viewport where the
1292 // original alignment was altered
1293 AlignmentI al = null;
1294 if (command instanceof EditCommand)
1296 EditCommand editCommand = (EditCommand) command;
1297 al = editCommand.getAlignment();
1298 Vector comps = (Vector) PaintRefresher.components.get(viewport
1299 .getSequenceSetId());
1301 for (int i = 0; i < comps.size(); i++)
1303 if (comps.elementAt(i) instanceof AlignmentPanel)
1305 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
1307 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1314 if (originalSource == null)
1316 // The original view is closed, we must validate
1317 // the current view against the closed view first
1320 PaintRefresher.validateSequences(al, viewport.alignment);
1323 originalSource = viewport;
1326 return originalSource;
1335 public void moveSelectedSequences(boolean up)
1337 SequenceGroup sg = viewport.getSelectionGroup();
1346 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1348 SequenceI seq = viewport.alignment.getSequenceAt(i);
1350 if (!sg.getSequences(null).contains(seq))
1355 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1357 if (sg.getSequences(null).contains(temp))
1362 viewport.alignment.getSequences().setElementAt(temp, i);
1363 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1368 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1370 SequenceI seq = viewport.alignment.getSequenceAt(i);
1372 if (!sg.getSequences(null).contains(seq))
1377 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1379 if (sg.getSequences(null).contains(temp))
1384 viewport.alignment.getSequences().setElementAt(temp, i);
1385 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1389 alignPanel.paintAlignment(true);
1392 synchronized void slideSequences(boolean right, int size)
1394 Vector sg = new Vector();
1395 if (viewport.cursorMode)
1397 sg.addElement(viewport.alignment
1398 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1400 else if (viewport.getSelectionGroup() != null
1401 && viewport.getSelectionGroup().getSize() != viewport.alignment
1404 sg = viewport.getSelectionGroup().getSequences(
1405 viewport.hiddenRepSequences);
1413 Vector invertGroup = new Vector();
1415 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1417 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
1418 invertGroup.add(viewport.alignment.getSequenceAt(i));
1421 SequenceI[] seqs1 = new SequenceI[sg.size()];
1422 for (int i = 0; i < sg.size(); i++)
1423 seqs1[i] = (SequenceI) sg.elementAt(i);
1425 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1426 for (int i = 0; i < invertGroup.size(); i++)
1427 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1429 SlideSequencesCommand ssc;
1431 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1432 size, viewport.getGapCharacter());
1434 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1435 size, viewport.getGapCharacter());
1437 int groupAdjustment = 0;
1438 if (ssc.getGapsInsertedBegin() && right)
1440 if (viewport.cursorMode)
1441 alignPanel.seqPanel.moveCursor(size, 0);
1443 groupAdjustment = size;
1445 else if (!ssc.getGapsInsertedBegin() && !right)
1447 if (viewport.cursorMode)
1448 alignPanel.seqPanel.moveCursor(-size, 0);
1450 groupAdjustment = -size;
1453 if (groupAdjustment != 0)
1455 viewport.getSelectionGroup().setStartRes(
1456 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1457 viewport.getSelectionGroup().setEndRes(
1458 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1461 boolean appendHistoryItem = false;
1462 if (viewport.historyList != null && viewport.historyList.size() > 0
1463 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1465 appendHistoryItem = ssc
1466 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1470 if (!appendHistoryItem)
1471 addHistoryItem(ssc);
1482 protected void copy_actionPerformed(ActionEvent e)
1485 if (viewport.getSelectionGroup() == null)
1489 // TODO: preserve the ordering of displayed alignment annotation in any
1490 // internal paste (particularly sequence associated annotation)
1491 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1492 String[] omitHidden = null;
1494 if (viewport.hasHiddenColumns)
1496 omitHidden = viewport.getViewAsString(true);
1499 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1502 StringSelection ss = new StringSelection(output);
1506 jalview.gui.Desktop.internalCopy = true;
1507 // Its really worth setting the clipboard contents
1508 // to empty before setting the large StringSelection!!
1509 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
1510 new StringSelection(""), null);
1512 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1514 } catch (OutOfMemoryError er)
1516 new OOMWarning("copying region", er);
1520 Vector hiddenColumns = null;
1521 if (viewport.hasHiddenColumns)
1523 hiddenColumns = new Vector();
1524 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1525 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1528 int[] region = (int[]) viewport.getColumnSelection()
1529 .getHiddenColumns().elementAt(i);
1531 hiddenColumns.addElement(new int[]
1532 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1536 Desktop.jalviewClipboard = new Object[]
1537 { seqs, viewport.alignment.getDataset(), hiddenColumns };
1538 statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
1547 protected void pasteNew_actionPerformed(ActionEvent e)
1558 protected void pasteThis_actionPerformed(ActionEvent e)
1564 * Paste contents of Jalview clipboard
1566 * @param newAlignment
1567 * true to paste to a new alignment, otherwise add to this.
1569 void paste(boolean newAlignment)
1571 boolean externalPaste = true;
1574 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1575 Transferable contents = c.getContents(this);
1577 if (contents == null)
1585 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1586 if (str.length() < 1)
1591 format = new IdentifyFile().Identify(str, "Paste");
1593 } catch (OutOfMemoryError er)
1595 new OOMWarning("Out of memory pasting sequences!!", er);
1599 SequenceI[] sequences;
1600 boolean annotationAdded = false;
1601 AlignmentI alignment = null;
1603 if (Desktop.jalviewClipboard != null)
1605 // The clipboard was filled from within Jalview, we must use the
1607 // And dataset from the copied alignment
1608 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1609 // be doubly sure that we create *new* sequence objects.
1610 sequences = new SequenceI[newseq.length];
1611 for (int i = 0; i < newseq.length; i++)
1613 sequences[i] = new Sequence(newseq[i]);
1615 alignment = new Alignment(sequences);
1616 externalPaste = false;
1620 // parse the clipboard as an alignment.
1621 alignment = new FormatAdapter().readFile(str, "Paste", format);
1622 sequences = alignment.getSequencesArray();
1630 if (Desktop.jalviewClipboard != null)
1632 // dataset is inherited
1633 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1637 // new dataset is constructed
1638 alignment.setDataset(null);
1640 alwidth = alignment.getWidth() + 1;
1644 AlignmentI pastedal = alignment; // preserve pasted alignment object
1645 // Add pasted sequences and dataset into existing alignment.
1646 alignment = viewport.getAlignment();
1647 alwidth = alignment.getWidth() + 1;
1648 // decide if we need to import sequences from an existing dataset
1649 boolean importDs = Desktop.jalviewClipboard != null
1650 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1651 // importDs==true instructs us to copy over new dataset sequences from
1652 // an existing alignment
1653 Vector newDs = (importDs) ? new Vector() : null; // used to create
1654 // minimum dataset set
1656 for (int i = 0; i < sequences.length; i++)
1660 newDs.addElement(null);
1662 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1664 if (importDs && ds != null)
1666 if (!newDs.contains(ds))
1668 newDs.setElementAt(ds, i);
1669 ds = new Sequence(ds);
1670 // update with new dataset sequence
1671 sequences[i].setDatasetSequence(ds);
1675 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1680 // copy and derive new dataset sequence
1681 sequences[i] = sequences[i].deriveSequence();
1682 alignment.getDataset().addSequence(
1683 sequences[i].getDatasetSequence());
1684 // TODO: avoid creation of duplicate dataset sequences with a
1685 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1687 alignment.addSequence(sequences[i]); // merges dataset
1691 newDs.clear(); // tidy up
1693 if (pastedal.getAlignmentAnnotation() != null)
1695 // Add any annotation attached to alignment.
1696 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1697 for (int i = 0; i < alann.length; i++)
1699 annotationAdded = true;
1700 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1702 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1703 newann.padAnnotation(alwidth);
1704 alignment.addAnnotation(newann);
1714 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1715 sequences, 0, alignment.getWidth(), alignment));
1717 // Add any annotations attached to sequences
1718 for (int i = 0; i < sequences.length; i++)
1720 if (sequences[i].getAnnotation() != null)
1722 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1724 annotationAdded = true;
1725 sequences[i].getAnnotation()[a].adjustForAlignment();
1726 sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1727 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1732 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1739 // propagate alignment changed.
1740 viewport.setEndSeq(alignment.getHeight());
1741 if (annotationAdded)
1743 // Duplicate sequence annotation in all views.
1744 AlignmentI[] alview = this.getViewAlignments();
1745 for (int i = 0; i < sequences.length; i++)
1747 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1750 for (int avnum = 0; avnum < alview.length; avnum++)
1752 if (alview[avnum] != alignment)
1754 // duplicate in a view other than the one with input focus
1755 int avwidth = alview[avnum].getWidth() + 1;
1756 // this relies on sann being preserved after we
1757 // modify the sequence's annotation array for each duplication
1758 for (int a = 0; a < sann.length; a++)
1760 AlignmentAnnotation newann = new AlignmentAnnotation(
1762 sequences[i].addAlignmentAnnotation(newann);
1763 newann.padAnnotation(avwidth);
1764 alview[avnum].addAnnotation(newann); // annotation was
1765 // duplicated earlier
1766 alview[avnum].setAnnotationIndex(newann, a);
1771 buildSortByAnnotationScoresMenu();
1773 viewport.firePropertyChange("alignment", null, alignment
1779 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
1781 String newtitle = new String("Copied sequences");
1783 if (Desktop.jalviewClipboard != null
1784 && Desktop.jalviewClipboard[2] != null)
1786 Vector hc = (Vector) Desktop.jalviewClipboard[2];
1787 for (int i = 0; i < hc.size(); i++)
1789 int[] region = (int[]) hc.elementAt(i);
1790 af.viewport.hideColumns(region[0], region[1]);
1794 // >>>This is a fix for the moment, until a better solution is
1796 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
1798 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1800 // TODO: maintain provenance of an alignment, rather than just make the
1801 // title a concatenation of operations.
1804 if (title.startsWith("Copied sequences"))
1810 newtitle = newtitle.concat("- from " + title);
1815 newtitle = new String("Pasted sequences");
1818 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1823 } catch (Exception ex)
1825 ex.printStackTrace();
1826 System.out.println("Exception whilst pasting: " + ex);
1827 // could be anything being pasted in here
1838 protected void cut_actionPerformed(ActionEvent e)
1840 copy_actionPerformed(null);
1841 delete_actionPerformed(null);
1850 protected void delete_actionPerformed(ActionEvent evt)
1853 SequenceGroup sg = viewport.getSelectionGroup();
1859 Vector seqs = new Vector();
1861 for (int i = 0; i < sg.getSize(); i++)
1863 seq = sg.getSequenceAt(i);
1864 seqs.addElement(seq);
1867 // If the cut affects all sequences, remove highlighted columns
1868 if (sg.getSize() == viewport.alignment.getHeight())
1870 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1871 sg.getEndRes() + 1);
1874 SequenceI[] cut = new SequenceI[seqs.size()];
1875 for (int i = 0; i < seqs.size(); i++)
1877 cut[i] = (SequenceI) seqs.elementAt(i);
1881 * //ADD HISTORY ITEM
1883 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1884 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1885 viewport.alignment));
1887 viewport.setSelectionGroup(null);
1888 viewport.sendSelection();
1889 viewport.alignment.deleteGroup(sg);
1891 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1893 if (viewport.getAlignment().getHeight() < 1)
1897 this.setClosed(true);
1898 } catch (Exception ex)
1910 protected void deleteGroups_actionPerformed(ActionEvent e)
1912 viewport.alignment.deleteAllGroups();
1913 viewport.sequenceColours = null;
1914 viewport.setSelectionGroup(null);
1915 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1916 alignPanel.updateAnnotation();
1917 alignPanel.paintAlignment(true);
1926 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1928 SequenceGroup sg = new SequenceGroup();
1930 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1932 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1935 sg.setEndRes(viewport.alignment.getWidth() - 1);
1936 viewport.setSelectionGroup(sg);
1937 viewport.sendSelection();
1938 alignPanel.paintAlignment(true);
1939 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1948 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1950 if (viewport.cursorMode)
1952 alignPanel.seqPanel.keyboardNo1 = null;
1953 alignPanel.seqPanel.keyboardNo2 = null;
1955 viewport.setSelectionGroup(null);
1956 viewport.getColumnSelection().clear();
1957 viewport.setSelectionGroup(null);
1958 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1959 alignPanel.idPanel.idCanvas.searchResults = null;
1960 alignPanel.paintAlignment(true);
1961 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1970 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1972 SequenceGroup sg = viewport.getSelectionGroup();
1976 selectAllSequenceMenuItem_actionPerformed(null);
1981 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1983 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1986 alignPanel.paintAlignment(true);
1987 viewport.sendSelection();
1988 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1991 public void invertColSel_actionPerformed(ActionEvent e)
1993 viewport.invertColumnSelection();
1994 alignPanel.paintAlignment(true);
2003 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2005 trimAlignment(true);
2014 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2016 trimAlignment(false);
2019 void trimAlignment(boolean trimLeft)
2021 ColumnSelection colSel = viewport.getColumnSelection();
2024 if (colSel.size() > 0)
2028 column = colSel.getMin();
2032 column = colSel.getMax();
2036 if (viewport.getSelectionGroup() != null)
2038 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2039 viewport.hiddenRepSequences);
2043 seqs = viewport.alignment.getSequencesArray();
2046 TrimRegionCommand trimRegion;
2049 trimRegion = new TrimRegionCommand("Remove Left",
2050 TrimRegionCommand.TRIM_LEFT, seqs, column,
2051 viewport.alignment, viewport.colSel,
2052 viewport.selectionGroup);
2053 viewport.setStartRes(0);
2057 trimRegion = new TrimRegionCommand("Remove Right",
2058 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2059 viewport.alignment, viewport.colSel,
2060 viewport.selectionGroup);
2063 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2065 addHistoryItem(trimRegion);
2067 Vector groups = viewport.alignment.getGroups();
2069 for (int i = 0; i < groups.size(); i++)
2071 SequenceGroup sg = (SequenceGroup) groups.get(i);
2073 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2074 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2076 viewport.alignment.deleteGroup(sg);
2080 viewport.firePropertyChange("alignment", null, viewport
2081 .getAlignment().getSequences());
2091 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2093 int start = 0, end = viewport.alignment.getWidth() - 1;
2096 if (viewport.getSelectionGroup() != null)
2098 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2099 viewport.hiddenRepSequences);
2100 start = viewport.getSelectionGroup().getStartRes();
2101 end = viewport.getSelectionGroup().getEndRes();
2105 seqs = viewport.alignment.getSequencesArray();
2108 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2109 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
2111 addHistoryItem(removeGapCols);
2113 statusBar.setText("Removed " + removeGapCols.getSize()
2114 + " empty columns.");
2116 // This is to maintain viewport position on first residue
2117 // of first sequence
2118 SequenceI seq = viewport.alignment.getSequenceAt(0);
2119 int startRes = seq.findPosition(viewport.startRes);
2120 // ShiftList shifts;
2121 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2122 // edit.alColumnChanges=shifts.getInverse();
2123 // if (viewport.hasHiddenColumns)
2124 // viewport.getColumnSelection().compensateForEdits(shifts);
2125 viewport.setStartRes(seq.findIndex(startRes) - 1);
2126 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2137 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2139 int start = 0, end = viewport.alignment.getWidth() - 1;
2142 if (viewport.getSelectionGroup() != null)
2144 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2145 viewport.hiddenRepSequences);
2146 start = viewport.getSelectionGroup().getStartRes();
2147 end = viewport.getSelectionGroup().getEndRes();
2151 seqs = viewport.alignment.getSequencesArray();
2154 // This is to maintain viewport position on first residue
2155 // of first sequence
2156 SequenceI seq = viewport.alignment.getSequenceAt(0);
2157 int startRes = seq.findPosition(viewport.startRes);
2159 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2160 viewport.alignment));
2162 viewport.setStartRes(seq.findIndex(startRes) - 1);
2164 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2175 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2177 viewport.padGaps = padGapsMenuitem.isSelected();
2178 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2184 // if (justifySeqs>0)
2186 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2198 public void findMenuItem_actionPerformed(ActionEvent e)
2203 public void newView_actionPerformed(ActionEvent e)
2205 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2208 newap.av.gatherViewsHere = false;
2210 if (viewport.viewName == null)
2212 viewport.viewName = "Original";
2215 newap.av.historyList = viewport.historyList;
2216 newap.av.redoList = viewport.redoList;
2218 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2219 String newViewName = "View " + index;
2221 Vector comps = (Vector) PaintRefresher.components.get(viewport
2222 .getSequenceSetId());
2223 Vector existingNames = new Vector();
2224 for (int i = 0; i < comps.size(); i++)
2226 if (comps.elementAt(i) instanceof AlignmentPanel)
2228 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2229 if (!existingNames.contains(ap.av.viewName))
2231 existingNames.addElement(ap.av.viewName);
2236 while (existingNames.contains(newViewName))
2238 newViewName = "View " + (++index);
2241 newap.av.viewName = newViewName;
2243 addAlignmentPanel(newap, true);
2245 if (alignPanels.size() == 2)
2247 viewport.gatherViewsHere = true;
2249 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2252 public void expandViews_actionPerformed(ActionEvent e)
2254 Desktop.instance.explodeViews(this);
2257 public void gatherViews_actionPerformed(ActionEvent e)
2259 Desktop.instance.gatherViews(this);
2268 public void font_actionPerformed(ActionEvent e)
2270 new FontChooser(alignPanel);
2279 protected void seqLimit_actionPerformed(ActionEvent e)
2281 viewport.setShowJVSuffix(seqLimits.isSelected());
2283 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2284 .calculateIdWidth());
2285 alignPanel.paintAlignment(true);
2288 public void idRightAlign_actionPerformed(ActionEvent e)
2290 viewport.rightAlignIds = idRightAlign.isSelected();
2291 alignPanel.paintAlignment(true);
2294 public void centreColumnLabels_actionPerformed(ActionEvent e)
2296 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2297 alignPanel.paintAlignment(true);
2303 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2305 protected void followHighlight_actionPerformed()
2307 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2309 alignPanel.scrollToPosition(
2310 alignPanel.seqPanel.seqCanvas.searchResults, false);
2320 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2322 viewport.setColourText(colourTextMenuItem.isSelected());
2323 alignPanel.paintAlignment(true);
2332 public void wrapMenuItem_actionPerformed(ActionEvent e)
2334 scaleAbove.setVisible(wrapMenuItem.isSelected());
2335 scaleLeft.setVisible(wrapMenuItem.isSelected());
2336 scaleRight.setVisible(wrapMenuItem.isSelected());
2337 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2338 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2341 public void showAllSeqs_actionPerformed(ActionEvent e)
2343 viewport.showAllHiddenSeqs();
2346 public void showAllColumns_actionPerformed(ActionEvent e)
2348 viewport.showAllHiddenColumns();
2352 public void hideSelSequences_actionPerformed(ActionEvent e)
2354 viewport.hideAllSelectedSeqs();
2355 alignPanel.paintAlignment(true);
2358 * called by key handler and the hide all/show all menu items
2362 private void toggleHiddenRegions(boolean toggleSeqs,
2366 boolean hide = false;
2367 SequenceGroup sg = viewport.getSelectionGroup();
2368 if (!toggleSeqs && !toggleCols)
2370 // Hide everything by the current selection - this is a hack - we do the invert and then hide
2371 // first check that there will be visible columns after the invert.
2372 if ((viewport.colSel!=null && viewport.colSel.getSelected()!=null && viewport.colSel.getSelected().size()>0) || (sg!=null && sg.getSize()>0 && sg.getStartRes()<=sg.getEndRes()))
2374 // now invert the sequence set, if required - empty selection implies that no hiding is required.
2376 invertSequenceMenuItem_actionPerformed(null);
2377 sg = viewport.getSelectionGroup();
2381 viewport.expandColSelection(sg,true);
2382 // finally invert the column selection and get the new sequence selection.
2383 invertColSel_actionPerformed(null);
2391 && sg.getSize() != viewport.alignment.getHeight())
2393 hideSelSequences_actionPerformed(null);
2396 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
2398 showAllSeqs_actionPerformed(null);
2404 if (viewport.colSel.getSelected().size() > 0)
2406 hideSelColumns_actionPerformed(null);
2409 viewport.selectionGroup = sg;
2414 showAllColumns_actionPerformed(null);
2420 * @see jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.event.ActionEvent)
2422 public void hideAllButSelection_actionPerformed(ActionEvent e)
2424 toggleHiddenRegions(false, false);
2428 * @see jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event.ActionEvent)
2430 public void hideAllSelection_actionPerformed(ActionEvent e)
2432 SequenceGroup sg = viewport.getSelectionGroup();
2433 viewport.expandColSelection(sg,false);
2434 viewport.hideAllSelectedSeqs();
2435 viewport.hideSelectedColumns();
2436 alignPanel.paintAlignment(true);
2440 * @see jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.ActionEvent)
2442 public void showAllhidden_actionPerformed(ActionEvent e)
2444 viewport.showAllHiddenColumns();
2445 viewport.showAllHiddenSeqs();
2446 alignPanel.paintAlignment(true);
2449 public void hideSelColumns_actionPerformed(ActionEvent e)
2451 viewport.hideSelectedColumns();
2452 alignPanel.paintAlignment(true);
2455 public void hiddenMarkers_actionPerformed(ActionEvent e)
2457 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2467 protected void scaleAbove_actionPerformed(ActionEvent e)
2469 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2470 alignPanel.paintAlignment(true);
2479 protected void scaleLeft_actionPerformed(ActionEvent e)
2481 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2482 alignPanel.paintAlignment(true);
2491 protected void scaleRight_actionPerformed(ActionEvent e)
2493 viewport.setScaleRightWrapped(scaleRight.isSelected());
2494 alignPanel.paintAlignment(true);
2503 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2505 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2506 alignPanel.paintAlignment(true);
2515 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2517 viewport.setShowText(viewTextMenuItem.isSelected());
2518 alignPanel.paintAlignment(true);
2527 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2529 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2530 alignPanel.paintAlignment(true);
2533 public FeatureSettings featureSettings;
2535 public void featureSettings_actionPerformed(ActionEvent e)
2537 if (featureSettings != null)
2539 featureSettings.close();
2540 featureSettings = null;
2542 if (!showSeqFeatures.isSelected())
2544 // make sure features are actually displayed
2545 showSeqFeatures.setSelected(true);
2546 showSeqFeatures_actionPerformed(null);
2548 featureSettings = new FeatureSettings(this);
2552 * Set or clear 'Show Sequence Features'
2557 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2559 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2560 alignPanel.paintAlignment(true);
2561 if (alignPanel.getOverviewPanel() != null)
2563 alignPanel.getOverviewPanel().updateOverviewImage();
2568 * Set or clear 'Show Sequence Features'
2573 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2575 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2577 if (viewport.getShowSequenceFeaturesHeight())
2579 // ensure we're actually displaying features
2580 viewport.setShowSequenceFeatures(true);
2581 showSeqFeatures.setSelected(true);
2583 alignPanel.paintAlignment(true);
2584 if (alignPanel.getOverviewPanel() != null)
2586 alignPanel.getOverviewPanel().updateOverviewImage();
2596 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2598 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2599 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2602 public void alignmentProperties()
2604 JEditorPane editPane = new JEditorPane("text/html", "");
2605 editPane.setEditable(false);
2606 StringBuffer contents = new StringBuffer("<html>");
2609 int min = Integer.MAX_VALUE, max = 0;
2610 for (int i = 0; i < viewport.alignment.getHeight(); i++)
2612 int size = viewport.alignment.getSequenceAt(i).getEnd()
2613 - viewport.alignment.getSequenceAt(i).getStart();
2620 avg = avg / (float) viewport.alignment.getHeight();
2622 contents.append("<br>Sequences: " + viewport.alignment.getHeight());
2623 contents.append("<br>Minimum Sequence Length: " + min);
2624 contents.append("<br>Maximum Sequence Length: " + max);
2625 contents.append("<br>Average Length: " + (int) avg);
2627 if (((Alignment) viewport.alignment).getProperties() != null)
2629 Hashtable props = ((Alignment) viewport.alignment).getProperties();
2630 Enumeration en = props.keys();
2631 contents.append("<br><br><table border=\"1\">");
2632 while (en.hasMoreElements())
2634 String key = en.nextElement().toString();
2635 StringBuffer val = new StringBuffer();
2636 String vals = props.get(key).toString();
2640 npos = vals.indexOf("\n", pos);
2643 val.append(vals.substring(pos));
2647 val.append(vals.substring(pos, npos));
2651 } while (npos != -1);
2653 .append("<tr><td>" + key + "</td><td>" + val + "</td></tr>");
2655 contents.append("</table>");
2657 editPane.setText(contents.toString() + "</html>");
2658 JInternalFrame frame = new JInternalFrame();
2659 frame.getContentPane().add(new JScrollPane(editPane));
2661 Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
2662 + getTitle(), 500, 400);
2671 public void overviewMenuItem_actionPerformed(ActionEvent e)
2673 if (alignPanel.overviewPanel != null)
2678 JInternalFrame frame = new JInternalFrame();
2679 OverviewPanel overview = new OverviewPanel(alignPanel);
2680 frame.setContentPane(overview);
2681 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(), frame
2682 .getWidth(), frame.getHeight());
2684 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2686 .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2688 public void internalFrameClosed(
2689 javax.swing.event.InternalFrameEvent evt)
2691 alignPanel.setOverviewPanel(null);
2695 alignPanel.setOverviewPanel(overview);
2698 public void textColour_actionPerformed(ActionEvent e)
2700 new TextColourChooser().chooseColour(alignPanel, null);
2709 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2720 public void clustalColour_actionPerformed(ActionEvent e)
2722 changeColour(new ClustalxColourScheme(
2723 viewport.alignment.getSequences(), viewport.alignment
2733 public void zappoColour_actionPerformed(ActionEvent e)
2735 changeColour(new ZappoColourScheme());
2744 public void taylorColour_actionPerformed(ActionEvent e)
2746 changeColour(new TaylorColourScheme());
2755 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2757 changeColour(new HydrophobicColourScheme());
2766 public void helixColour_actionPerformed(ActionEvent e)
2768 changeColour(new HelixColourScheme());
2777 public void strandColour_actionPerformed(ActionEvent e)
2779 changeColour(new StrandColourScheme());
2788 public void turnColour_actionPerformed(ActionEvent e)
2790 changeColour(new TurnColourScheme());
2799 public void buriedColour_actionPerformed(ActionEvent e)
2801 changeColour(new BuriedColourScheme());
2810 public void nucleotideColour_actionPerformed(ActionEvent e)
2812 changeColour(new NucleotideColourScheme());
2815 public void annotationColour_actionPerformed(ActionEvent e)
2817 new AnnotationColourChooser(viewport, alignPanel);
2826 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2828 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2837 public void changeColour(ColourSchemeI cs)
2843 if (viewport.getAbovePIDThreshold())
2845 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2848 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2850 viewport.setGlobalColourScheme(cs);
2854 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2857 if (viewport.getConservationSelected())
2860 Alignment al = (Alignment) viewport.alignment;
2861 Conservation c = new Conservation("All",
2862 ResidueProperties.propHash, 3, al.getSequences(), 0, al
2866 c.verdict(false, viewport.ConsPercGaps);
2868 cs.setConservation(c);
2870 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
2875 cs.setConservation(null);
2878 cs.setConsensus(viewport.hconsensus);
2881 viewport.setGlobalColourScheme(cs);
2883 if (viewport.getColourAppliesToAllGroups())
2885 Vector groups = viewport.alignment.getGroups();
2887 for (int i = 0; i < groups.size(); i++)
2889 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2897 if (cs instanceof ClustalxColourScheme)
2899 sg.cs = new ClustalxColourScheme(sg
2900 .getSequences(viewport.hiddenRepSequences), sg.getWidth());
2902 else if (cs instanceof UserColourScheme)
2904 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
2910 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2911 } catch (Exception ex)
2916 if (viewport.getAbovePIDThreshold()
2917 || cs instanceof PIDColourScheme
2918 || cs instanceof Blosum62ColourScheme)
2920 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2922 sg.cs.setConsensus(AAFrequency.calculate(sg
2923 .getSequences(viewport.hiddenRepSequences), sg
2924 .getStartRes(), sg.getEndRes() + 1));
2928 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2931 if (viewport.getConservationSelected())
2933 Conservation c = new Conservation("Group",
2934 ResidueProperties.propHash, 3, sg
2935 .getSequences(viewport.hiddenRepSequences), sg
2936 .getStartRes(), sg.getEndRes() + 1);
2938 c.verdict(false, viewport.ConsPercGaps);
2939 sg.cs.setConservation(c);
2943 sg.cs.setConservation(null);
2948 if (alignPanel.getOverviewPanel() != null)
2950 alignPanel.getOverviewPanel().updateOverviewImage();
2953 alignPanel.paintAlignment(true);
2962 protected void modifyPID_actionPerformed(ActionEvent e)
2964 if (viewport.getAbovePIDThreshold()
2965 && viewport.globalColourScheme != null)
2967 SliderPanel.setPIDSliderSource(alignPanel, viewport
2968 .getGlobalColourScheme(), "Background");
2969 SliderPanel.showPIDSlider();
2979 protected void modifyConservation_actionPerformed(ActionEvent e)
2981 if (viewport.getConservationSelected()
2982 && viewport.globalColourScheme != null)
2984 SliderPanel.setConservationSlider(alignPanel,
2985 viewport.globalColourScheme, "Background");
2986 SliderPanel.showConservationSlider();
2996 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2998 viewport.setConservationSelected(conservationMenuItem.isSelected());
3000 viewport.setAbovePIDThreshold(false);
3001 abovePIDThreshold.setSelected(false);
3003 changeColour(viewport.getGlobalColourScheme());
3005 modifyConservation_actionPerformed(null);
3014 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3016 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3018 conservationMenuItem.setSelected(false);
3019 viewport.setConservationSelected(false);
3021 changeColour(viewport.getGlobalColourScheme());
3023 modifyPID_actionPerformed(null);
3032 public void userDefinedColour_actionPerformed(ActionEvent e)
3034 if (e.getActionCommand().equals("User Defined..."))
3036 new UserDefinedColours(alignPanel, null);
3040 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3041 .getUserColourSchemes().get(e.getActionCommand());
3047 public void updateUserColourMenu()
3050 Component[] menuItems = colourMenu.getMenuComponents();
3051 int i, iSize = menuItems.length;
3052 for (i = 0; i < iSize; i++)
3054 if (menuItems[i].getName() != null
3055 && menuItems[i].getName().equals("USER_DEFINED"))
3057 colourMenu.remove(menuItems[i]);
3061 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3063 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3064 .getUserColourSchemes().keys();
3066 while (userColours.hasMoreElements())
3068 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3069 userColours.nextElement().toString());
3070 radioItem.setName("USER_DEFINED");
3071 radioItem.addMouseListener(new MouseAdapter()
3073 public void mousePressed(MouseEvent evt)
3075 if (evt.isControlDown()
3076 || SwingUtilities.isRightMouseButton(evt))
3079 .removeActionListener(radioItem.getActionListeners()[0]);
3081 int option = JOptionPane.showInternalConfirmDialog(
3082 jalview.gui.Desktop.desktop,
3083 "Remove from default list?",
3084 "Remove user defined colour",
3085 JOptionPane.YES_NO_OPTION);
3086 if (option == JOptionPane.YES_OPTION)
3088 jalview.gui.UserDefinedColours
3089 .removeColourFromDefaults(radioItem.getText());
3090 colourMenu.remove(radioItem);
3094 radioItem.addActionListener(new ActionListener()
3096 public void actionPerformed(ActionEvent evt)
3098 userDefinedColour_actionPerformed(evt);
3105 radioItem.addActionListener(new ActionListener()
3107 public void actionPerformed(ActionEvent evt)
3109 userDefinedColour_actionPerformed(evt);
3113 colourMenu.insert(radioItem, 15);
3114 colours.add(radioItem);
3125 public void PIDColour_actionPerformed(ActionEvent e)
3127 changeColour(new PIDColourScheme());
3136 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3138 changeColour(new Blosum62ColourScheme());
3147 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3149 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3150 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3151 .getAlignment().getSequenceAt(0), null);
3152 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3153 viewport.alignment));
3154 alignPanel.paintAlignment(true);
3163 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3165 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3166 AlignmentSorter.sortByID(viewport.getAlignment());
3167 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
3168 alignPanel.paintAlignment(true);
3177 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3179 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3180 AlignmentSorter.sortByLength(viewport.getAlignment());
3181 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3182 viewport.alignment));
3183 alignPanel.paintAlignment(true);
3192 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3194 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3195 AlignmentSorter.sortByGroup(viewport.getAlignment());
3196 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3197 viewport.alignment));
3199 alignPanel.paintAlignment(true);
3208 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3210 new RedundancyPanel(alignPanel, this);
3219 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3221 if ((viewport.getSelectionGroup() == null)
3222 || (viewport.getSelectionGroup().getSize() < 2))
3224 JOptionPane.showInternalMessageDialog(this,
3225 "You must select at least 2 sequences.", "Invalid Selection",
3226 JOptionPane.WARNING_MESSAGE);
3230 JInternalFrame frame = new JInternalFrame();
3231 frame.setContentPane(new PairwiseAlignPanel(viewport));
3232 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
3242 public void PCAMenuItem_actionPerformed(ActionEvent e)
3244 if (((viewport.getSelectionGroup() != null)
3245 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3246 .getSelectionGroup().getSize() > 0))
3247 || (viewport.getAlignment().getHeight() < 4))
3249 JOptionPane.showInternalMessageDialog(this,
3250 "Principal component analysis must take\n"
3251 + "at least 4 input sequences.",
3252 "Sequence selection insufficient",
3253 JOptionPane.WARNING_MESSAGE);
3258 new PCAPanel(alignPanel);
3261 public void autoCalculate_actionPerformed(ActionEvent e)
3263 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3264 if (viewport.autoCalculateConsensus)
3266 viewport.firePropertyChange("alignment", null, viewport
3267 .getAlignment().getSequences());
3277 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3279 NewTreePanel("AV", "PID", "Average distance tree using PID");
3288 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3290 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3299 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3301 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3310 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3312 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3325 void NewTreePanel(String type, String pwType, String title)
3329 if (viewport.getSelectionGroup() != null)
3331 if (viewport.getSelectionGroup().getSize() < 3)
3336 "You need to have more than two sequences selected to build a tree!",
3337 "Not enough sequences", JOptionPane.WARNING_MESSAGE);
3342 SequenceGroup sg = viewport.getSelectionGroup();
3344 /* Decide if the selection is a column region */
3345 while (s < sg.getSize())
3347 if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
3353 "The selected region to create a tree may\nonly contain residues or gaps.\n"
3354 + "Try using the Pad function in the edit menu,\n"
3355 + "or one of the multiple sequence alignment web services.",
3356 "Sequences in selection are not aligned",
3357 JOptionPane.WARNING_MESSAGE);
3363 title = title + " on region";
3364 tp = new TreePanel(alignPanel, type, pwType);
3368 // are the visible sequences aligned?
3369 if (!viewport.alignment.isAligned(false))
3374 "The sequences must be aligned before creating a tree.\n"
3375 + "Try using the Pad function in the edit menu,\n"
3376 + "or one of the multiple sequence alignment web services.",
3377 "Sequences not aligned",
3378 JOptionPane.WARNING_MESSAGE);
3383 if (viewport.alignment.getHeight() < 2)
3388 tp = new TreePanel(alignPanel, type, pwType);
3393 if (viewport.viewName != null)
3395 title += viewport.viewName + " of ";
3398 title += this.title;
3400 Desktop.addInternalFrame(tp, title, 600, 500);
3411 public void addSortByOrderMenuItem(String title,
3412 final AlignmentOrder order)
3414 final JMenuItem item = new JMenuItem("by " + title);
3416 item.addActionListener(new java.awt.event.ActionListener()
3418 public void actionPerformed(ActionEvent e)
3420 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3422 // TODO: JBPNote - have to map order entries to curent SequenceI
3424 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3426 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3427 viewport.alignment));
3429 alignPanel.paintAlignment(true);
3435 * Add a new sort by annotation score menu item
3438 * the menu to add the option to
3440 * the label used to retrieve scores for each sequence on the
3443 public void addSortByAnnotScoreMenuItem(JMenu sort,
3444 final String scoreLabel)
3446 final JMenuItem item = new JMenuItem(scoreLabel);
3448 item.addActionListener(new java.awt.event.ActionListener()
3450 public void actionPerformed(ActionEvent e)
3452 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3453 AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport
3454 .getAlignment());// ,viewport.getSelectionGroup());
3455 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3456 viewport.alignment));
3457 alignPanel.paintAlignment(true);
3463 * last hash for alignment's annotation array - used to minimise cost of
3466 protected int _annotationScoreVectorHash;
3469 * search the alignment and rebuild the sort by annotation score submenu the
3470 * last alignment annotation vector hash is stored to minimize cost of
3471 * rebuilding in subsequence calls.
3474 public void buildSortByAnnotationScoresMenu()
3476 if (viewport.alignment.getAlignmentAnnotation() == null)
3481 if (viewport.alignment.getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3483 sortByAnnotScore.removeAll();
3484 // almost certainly a quicker way to do this - but we keep it simple
3485 Hashtable scoreSorts = new Hashtable();
3486 AlignmentAnnotation aann[];
3487 Enumeration sq = viewport.alignment.getSequences().elements();
3488 while (sq.hasMoreElements())
3490 aann = ((SequenceI) sq.nextElement()).getAnnotation();
3491 for (int i = 0; aann != null && i < aann.length; i++)
3493 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3495 scoreSorts.put(aann[i].label, aann[i].label);
3499 Enumeration labels = scoreSorts.keys();
3500 while (labels.hasMoreElements())
3502 addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels
3505 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3508 _annotationScoreVectorHash = viewport.alignment
3509 .getAlignmentAnnotation().hashCode();
3514 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3515 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3516 * call. Listeners are added to remove the menu item when the treePanel is
3517 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3521 * Displayed tree window.
3523 * SortBy menu item title.
3525 public void buildTreeMenu()
3527 sortByTreeMenu.removeAll();
3529 Vector comps = (Vector) PaintRefresher.components.get(viewport
3530 .getSequenceSetId());
3531 Vector treePanels = new Vector();
3532 int i, iSize = comps.size();
3533 for (i = 0; i < iSize; i++)
3535 if (comps.elementAt(i) instanceof TreePanel)
3537 treePanels.add(comps.elementAt(i));
3541 iSize = treePanels.size();
3545 sortByTreeMenu.setVisible(false);
3549 sortByTreeMenu.setVisible(true);
3551 for (i = 0; i < treePanels.size(); i++)
3553 TreePanel tp = (TreePanel) treePanels.elementAt(i);
3554 final JMenuItem item = new JMenuItem(tp.getTitle());
3555 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3556 item.addActionListener(new java.awt.event.ActionListener()
3558 public void actionPerformed(ActionEvent e)
3560 SequenceI[] oldOrder = viewport.getAlignment()
3561 .getSequencesArray();
3562 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
3564 addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
3565 viewport.alignment));
3567 alignPanel.paintAlignment(true);
3571 sortByTreeMenu.add(item);
3576 * Work out whether the whole set of sequences or just the selected set will
3577 * be submitted for multiple alignment.
3580 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3582 // Now, check we have enough sequences
3583 AlignmentView msa = null;
3585 if ((viewport.getSelectionGroup() != null)
3586 && (viewport.getSelectionGroup().getSize() > 1))
3588 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3589 // some common interface!
3591 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3592 * SequenceI[sz = seqs.getSize(false)];
3594 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3595 * seqs.getSequenceAt(i); }
3597 msa = viewport.getAlignmentView(true);
3602 * Vector seqs = viewport.getAlignment().getSequences();
3604 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3606 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3607 * seqs.elementAt(i); } }
3609 msa = viewport.getAlignmentView(false);
3615 * Decides what is submitted to a secondary structure prediction service: the
3616 * first sequence in the alignment, or in the current selection, or, if the
3617 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3618 * region or the whole alignment. (where the first sequence in the set is the
3619 * one that the prediction will be for).
3621 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3623 AlignmentView seqs = null;
3625 if ((viewport.getSelectionGroup() != null)
3626 && (viewport.getSelectionGroup().getSize() > 0))
3628 seqs = viewport.getAlignmentView(true);
3632 seqs = viewport.getAlignmentView(false);
3634 // limit sequences - JBPNote in future - could spawn multiple prediction
3636 // TODO: viewport.alignment.isAligned is a global state - the local
3637 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3638 if (!viewport.alignment.isAligned(false))
3640 seqs.setSequences(new SeqCigar[]
3641 { seqs.getSequences()[0] });
3642 // TODO: if seqs.getSequences().length>1 then should really have warned user!
3654 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3656 // Pick the tree file
3657 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
3658 .getProperty("LAST_DIRECTORY"));
3659 chooser.setFileView(new JalviewFileView());
3660 chooser.setDialogTitle("Select a newick-like tree file");
3661 chooser.setToolTipText("Load a tree file");
3663 int value = chooser.showOpenDialog(null);
3665 if (value == JalviewFileChooser.APPROVE_OPTION)
3667 String choice = chooser.getSelectedFile().getPath();
3668 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3669 jalview.io.NewickFile fin = null;
3672 fin = new jalview.io.NewickFile(choice, "File");
3673 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3674 } catch (Exception ex)
3676 JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3677 "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
3678 ex.printStackTrace();
3680 if (fin != null && fin.hasWarningMessage())
3682 JOptionPane.showMessageDialog(Desktop.desktop, fin
3683 .getWarningMessage(), "Possible problem with tree file",
3684 JOptionPane.WARNING_MESSAGE);
3689 public TreePanel ShowNewickTree(NewickFile nf, String title)
3691 return ShowNewickTree(nf, title, 600, 500, 4, 5);
3694 public TreePanel ShowNewickTree(NewickFile nf, String title,
3695 AlignmentView input)
3697 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
3700 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
3701 int h, int x, int y)
3703 return ShowNewickTree(nf, title, null, w, h, x, y);
3707 * Add a treeviewer for the tree extracted from a newick file object to the
3708 * current alignment view
3715 * Associated alignment input data (or null)
3724 * @return TreePanel handle
3726 public TreePanel ShowNewickTree(NewickFile nf, String title,
3727 AlignmentView input, int w, int h, int x, int y)
3729 TreePanel tp = null;
3735 if (nf.getTree() != null)
3737 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
3743 tp.setLocation(x, y);
3746 Desktop.addInternalFrame(tp, title, w, h);
3748 } catch (Exception ex)
3750 ex.printStackTrace();
3757 * Generates menu items and listener event actions for web service clients
3760 public void BuildWebServiceMenu()
3762 // TODO: add support for context dependent disabling of services based on
3763 // alignment and current selection
3764 // TODO: add additional serviceHandle parameter to specify abstract handler
3765 // class independently of AbstractName
3766 // TODO: add in rediscovery GUI function to restart discoverer
3767 // TODO: group services by location as well as function and/or introduce
3768 // object broker mechanism.
3769 if ((Discoverer.services != null) && (Discoverer.services.size() > 0))
3771 // TODO: refactor to allow list of AbstractName/Handler bindings to be
3772 // stored or retrieved from elsewhere
3773 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
3774 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
3775 Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
3776 // TODO: move GUI generation code onto service implementation - so a
3777 // client instance attaches itself to the GUI with method call like
3778 // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
3780 Vector wsmenu = new Vector();
3781 final IProgressIndicator af = this;
3784 // Add any Multiple Sequence Alignment Services
3785 final JMenu msawsmenu = new JMenu("Alignment");
3786 for (int i = 0, j = msaws.size(); i < j; i++)
3788 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
3790 jalview.ws.WSClient impl = jalview.ws.Discoverer
3791 .getServiceClient(sh);
3792 impl.attachWSMenuEntry(msawsmenu, this);
3795 wsmenu.add(msawsmenu);
3797 if (secstrpr != null)
3799 // Add any secondary structure prediction services
3800 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
3801 for (int i = 0, j = secstrpr.size(); i < j; i++)
3803 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
3805 jalview.ws.WSClient impl = jalview.ws.Discoverer
3806 .getServiceClient(sh);
3807 impl.attachWSMenuEntry(secstrmenu, this);
3809 wsmenu.add(secstrmenu);
3811 if (seqsrch != null)
3813 // Add any sequence search services
3814 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
3815 for (int i = 0, j = seqsrch.size(); i < j; i++)
3817 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
3819 jalview.ws.WSClient impl = jalview.ws.Discoverer
3820 .getServiceClient(sh);
3821 impl.attachWSMenuEntry(seqsrchmenu, this);
3823 wsmenu.add(seqsrchmenu);
3825 // finally, add the whole shebang onto the webservices menu
3826 resetWebServiceMenu();
3827 for (int i = 0, j = wsmenu.size(); i < j; i++)
3829 webService.add((JMenu) wsmenu.get(i));
3834 resetWebServiceMenu();
3835 this.webService.add(this.webServiceNoServices);
3840 * empty the web service menu and add any ad-hoc functions not dynamically
3844 private void resetWebServiceMenu()
3846 webService.removeAll();
3847 build_fetchdbmenu(webService);
3848 build_urlServiceMenu(webService);
3852 * construct any groupURL type service menu entries.
3855 private void build_urlServiceMenu(JMenu webService)
3857 jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(webService, this);
3861 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
3862 * chooser = new JalviewFileChooser(jalview.bin.Cache.
3863 * getProperty("LAST_DIRECTORY"));
3865 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
3866 * to Vamsas file"); chooser.setToolTipText("Export");
3868 * int value = chooser.showSaveDialog(this);
3870 * if (value == JalviewFileChooser.APPROVE_OPTION) {
3871 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
3872 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
3873 * chooser.getSelectedFile().getAbsolutePath(), this); } }
3876 * prototype of an automatically enabled/disabled analysis function
3879 protected void setShowProductsEnabled()
3881 SequenceI[] selection = viewport.getSequenceSelection();
3882 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
3883 viewport.getAlignment().getDataset()))
3885 showProducts.setEnabled(true);
3890 showProducts.setEnabled(false);
3895 * search selection for sequence xRef products and build the show products
3900 * @return true if showProducts menu should be enabled.
3902 public boolean canShowProducts(SequenceI[] selection,
3903 boolean isRegionSelection, Alignment dataset)
3905 boolean showp = false;
3908 showProducts.removeAll();
3909 final boolean dna = viewport.getAlignment().isNucleotide();
3910 final Alignment ds = dataset;
3911 String[] ptypes = (selection == null || selection.length == 0) ? null
3912 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
3914 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
3915 // selection, dataset, true);
3916 final SequenceI[] sel = selection;
3917 for (int t = 0; ptypes != null && t < ptypes.length; t++)
3920 final boolean isRegSel = isRegionSelection;
3921 final AlignFrame af = this;
3922 final String source = ptypes[t];
3923 JMenuItem xtype = new JMenuItem(ptypes[t]);
3924 xtype.addActionListener(new ActionListener()
3927 public void actionPerformed(ActionEvent e)
3929 // TODO: new thread for this call with vis-delay
3930 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
3931 isRegSel, dna, source);
3935 showProducts.add(xtype);
3937 showProducts.setVisible(showp);
3938 showProducts.setEnabled(showp);
3939 } catch (Exception e)
3941 jalview.bin.Cache.log
3943 "canTranslate threw an exception - please report to help@jalview.org",
3950 protected void showProductsFor(SequenceI[] sel, Alignment ds,
3951 boolean isRegSel, boolean dna, String source)
3953 final boolean fisRegSel = isRegSel;
3954 final boolean fdna = dna;
3955 final String fsrc = source;
3956 final AlignFrame ths = this;
3957 final SequenceI[] fsel = sel;
3958 Runnable foo = new Runnable()
3963 final long sttime = System.currentTimeMillis();
3964 ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
3967 Alignment ds = ths.getViewport().alignment.getDataset(); // update
3971 Alignment prods = CrossRef
3972 .findXrefSequences(fsel, fdna, fsrc, ds);
3975 SequenceI[] sprods = new SequenceI[prods.getHeight()];
3976 for (int s = 0; s < sprods.length; s++)
3978 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
3979 if (ds.getSequences() == null
3980 || !ds.getSequences().contains(
3981 sprods[s].getDatasetSequence()))
3982 ds.addSequence(sprods[s].getDatasetSequence());
3983 sprods[s].updatePDBIds();
3985 Alignment al = new Alignment(sprods);
3986 AlignedCodonFrame[] cf = prods.getCodonFrames();
3988 for (int s = 0; cf != null && s < cf.length; s++)
3990 al.addCodonFrame(cf[s]);
3993 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
3995 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
3996 + " for " + ((fisRegSel) ? "selected region of " : "")
3998 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4003 System.err.println("No Sequences generated for xRef type "
4006 } catch (Exception e)
4008 jalview.bin.Cache.log.error(
4009 "Exception when finding crossreferences", e);
4010 } catch (OutOfMemoryError e)
4012 new OOMWarning("whilst fetching crossreferences", e);
4015 jalview.bin.Cache.log.error("Error when finding crossreferences",
4018 ths.setProgressBar("Finished searching for sequences from " + fsrc,
4023 Thread frunner = new Thread(foo);
4027 public boolean canShowTranslationProducts(SequenceI[] selection,
4028 AlignmentI alignment)
4033 return (jalview.analysis.Dna.canTranslate(selection, viewport
4034 .getViewAsVisibleContigs(true)));
4035 } catch (Exception e)
4037 jalview.bin.Cache.log
4039 "canTranslate threw an exception - please report to help@jalview.org",
4045 public void showProducts_actionPerformed(ActionEvent e)
4047 // /////////////////////////////
4048 // Collect Data to be translated/transferred
4050 SequenceI[] selection = viewport.getSequenceSelection();
4051 AlignmentI al = null;
4054 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4055 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4056 viewport.getAlignment().getDataset());
4057 } catch (Exception ex)
4060 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4067 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4068 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4072 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4073 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4074 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4078 public void showTranslation_actionPerformed(ActionEvent e)
4080 // /////////////////////////////
4081 // Collect Data to be translated/transferred
4083 SequenceI[] selection = viewport.getSequenceSelection();
4084 String[] seqstring = viewport.getViewAsString(true);
4085 AlignmentI al = null;
4088 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4089 viewport.getViewAsVisibleContigs(true), viewport
4090 .getGapCharacter(), viewport.alignment
4091 .getAlignmentAnnotation(), viewport.alignment
4092 .getWidth(), viewport.getAlignment().getDataset());
4093 } catch (Exception ex)
4096 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4103 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4104 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4108 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4109 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4110 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4115 * Try to load a features file onto the alignment.
4118 * contents or path to retrieve file
4120 * access mode of file (see jalview.io.AlignFile)
4121 * @return true if features file was parsed corectly.
4123 public boolean parseFeaturesFile(String file, String type)
4125 boolean featuresFile = false;
4128 featuresFile = new FeaturesFile(file, type).parse(viewport.alignment
4129 .getDataset(), alignPanel.seqPanel.seqCanvas
4130 .getFeatureRenderer().featureColours, false);
4131 } catch (Exception ex)
4133 ex.printStackTrace();
4138 viewport.showSequenceFeatures = true;
4139 showSeqFeatures.setSelected(true);
4140 if (alignPanel.seqPanel.seqCanvas.fr != null)
4142 // update the min/max ranges where necessary
4143 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4145 if (featureSettings!=null)
4147 featureSettings.setTableData();
4149 alignPanel.paintAlignment(true);
4152 return featuresFile;
4155 public void dragEnter(DropTargetDragEvent evt)
4159 public void dragExit(DropTargetEvent evt)
4163 public void dragOver(DropTargetDragEvent evt)
4167 public void dropActionChanged(DropTargetDragEvent evt)
4171 public void drop(DropTargetDropEvent evt)
4173 Transferable t = evt.getTransferable();
4174 java.util.List files = null;
4178 DataFlavor uriListFlavor = new DataFlavor(
4179 "text/uri-list;class=java.lang.String");
4180 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4182 // Works on Windows and MacOSX
4183 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4184 files = (java.util.List) t
4185 .getTransferData(DataFlavor.javaFileListFlavor);
4187 else if (t.isDataFlavorSupported(uriListFlavor))
4189 // This is used by Unix drag system
4190 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4191 String data = (String) t.getTransferData(uriListFlavor);
4192 files = new java.util.ArrayList(1);
4193 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4194 data, "\r\n"); st.hasMoreTokens();)
4196 String s = st.nextToken();
4197 if (s.startsWith("#"))
4199 // the line is a comment (as per the RFC 2483)
4203 java.net.URI uri = new java.net.URI(s);
4204 // check to see if we can handle this kind of URI
4205 if (uri.getScheme().toLowerCase().startsWith("http"))
4207 files.add(uri.toString());
4211 // otherwise preserve old behaviour: catch all for file objects
4212 java.io.File file = new java.io.File(uri);
4213 files.add(file.toString());
4217 } catch (Exception e)
4219 e.printStackTrace();
4226 for (int i = 0; i < files.size(); i++)
4228 loadJalviewDataFile(files.get(i).toString());
4230 } catch (Exception ex)
4232 ex.printStackTrace();
4238 * Attempt to load a "dropped" file or URL string: First by testing whether
4239 * it's and Annotation file, then a JNet file, and finally a features file. If
4240 * all are false then the user may have dropped an alignment file onto this
4244 * either a filename or a URL string.
4246 public void loadJalviewDataFile(String file)
4250 String protocol = jalview.io.FormatAdapter.FILE;
4251 String f = file.toLowerCase();
4252 if (f.indexOf("http:") == 0 || f.indexOf("https:") == 0
4253 || f.indexOf("file:") == 0)
4255 protocol = jalview.io.FormatAdapter.URL;
4258 boolean isAnnotation = new AnnotationFile().readAnnotationFile(
4259 viewport.alignment, file, protocol);
4263 // try to see if its a JNet 'concise' style annotation file *before* we
4264 // try to parse it as a features file
4265 String format = new IdentifyFile().Identify(file, protocol);
4266 if (format.equalsIgnoreCase("JnetFile"))
4268 jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
4270 new JnetAnnotationMaker().add_annotation(predictions, viewport
4271 .getAlignment(), 0, false);
4272 isAnnotation = true;
4276 // try to parse it as a features file
4277 boolean isGroupsFile = parseFeaturesFile(file, protocol);
4278 // if it wasn't a features file then we just treat it as a general
4279 // alignment file to load into the current view.
4282 new FileLoader().LoadFile(viewport, file, protocol, format);
4286 alignPanel.paintAlignment(true);
4293 alignPanel.adjustAnnotationHeight();
4294 viewport.updateSequenceIdColours();
4295 buildSortByAnnotationScoresMenu();
4296 alignPanel.paintAlignment(true);
4298 } catch (Exception ex)
4300 ex.printStackTrace();
4304 public void tabSelectionChanged(int index)
4308 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
4309 viewport = alignPanel.av;
4310 setMenusFromViewport(viewport);
4314 public void tabbedPane_mousePressed(MouseEvent e)
4316 if (SwingUtilities.isRightMouseButton(e))
4318 String reply = JOptionPane.showInternalInputDialog(this,
4319 "Enter View Name", "Edit View Name",
4320 JOptionPane.QUESTION_MESSAGE);
4324 viewport.viewName = reply;
4325 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4330 public AlignViewport getCurrentView()
4336 * Open the dialog for regex description parsing.
4338 protected void extractScores_actionPerformed(ActionEvent e)
4340 ParseProperties pp = new jalview.analysis.ParseProperties(
4341 viewport.alignment);
4342 // TODO: verify regex and introduce GUI dialog for version 2.5
4343 // if (pp.getScoresFromDescription("col", "score column ",
4344 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4346 if (pp.getScoresFromDescription("description column",
4347 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4349 buildSortByAnnotationScoresMenu();
4357 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4360 protected void showDbRefs_actionPerformed(ActionEvent e)
4362 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
4368 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4371 protected void showNpFeats_actionPerformed(ActionEvent e)
4373 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
4377 * find the viewport amongst the tabs in this alignment frame and close that
4382 public boolean closeView(AlignViewport av)
4386 this.closeMenuItem_actionPerformed(false);
4389 Component[] comp = tabbedPane.getComponents();
4390 for (int i = 0; comp != null && i < comp.length; i++)
4392 if (comp[i] instanceof AlignmentPanel)
4394 if (((AlignmentPanel) comp[i]).av == av)
4397 closeView((AlignmentPanel) comp[i]);
4405 protected void build_fetchdbmenu(JMenu webService)
4407 // Temporary hack - DBRef Fetcher always top level ws entry.
4408 // TODO We probably want to store a sequence database checklist in
4409 // preferences and have checkboxes.. rather than individual sources selected
4411 JMenu rfetch = new JMenu("Fetch DB References");
4413 .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
4414 webService.add(rfetch);
4416 JMenuItem fetchr = new JMenuItem("Standard Databases");
4418 .setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
4419 fetchr.addActionListener(new ActionListener()
4422 public void actionPerformed(ActionEvent e)
4424 new Thread(new Runnable()
4429 new jalview.ws.DBRefFetcher(alignPanel.av
4430 .getSequenceSelection(), alignPanel.alignFrame)
4431 .fetchDBRefs(false);
4439 JMenu dfetch = new JMenu();
4441 jalview.ws.SequenceFetcher sf = SequenceFetcher
4442 .getSequenceFetcherSingleton(this);
4443 String[] otherdb = sf.getOrderedSupportedSources();
4444 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4445 // jalview.util.QuickSort.sort(otherdb, otherdb);
4446 int comp = 0, mcomp = 15;
4447 String mname = null;
4448 if (otherdb != null && otherdb.length > 0)
4450 for (int i = 0; i < otherdb.length; i++)
4452 String dbname = sf.getSourceProxy(otherdb[i]).getDbName();
4455 mname = "from '" + dbname + "'";
4457 fetchr = new JMenuItem(otherdb[i]);
4458 final String[] dassource = new String[]
4460 fetchr.addActionListener(new ActionListener()
4463 public void actionPerformed(ActionEvent e)
4465 new Thread(new Runnable()
4470 new jalview.ws.DBRefFetcher(alignPanel.av
4471 .getSequenceSelection(), alignPanel.alignFrame,
4472 dassource).fetchDBRefs(false);
4478 fetchr.setToolTipText("Retrieve from " + dbname);
4480 if (comp++ == mcomp || i == (otherdb.length - 1))
4482 dfetch.setText(mname + " to '" + dbname + "'");
4484 dfetch = new JMenu();
4493 * Left justify the whole alignment.
4495 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
4497 AlignmentI al = viewport.getAlignment();
4499 viewport.firePropertyChange("alignment", null, al);
4503 * Right justify the whole alignment.
4505 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
4507 AlignmentI al = viewport.getAlignment();
4509 viewport.firePropertyChange("alignment", null, al);
4512 public void setShowSeqFeatures(boolean b)
4514 showSeqFeatures.setSelected(true);
4515 viewport.setShowSequenceFeatures(true);
4522 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
4523 * awt.event.ActionEvent)
4525 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
4527 viewport.setShowUnconserved(showUnconservedMenuItem.getState());
4528 alignPanel.paintAlignment(true);
4535 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
4538 protected void showGroupConsensus_actionPerformed(ActionEvent e)
4540 viewport.setShowGroupConsensus(showGroupConsensus.getState());
4541 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4549 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
4550 * .event.ActionEvent)
4552 protected void showGroupConservation_actionPerformed(ActionEvent e)
4554 viewport.setShowGroupConservation(showGroupConservation.getState());
4555 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4559 * @see jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt.event.ActionEvent)
4561 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
4563 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
4564 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4568 * @see jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt.event.ActionEvent)
4570 protected void showSequenceLogo_actionPerformed(ActionEvent e)
4572 viewport.setShowSequenceLogo(showSequenceLogo.getState());
4573 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4575 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
4577 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4584 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
4585 * .event.ActionEvent)
4587 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
4589 if (viewport.getSelectionGroup() != null)
4591 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
4592 viewport.getSequenceSelection(), viewport.getAlignmentView(
4593 true).getSequenceStrings(viewport.getGapCharacter()),
4594 viewport.alignment.getGroups());
4595 viewport.alignment.deleteAllGroups();
4596 viewport.sequenceColours = null;
4597 viewport.setSelectionGroup(null);
4598 // set view properties for each group
4599 for (int g = 0; g < gps.length; g++)
4601 gps[g].setShowunconserved(viewport.getShowUnconserved());
4602 gps[g].setIncludeAllConsSymbols(viewport.isIncludeAllConsensusSymbols());
4603 viewport.alignment.addGroup(gps[g]);
4604 Color col = new Color((int) (Math.random() * 255), (int) (Math
4605 .random() * 255), (int) (Math.random() * 255));
4606 col = col.brighter();
4607 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
4608 .hasMoreElements(); viewport.setSequenceColour(
4609 (SequenceI) sq.nextElement(), col))
4612 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
4613 alignPanel.updateAnnotation();
4614 alignPanel.paintAlignment(true);
4619 class PrintThread extends Thread
4623 public PrintThread(AlignmentPanel ap)
4628 static PageFormat pf;
4632 PrinterJob printJob = PrinterJob.getPrinterJob();
4636 printJob.setPrintable(ap, pf);
4640 printJob.setPrintable(ap);
4643 if (printJob.printDialog())
4648 } catch (Exception PrintException)
4650 PrintException.printStackTrace();