2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
25 import java.awt.datatransfer.*;
26 import java.awt.dnd.*;
27 import java.awt.event.*;
28 import java.awt.print.*;
30 import javax.swing.event.MenuEvent;
32 import jalview.analysis.*;
33 import jalview.bin.Cache;
34 import jalview.commands.*;
35 import jalview.datamodel.*;
37 import jalview.jbgui.*;
38 import jalview.schemes.*;
40 import jalview.ws.jws1.Discoverer;
41 import jalview.ws.jws2.Jws2Discoverer;
49 public class AlignFrame extends GAlignFrame implements DropTargetListener,
54 public static final int DEFAULT_WIDTH = 700;
57 public static final int DEFAULT_HEIGHT = 500;
59 public AlignmentPanel alignPanel;
61 AlignViewport viewport;
63 Vector alignPanels = new Vector();
66 * Last format used to load or save alignments in this window
68 String currentFileFormat = null;
71 * Current filename for this alignment
73 String fileName = null;
76 * Creates a new AlignFrame object with specific width and height.
82 public AlignFrame(AlignmentI al, int width, int height)
84 this(al, null, width, height);
88 * Creates a new AlignFrame object with specific width, height and
94 * @param sequenceSetId
96 public AlignFrame(AlignmentI al, int width, int height,
99 this(al, null, width, height, sequenceSetId);
103 * Creates a new AlignFrame object with specific width, height and
109 * @param sequenceSetId
112 public AlignFrame(AlignmentI al, int width, int height,
113 String sequenceSetId, String viewId)
115 this(al, null, width, height, sequenceSetId, viewId);
119 * new alignment window with hidden columns
123 * @param hiddenColumns
124 * ColumnSelection or null
126 * Width of alignment frame
130 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
131 int width, int height)
133 this(al, hiddenColumns, width, height, null);
137 * Create alignment frame for al with hiddenColumns, a specific width and
138 * height, and specific sequenceId
141 * @param hiddenColumns
144 * @param sequenceSetId
147 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
148 int width, int height, String sequenceSetId)
150 this(al, hiddenColumns, width, height, sequenceSetId, null);
154 * Create alignment frame for al with hiddenColumns, a specific width and
155 * height, and specific sequenceId
158 * @param hiddenColumns
161 * @param sequenceSetId
166 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
167 int width, int height, String sequenceSetId, String viewId)
169 setSize(width, height);
170 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
172 alignPanel = new AlignmentPanel(this, viewport);
174 if (al.getDataset() == null)
179 addAlignmentPanel(alignPanel, true);
184 * Make a new AlignFrame from exisiting alignmentPanels
191 public AlignFrame(AlignmentPanel ap)
195 addAlignmentPanel(ap, false);
200 * initalise the alignframe from the underlying viewport data and the
205 if (viewport.conservation == null)
207 BLOSUM62Colour.setEnabled(false);
208 conservationMenuItem.setEnabled(false);
209 modifyConservation.setEnabled(false);
210 // PIDColour.setEnabled(false);
211 // abovePIDThreshold.setEnabled(false);
212 // modifyPID.setEnabled(false);
215 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
218 if (sortby.equals("Id"))
220 sortIDMenuItem_actionPerformed(null);
222 else if (sortby.equals("Pairwise Identity"))
224 sortPairwiseMenuItem_actionPerformed(null);
227 if (Desktop.desktop != null)
229 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
230 addServiceListeners();
231 setGUINucleotide(viewport.alignment.isNucleotide());
234 setMenusFromViewport(viewport);
235 buildSortByAnnotationScoresMenu();
236 if (viewport.wrapAlignment)
238 wrapMenuItem_actionPerformed(null);
241 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
243 this.overviewMenuItem_actionPerformed(null);
251 * Change the filename and format for the alignment, and enable the 'reload'
252 * button functionality.
259 public void setFileName(String file, String format)
262 currentFileFormat = format;
263 reload.setEnabled(true);
266 void addKeyListener()
268 addKeyListener(new KeyAdapter()
270 public void keyPressed(KeyEvent evt)
272 if (viewport.cursorMode
273 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
274 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
275 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
276 && Character.isDigit(evt.getKeyChar()))
277 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
279 switch (evt.getKeyCode())
282 case 27: // escape key
283 deselectAllSequenceMenuItem_actionPerformed(null);
287 case KeyEvent.VK_DOWN:
288 if (evt.isAltDown() || !viewport.cursorMode)
289 moveSelectedSequences(false);
290 if (viewport.cursorMode)
291 alignPanel.seqPanel.moveCursor(0, 1);
295 if (evt.isAltDown() || !viewport.cursorMode)
296 moveSelectedSequences(true);
297 if (viewport.cursorMode)
298 alignPanel.seqPanel.moveCursor(0, -1);
302 case KeyEvent.VK_LEFT:
303 if (evt.isAltDown() || !viewport.cursorMode)
304 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
306 alignPanel.seqPanel.moveCursor(-1, 0);
310 case KeyEvent.VK_RIGHT:
311 if (evt.isAltDown() || !viewport.cursorMode)
312 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
314 alignPanel.seqPanel.moveCursor(1, 0);
317 case KeyEvent.VK_SPACE:
318 if (viewport.cursorMode)
320 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
321 || evt.isShiftDown() || evt.isAltDown());
325 case KeyEvent.VK_DELETE:
326 case KeyEvent.VK_BACK_SPACE:
327 if (!viewport.cursorMode)
329 cut_actionPerformed(null);
333 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
334 || evt.isShiftDown() || evt.isAltDown());
340 if (viewport.cursorMode)
342 alignPanel.seqPanel.setCursorRow();
346 if (viewport.cursorMode && !evt.isControlDown())
348 alignPanel.seqPanel.setCursorColumn();
352 if (viewport.cursorMode)
354 alignPanel.seqPanel.setCursorPosition();
358 case KeyEvent.VK_ENTER:
359 case KeyEvent.VK_COMMA:
360 if (viewport.cursorMode)
362 alignPanel.seqPanel.setCursorRowAndColumn();
367 if (viewport.cursorMode)
369 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
373 if (viewport.cursorMode)
375 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
380 viewport.cursorMode = !viewport.cursorMode;
381 statusBar.setText("Keyboard editing mode is "
382 + (viewport.cursorMode ? "on" : "off"));
383 if (viewport.cursorMode)
385 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
386 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
388 alignPanel.seqPanel.seqCanvas.repaint();
394 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
395 java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
397 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
399 javax.help.HelpBroker hb = hs.createHelpBroker();
400 hb.setCurrentID("home");
401 hb.setDisplayed(true);
402 } catch (Exception ex)
404 ex.printStackTrace();
409 boolean toggleSeqs = !evt.isControlDown();
410 boolean toggleCols = !evt.isShiftDown();
411 toggleHiddenRegions(toggleSeqs, toggleCols);
414 case KeyEvent.VK_PAGE_UP:
415 if (viewport.wrapAlignment)
417 alignPanel.scrollUp(true);
421 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
422 - viewport.endSeq + viewport.startSeq);
425 case KeyEvent.VK_PAGE_DOWN:
426 if (viewport.wrapAlignment)
428 alignPanel.scrollUp(false);
432 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
433 + viewport.endSeq - viewport.startSeq);
439 public void keyReleased(KeyEvent evt)
441 switch (evt.getKeyCode())
443 case KeyEvent.VK_LEFT:
444 if (evt.isAltDown() || !viewport.cursorMode)
445 viewport.firePropertyChange("alignment", null, viewport
446 .getAlignment().getSequences());
449 case KeyEvent.VK_RIGHT:
450 if (evt.isAltDown() || !viewport.cursorMode)
451 viewport.firePropertyChange("alignment", null, viewport
452 .getAlignment().getSequences());
459 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
461 ap.alignFrame = this;
463 alignPanels.addElement(ap);
465 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
467 int aSize = alignPanels.size();
469 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
471 if (aSize == 1 && ap.av.viewName == null)
473 this.getContentPane().add(ap, BorderLayout.CENTER);
479 setInitialTabVisible();
482 expandViews.setEnabled(true);
483 gatherViews.setEnabled(true);
484 tabbedPane.addTab(ap.av.viewName, ap);
486 ap.setVisible(false);
493 ap.av.alignment.padGaps();
495 ap.av.updateConservation(ap);
496 ap.av.updateConsensus(ap);
500 public void setInitialTabVisible()
502 expandViews.setEnabled(true);
503 gatherViews.setEnabled(true);
504 tabbedPane.setVisible(true);
505 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
506 tabbedPane.addTab(first.av.viewName, first);
507 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
510 public AlignViewport getViewport()
515 /* Set up intrinsic listeners for dynamically generated GUI bits. */
516 private void addServiceListeners()
518 final java.beans.PropertyChangeListener thisListener;
519 Desktop.instance.addJalviewPropertyChangeListener("services",
520 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 SwingUtilities.invokeLater(new Runnable()
533 .println("Rebuild WS Menu for service change");
534 BuildWebServiceMenu();
541 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
543 public void internalFrameClosed(
544 javax.swing.event.InternalFrameEvent evt)
546 System.out.println("deregistering discoverer listener");
547 Desktop.instance.removeJalviewPropertyChangeListener("services",
549 closeMenuItem_actionPerformed(true);
552 // Finally, build the menu once to get current service state
553 new Thread(new Runnable()
557 BuildWebServiceMenu();
562 public void setGUINucleotide(boolean nucleotide)
564 showTranslation.setVisible(nucleotide);
565 conservationMenuItem.setEnabled(!nucleotide);
566 modifyConservation.setEnabled(!nucleotide);
567 showGroupConservation.setEnabled(!nucleotide);
568 // Remember AlignFrame always starts as protein
571 calculateMenu.remove(calculateMenu.getItemCount() - 2);
576 * set up menus for the currently viewport. This may be called after any
577 * operation that affects the data in the current view (selection changed,
578 * etc) to update the menus to reflect the new state.
580 public void setMenusForViewport()
582 setMenusFromViewport(viewport);
586 * Need to call this method when tabs are selected for multiple views, or when
587 * loading from Jalview2XML.java
592 void setMenusFromViewport(AlignViewport av)
594 padGapsMenuitem.setSelected(av.padGaps);
595 colourTextMenuItem.setSelected(av.showColourText);
596 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
597 conservationMenuItem.setSelected(av.getConservationSelected());
598 seqLimits.setSelected(av.getShowJVSuffix());
599 idRightAlign.setSelected(av.rightAlignIds);
600 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
601 renderGapsMenuItem.setSelected(av.renderGaps);
602 wrapMenuItem.setSelected(av.wrapAlignment);
603 scaleAbove.setVisible(av.wrapAlignment);
604 scaleLeft.setVisible(av.wrapAlignment);
605 scaleRight.setVisible(av.wrapAlignment);
606 annotationPanelMenuItem.setState(av.showAnnotation);
607 viewBoxesMenuItem.setSelected(av.showBoxes);
608 viewTextMenuItem.setSelected(av.showText);
609 showNonconservedMenuItem.setSelected(av.showUnconserved);
610 showGroupConsensus.setSelected(av.showGroupConsensus);
611 showGroupConservation.setSelected(av.showGroupConservation);
612 showConsensusHistogram.setSelected(av.showConsensusHistogram);
613 showSequenceLogo.setSelected(av.showSequenceLogo);
614 setColourSelected(ColourSchemeProperty.getColourName(av
615 .getGlobalColourScheme()));
617 showSeqFeatures.setSelected(av.showSequenceFeatures);
618 hiddenMarkers.setState(av.showHiddenMarkers);
619 applyToAllGroups.setState(av.colourAppliesToAllGroups);
620 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
621 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
623 setShowProductsEnabled();
628 Hashtable progressBars, progressBarHandlers;
633 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
635 public void setProgressBar(String message, long id)
637 if (progressBars == null)
639 progressBars = new Hashtable();
640 progressBarHandlers = new Hashtable();
643 JPanel progressPanel;
644 Long lId = new Long(id);
645 GridLayout layout = (GridLayout) statusPanel.getLayout();
646 if (progressBars.get(lId) != null)
648 progressPanel = (JPanel) progressBars.get(new Long(id));
649 statusPanel.remove(progressPanel);
650 progressBars.remove(lId);
651 progressPanel = null;
654 statusBar.setText(message);
656 if (progressBarHandlers.contains(lId))
658 progressBarHandlers.remove(lId);
660 layout.setRows(layout.getRows() - 1);
664 progressPanel = new JPanel(new BorderLayout(10, 5));
666 JProgressBar progressBar = new JProgressBar();
667 progressBar.setIndeterminate(true);
669 progressPanel.add(new JLabel(message), BorderLayout.WEST);
670 progressPanel.add(progressBar, BorderLayout.CENTER);
672 layout.setRows(layout.getRows() + 1);
673 statusPanel.add(progressPanel);
675 progressBars.put(lId, progressPanel);
678 setMenusForViewport();
682 public void registerHandler(final long id,
683 final IProgressIndicatorHandler handler)
685 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
688 "call setProgressBar before registering the progress bar's handler.");
690 progressBarHandlers.put(new Long(id), handler);
691 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
692 if (handler.canCancel())
694 JButton cancel = new JButton("Cancel");
695 final IProgressIndicator us = this;
696 cancel.addActionListener(new ActionListener()
699 public void actionPerformed(ActionEvent e)
701 handler.cancelActivity(id);
704 + ((JLabel) progressPanel.getComponent(0))
708 progressPanel.add(cancel, BorderLayout.EAST);
714 * @return true if any progress bars are still active
716 public boolean operationInProgress()
718 if (progressBars != null && progressBars.size() > 0)
726 * Added so Castor Mapping file can obtain Jalview Version
728 public String getVersion()
730 return jalview.bin.Cache.getProperty("VERSION");
733 public FeatureRenderer getFeatureRenderer()
735 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
738 public void fetchSequence_actionPerformed(ActionEvent e)
740 new SequenceFetcher(this);
743 public void addFromFile_actionPerformed(ActionEvent e)
745 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
748 public void reload_actionPerformed(ActionEvent e)
750 if (fileName != null)
752 // TODO: work out how to recover feature settings for correct view(s) when
754 if (currentFileFormat.equals("Jalview"))
756 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
757 for (int i = 0; i < frames.length; i++)
759 if (frames[i] instanceof AlignFrame && frames[i] != this
760 && ((AlignFrame) frames[i]).fileName.equals(fileName))
764 frames[i].setSelected(true);
765 Desktop.instance.closeAssociatedWindows();
766 } catch (java.beans.PropertyVetoException ex)
772 Desktop.instance.closeAssociatedWindows();
774 FileLoader loader = new FileLoader();
775 String protocol = fileName.startsWith("http:") ? "URL" : "File";
776 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
780 Rectangle bounds = this.getBounds();
782 FileLoader loader = new FileLoader();
783 String protocol = fileName.startsWith("http:") ? "URL" : "File";
784 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
785 protocol, currentFileFormat);
787 newframe.setBounds(bounds);
788 if (featureSettings != null && featureSettings.isShowing())
790 final Rectangle fspos = featureSettings.frame.getBounds();
791 // TODO: need a 'show feature settings' function that takes bounds -
792 // need to refactor Desktop.addFrame
793 newframe.featureSettings_actionPerformed(null);
794 final FeatureSettings nfs = newframe.featureSettings;
795 SwingUtilities.invokeLater(new Runnable()
799 nfs.frame.setBounds(fspos);
802 this.featureSettings.close();
803 this.featureSettings = null;
805 this.closeMenuItem_actionPerformed(true);
810 public void addFromText_actionPerformed(ActionEvent e)
812 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
815 public void addFromURL_actionPerformed(ActionEvent e)
817 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
820 public void save_actionPerformed(ActionEvent e)
823 || (currentFileFormat == null || !jalview.io.FormatAdapter
824 .isValidIOFormat(currentFileFormat, true))
825 || fileName.startsWith("http"))
827 saveAs_actionPerformed(null);
831 saveAlignment(fileName, currentFileFormat);
841 public void saveAs_actionPerformed(ActionEvent e)
843 JalviewFileChooser chooser = new JalviewFileChooser(
844 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
845 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
846 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
847 currentFileFormat, false);
849 chooser.setFileView(new JalviewFileView());
850 chooser.setDialogTitle("Save Alignment to file");
851 chooser.setToolTipText("Save");
853 int value = chooser.showSaveDialog(this);
855 if (value == JalviewFileChooser.APPROVE_OPTION)
857 currentFileFormat = chooser.getSelectedFormat();
858 if (currentFileFormat == null)
860 JOptionPane.showInternalMessageDialog(Desktop.desktop,
861 "You must select a file format before saving!",
862 "File format not specified", JOptionPane.WARNING_MESSAGE);
863 value = chooser.showSaveDialog(this);
867 fileName = chooser.getSelectedFile().getPath();
869 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
872 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
873 if (currentFileFormat.indexOf(" ") > -1)
875 currentFileFormat = currentFileFormat.substring(0,
876 currentFileFormat.indexOf(" "));
878 saveAlignment(fileName, currentFileFormat);
882 public boolean saveAlignment(String file, String format)
884 boolean success = true;
886 if (format.equalsIgnoreCase("Jalview"))
888 String shortName = title;
890 if (shortName.indexOf(java.io.File.separatorChar) > -1)
892 shortName = shortName.substring(shortName
893 .lastIndexOf(java.io.File.separatorChar) + 1);
896 success = new Jalview2XML().SaveAlignment(this, file, shortName);
898 statusBar.setText("Successfully saved to file: " + fileName + " in "
899 + format + " format.");
904 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
906 warningMessage("Cannot save file " + fileName + " using format "
907 + format, "Alignment output format not supported");
908 saveAs_actionPerformed(null);
909 // JBPNote need to have a raise_gui flag here
913 String[] omitHidden = null;
915 if (viewport.hasHiddenColumns)
917 int reply = JOptionPane
918 .showInternalConfirmDialog(
920 "The Alignment contains hidden columns."
921 + "\nDo you want to save only the visible alignment?",
922 "Save / Omit Hidden Columns",
923 JOptionPane.YES_NO_OPTION,
924 JOptionPane.QUESTION_MESSAGE);
926 if (reply == JOptionPane.YES_OPTION)
928 omitHidden = viewport.getViewAsString(false);
931 FormatAdapter f = new FormatAdapter();
932 String output = f.formatSequences(format,
933 (Alignment) viewport.alignment, // class cast exceptions will
934 // occur in the distant future
935 omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
945 java.io.PrintWriter out = new java.io.PrintWriter(
946 new java.io.FileWriter(file));
951 statusBar.setText("Successfully saved to file: " + fileName
952 + " in " + format + " format.");
953 } catch (Exception ex)
956 ex.printStackTrace();
963 JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
964 + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
970 private void warningMessage(String warning, String title)
972 if (new jalview.util.Platform().isHeadless())
974 System.err.println("Warning: " + title + "\nWarning: " + warning);
979 JOptionPane.showInternalMessageDialog(this, warning, title,
980 JOptionPane.WARNING_MESSAGE);
991 protected void outputText_actionPerformed(ActionEvent e)
993 String[] omitHidden = null;
995 if (viewport.hasHiddenColumns)
997 int reply = JOptionPane
998 .showInternalConfirmDialog(
1000 "The Alignment contains hidden columns."
1001 + "\nDo you want to output only the visible alignment?",
1002 "Save / Omit Hidden Columns",
1003 JOptionPane.YES_NO_OPTION,
1004 JOptionPane.QUESTION_MESSAGE);
1006 if (reply == JOptionPane.YES_OPTION)
1008 omitHidden = viewport.getViewAsString(false);
1012 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1013 cap.setForInput(null);
1017 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1018 viewport.alignment, omitHidden, viewport.colSel));
1019 Desktop.addInternalFrame(cap,
1020 "Alignment output - " + e.getActionCommand(), 600, 500);
1021 } catch (OutOfMemoryError oom)
1023 new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1035 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1037 new HTMLOutput(alignPanel,
1038 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1039 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1042 public void createImageMap(File file, String image)
1044 alignPanel.makePNGImageMap(file, image);
1053 public void createPNG(File f)
1055 alignPanel.makePNG(f);
1064 public void createEPS(File f)
1066 alignPanel.makeEPS(f);
1069 public void pageSetup_actionPerformed(ActionEvent e)
1071 PrinterJob printJob = PrinterJob.getPrinterJob();
1072 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1081 public void printMenuItem_actionPerformed(ActionEvent e)
1083 // Putting in a thread avoids Swing painting problems
1084 PrintThread thread = new PrintThread(alignPanel);
1088 public void exportFeatures_actionPerformed(ActionEvent e)
1090 new AnnotationExporter().exportFeatures(alignPanel);
1093 public void exportAnnotations_actionPerformed(ActionEvent e)
1095 new AnnotationExporter().exportAnnotations(
1097 viewport.showAnnotation ? viewport.alignment
1098 .getAlignmentAnnotation() : null, viewport.alignment
1100 ((Alignment) viewport.alignment).alignmentProperties);
1103 public void associatedData_actionPerformed(ActionEvent e)
1105 // Pick the tree file
1106 JalviewFileChooser chooser = new JalviewFileChooser(
1107 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1108 chooser.setFileView(new JalviewFileView());
1109 chooser.setDialogTitle("Load Jalview Annotations or Features File");
1110 chooser.setToolTipText("Load Jalview Annotations / Features file");
1112 int value = chooser.showOpenDialog(null);
1114 if (value == JalviewFileChooser.APPROVE_OPTION)
1116 String choice = chooser.getSelectedFile().getPath();
1117 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1118 loadJalviewDataFile(choice);
1124 * Close the current view or all views in the alignment frame. If the frame
1125 * only contains one view then the alignment will be removed from memory.
1127 * @param closeAllTabs
1129 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1131 if (alignPanels != null && alignPanels.size() < 2)
1133 closeAllTabs = true;
1138 if (alignPanels != null)
1142 if (this.isClosed())
1144 // really close all the windows - otherwise wait till
1145 // setClosed(true) is called
1146 for (int i = 0; i < alignPanels.size(); i++)
1148 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1155 closeView(alignPanel);
1161 this.setClosed(true);
1163 } catch (Exception ex)
1165 ex.printStackTrace();
1170 * close alignPanel2 and shuffle tabs appropriately.
1172 * @param alignPanel2
1174 public void closeView(AlignmentPanel alignPanel2)
1176 int index = tabbedPane.getSelectedIndex();
1177 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1178 alignPanels.removeElement(alignPanel2);
1180 // if (viewport == alignPanel2.av)
1184 alignPanel2.closePanel();
1187 tabbedPane.removeTabAt(closedindex);
1188 tabbedPane.validate();
1190 if (index > closedindex || index == tabbedPane.getTabCount())
1192 // modify currently selected tab index if necessary.
1196 this.tabSelectionChanged(index);
1202 void updateEditMenuBar()
1205 if (viewport.historyList.size() > 0)
1207 undoMenuItem.setEnabled(true);
1208 CommandI command = (CommandI) viewport.historyList.peek();
1209 undoMenuItem.setText("Undo " + command.getDescription());
1213 undoMenuItem.setEnabled(false);
1214 undoMenuItem.setText("Undo");
1217 if (viewport.redoList.size() > 0)
1219 redoMenuItem.setEnabled(true);
1221 CommandI command = (CommandI) viewport.redoList.peek();
1222 redoMenuItem.setText("Redo " + command.getDescription());
1226 redoMenuItem.setEnabled(false);
1227 redoMenuItem.setText("Redo");
1231 public void addHistoryItem(CommandI command)
1233 if (command.getSize() > 0)
1235 viewport.historyList.push(command);
1236 viewport.redoList.clear();
1237 updateEditMenuBar();
1238 viewport.hasHiddenColumns = (viewport.colSel != null
1239 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1240 .getHiddenColumns().size() > 0);
1246 * @return alignment objects for all views
1248 AlignmentI[] getViewAlignments()
1250 if (alignPanels != null)
1252 Enumeration e = alignPanels.elements();
1253 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1254 for (int i = 0; e.hasMoreElements(); i++)
1256 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1260 if (viewport != null)
1262 return new AlignmentI[]
1263 { viewport.alignment };
1274 protected void undoMenuItem_actionPerformed(ActionEvent e)
1276 if (viewport.historyList.empty())
1278 CommandI command = (CommandI) viewport.historyList.pop();
1279 viewport.redoList.push(command);
1280 command.undoCommand(getViewAlignments());
1282 AlignViewport originalSource = getOriginatingSource(command);
1283 updateEditMenuBar();
1285 if (originalSource != null)
1287 originalSource.hasHiddenColumns = (viewport.colSel != null
1288 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1289 .getHiddenColumns().size() > 0);
1290 originalSource.firePropertyChange("alignment", null,
1291 originalSource.alignment.getSequences());
1301 protected void redoMenuItem_actionPerformed(ActionEvent e)
1303 if (viewport.redoList.size() < 1)
1308 CommandI command = (CommandI) viewport.redoList.pop();
1309 viewport.historyList.push(command);
1310 command.doCommand(getViewAlignments());
1312 AlignViewport originalSource = getOriginatingSource(command);
1313 updateEditMenuBar();
1315 if (originalSource != null)
1317 originalSource.hasHiddenColumns = (viewport.colSel != null
1318 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1319 .getHiddenColumns().size() > 0);
1320 originalSource.firePropertyChange("alignment", null,
1321 originalSource.alignment.getSequences());
1325 AlignViewport getOriginatingSource(CommandI command)
1327 AlignViewport originalSource = null;
1328 // For sequence removal and addition, we need to fire
1329 // the property change event FROM the viewport where the
1330 // original alignment was altered
1331 AlignmentI al = null;
1332 if (command instanceof EditCommand)
1334 EditCommand editCommand = (EditCommand) command;
1335 al = editCommand.getAlignment();
1336 Vector comps = (Vector) PaintRefresher.components.get(viewport
1337 .getSequenceSetId());
1339 for (int i = 0; i < comps.size(); i++)
1341 if (comps.elementAt(i) instanceof AlignmentPanel)
1343 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
1345 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1352 if (originalSource == null)
1354 // The original view is closed, we must validate
1355 // the current view against the closed view first
1358 PaintRefresher.validateSequences(al, viewport.alignment);
1361 originalSource = viewport;
1364 return originalSource;
1373 public void moveSelectedSequences(boolean up)
1375 SequenceGroup sg = viewport.getSelectionGroup();
1384 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1386 SequenceI seq = viewport.alignment.getSequenceAt(i);
1388 if (!sg.getSequences(null).contains(seq))
1393 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1395 if (sg.getSequences(null).contains(temp))
1400 viewport.alignment.getSequences().setElementAt(temp, i);
1401 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1406 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1408 SequenceI seq = viewport.alignment.getSequenceAt(i);
1410 if (!sg.getSequences(null).contains(seq))
1415 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1417 if (sg.getSequences(null).contains(temp))
1422 viewport.alignment.getSequences().setElementAt(temp, i);
1423 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1427 alignPanel.paintAlignment(true);
1430 synchronized void slideSequences(boolean right, int size)
1432 Vector sg = new Vector();
1433 if (viewport.cursorMode)
1435 sg.addElement(viewport.alignment
1436 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1438 else if (viewport.getSelectionGroup() != null
1439 && viewport.getSelectionGroup().getSize() != viewport.alignment
1442 sg = viewport.getSelectionGroup().getSequences(
1443 viewport.hiddenRepSequences);
1451 Vector invertGroup = new Vector();
1453 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1455 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
1456 invertGroup.add(viewport.alignment.getSequenceAt(i));
1459 SequenceI[] seqs1 = new SequenceI[sg.size()];
1460 for (int i = 0; i < sg.size(); i++)
1461 seqs1[i] = (SequenceI) sg.elementAt(i);
1463 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1464 for (int i = 0; i < invertGroup.size(); i++)
1465 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1467 SlideSequencesCommand ssc;
1469 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1470 size, viewport.getGapCharacter());
1472 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1473 size, viewport.getGapCharacter());
1475 int groupAdjustment = 0;
1476 if (ssc.getGapsInsertedBegin() && right)
1478 if (viewport.cursorMode)
1479 alignPanel.seqPanel.moveCursor(size, 0);
1481 groupAdjustment = size;
1483 else if (!ssc.getGapsInsertedBegin() && !right)
1485 if (viewport.cursorMode)
1486 alignPanel.seqPanel.moveCursor(-size, 0);
1488 groupAdjustment = -size;
1491 if (groupAdjustment != 0)
1493 viewport.getSelectionGroup().setStartRes(
1494 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1495 viewport.getSelectionGroup().setEndRes(
1496 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1499 boolean appendHistoryItem = false;
1500 if (viewport.historyList != null && viewport.historyList.size() > 0
1501 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1503 appendHistoryItem = ssc
1504 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1508 if (!appendHistoryItem)
1509 addHistoryItem(ssc);
1520 protected void copy_actionPerformed(ActionEvent e)
1523 if (viewport.getSelectionGroup() == null)
1527 // TODO: preserve the ordering of displayed alignment annotation in any
1528 // internal paste (particularly sequence associated annotation)
1529 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1530 String[] omitHidden = null;
1532 if (viewport.hasHiddenColumns)
1534 omitHidden = viewport.getViewAsString(true);
1537 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1540 StringSelection ss = new StringSelection(output);
1544 jalview.gui.Desktop.internalCopy = true;
1545 // Its really worth setting the clipboard contents
1546 // to empty before setting the large StringSelection!!
1547 Toolkit.getDefaultToolkit().getSystemClipboard()
1548 .setContents(new StringSelection(""), null);
1550 Toolkit.getDefaultToolkit().getSystemClipboard()
1551 .setContents(ss, Desktop.instance);
1552 } catch (OutOfMemoryError er)
1554 new OOMWarning("copying region", er);
1558 Vector hiddenColumns = null;
1559 if (viewport.hasHiddenColumns)
1561 hiddenColumns = new Vector();
1562 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1563 .getSelectionGroup().getEndRes();
1564 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1567 int[] region = (int[]) viewport.getColumnSelection()
1568 .getHiddenColumns().elementAt(i);
1569 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1571 hiddenColumns.addElement(new int[]
1572 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1577 Desktop.jalviewClipboard = new Object[]
1578 { seqs, viewport.alignment.getDataset(), hiddenColumns };
1579 statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
1588 protected void pasteNew_actionPerformed(ActionEvent e)
1599 protected void pasteThis_actionPerformed(ActionEvent e)
1605 * Paste contents of Jalview clipboard
1607 * @param newAlignment
1608 * true to paste to a new alignment, otherwise add to this.
1610 void paste(boolean newAlignment)
1612 boolean externalPaste = true;
1615 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1616 Transferable contents = c.getContents(this);
1618 if (contents == null)
1626 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1627 if (str.length() < 1)
1632 format = new IdentifyFile().Identify(str, "Paste");
1634 } catch (OutOfMemoryError er)
1636 new OOMWarning("Out of memory pasting sequences!!", er);
1640 SequenceI[] sequences;
1641 boolean annotationAdded = false;
1642 AlignmentI alignment = null;
1644 if (Desktop.jalviewClipboard != null)
1646 // The clipboard was filled from within Jalview, we must use the
1648 // And dataset from the copied alignment
1649 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1650 // be doubly sure that we create *new* sequence objects.
1651 sequences = new SequenceI[newseq.length];
1652 for (int i = 0; i < newseq.length; i++)
1654 sequences[i] = new Sequence(newseq[i]);
1656 alignment = new Alignment(sequences);
1657 externalPaste = false;
1661 // parse the clipboard as an alignment.
1662 alignment = new FormatAdapter().readFile(str, "Paste", format);
1663 sequences = alignment.getSequencesArray();
1671 if (Desktop.jalviewClipboard != null)
1673 // dataset is inherited
1674 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1678 // new dataset is constructed
1679 alignment.setDataset(null);
1681 alwidth = alignment.getWidth() + 1;
1685 AlignmentI pastedal = alignment; // preserve pasted alignment object
1686 // Add pasted sequences and dataset into existing alignment.
1687 alignment = viewport.getAlignment();
1688 alwidth = alignment.getWidth() + 1;
1689 // decide if we need to import sequences from an existing dataset
1690 boolean importDs = Desktop.jalviewClipboard != null
1691 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1692 // importDs==true instructs us to copy over new dataset sequences from
1693 // an existing alignment
1694 Vector newDs = (importDs) ? new Vector() : null; // used to create
1695 // minimum dataset set
1697 for (int i = 0; i < sequences.length; i++)
1701 newDs.addElement(null);
1703 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1705 if (importDs && ds != null)
1707 if (!newDs.contains(ds))
1709 newDs.setElementAt(ds, i);
1710 ds = new Sequence(ds);
1711 // update with new dataset sequence
1712 sequences[i].setDatasetSequence(ds);
1716 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1721 // copy and derive new dataset sequence
1722 sequences[i] = sequences[i].deriveSequence();
1723 alignment.getDataset().addSequence(
1724 sequences[i].getDatasetSequence());
1725 // TODO: avoid creation of duplicate dataset sequences with a
1726 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1728 alignment.addSequence(sequences[i]); // merges dataset
1732 newDs.clear(); // tidy up
1734 if (pastedal.getAlignmentAnnotation() != null)
1736 // Add any annotation attached to alignment.
1737 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1738 for (int i = 0; i < alann.length; i++)
1740 annotationAdded = true;
1741 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1743 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1744 newann.padAnnotation(alwidth);
1745 alignment.addAnnotation(newann);
1755 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1756 sequences, 0, alignment.getWidth(), alignment));
1758 // Add any annotations attached to sequences
1759 for (int i = 0; i < sequences.length; i++)
1761 if (sequences[i].getAnnotation() != null)
1763 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1765 annotationAdded = true;
1766 sequences[i].getAnnotation()[a].adjustForAlignment();
1767 sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1768 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1773 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1780 // propagate alignment changed.
1781 viewport.setEndSeq(alignment.getHeight());
1782 if (annotationAdded)
1784 // Duplicate sequence annotation in all views.
1785 AlignmentI[] alview = this.getViewAlignments();
1786 for (int i = 0; i < sequences.length; i++)
1788 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1791 for (int avnum = 0; avnum < alview.length; avnum++)
1793 if (alview[avnum] != alignment)
1795 // duplicate in a view other than the one with input focus
1796 int avwidth = alview[avnum].getWidth() + 1;
1797 // this relies on sann being preserved after we
1798 // modify the sequence's annotation array for each duplication
1799 for (int a = 0; a < sann.length; a++)
1801 AlignmentAnnotation newann = new AlignmentAnnotation(
1803 sequences[i].addAlignmentAnnotation(newann);
1804 newann.padAnnotation(avwidth);
1805 alview[avnum].addAnnotation(newann); // annotation was
1806 // duplicated earlier
1807 alview[avnum].setAnnotationIndex(newann, a);
1812 buildSortByAnnotationScoresMenu();
1814 viewport.firePropertyChange("alignment", null,
1815 alignment.getSequences());
1820 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
1822 String newtitle = new String("Copied sequences");
1824 if (Desktop.jalviewClipboard != null
1825 && Desktop.jalviewClipboard[2] != null)
1827 Vector hc = (Vector) Desktop.jalviewClipboard[2];
1828 for (int i = 0; i < hc.size(); i++)
1830 int[] region = (int[]) hc.elementAt(i);
1831 af.viewport.hideColumns(region[0], region[1]);
1835 // >>>This is a fix for the moment, until a better solution is
1837 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
1839 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1841 // TODO: maintain provenance of an alignment, rather than just make the
1842 // title a concatenation of operations.
1845 if (title.startsWith("Copied sequences"))
1851 newtitle = newtitle.concat("- from " + title);
1856 newtitle = new String("Pasted sequences");
1859 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1864 } catch (Exception ex)
1866 ex.printStackTrace();
1867 System.out.println("Exception whilst pasting: " + ex);
1868 // could be anything being pasted in here
1879 protected void cut_actionPerformed(ActionEvent e)
1881 copy_actionPerformed(null);
1882 delete_actionPerformed(null);
1891 protected void delete_actionPerformed(ActionEvent evt)
1894 SequenceGroup sg = viewport.getSelectionGroup();
1900 Vector seqs = new Vector();
1902 for (int i = 0; i < sg.getSize(); i++)
1904 seq = sg.getSequenceAt(i);
1905 seqs.addElement(seq);
1908 // If the cut affects all sequences, remove highlighted columns
1909 if (sg.getSize() == viewport.alignment.getHeight())
1911 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1912 sg.getEndRes() + 1);
1915 SequenceI[] cut = new SequenceI[seqs.size()];
1916 for (int i = 0; i < seqs.size(); i++)
1918 cut[i] = (SequenceI) seqs.elementAt(i);
1922 * //ADD HISTORY ITEM
1924 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1925 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1926 viewport.alignment));
1928 viewport.setSelectionGroup(null);
1929 viewport.sendSelection();
1930 viewport.alignment.deleteGroup(sg);
1932 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1934 if (viewport.getAlignment().getHeight() < 1)
1938 this.setClosed(true);
1939 } catch (Exception ex)
1951 protected void deleteGroups_actionPerformed(ActionEvent e)
1953 viewport.alignment.deleteAllGroups();
1954 viewport.sequenceColours = null;
1955 viewport.setSelectionGroup(null);
1956 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1957 alignPanel.updateAnnotation();
1958 alignPanel.paintAlignment(true);
1967 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1969 SequenceGroup sg = new SequenceGroup();
1971 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1973 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1976 sg.setEndRes(viewport.alignment.getWidth() - 1);
1977 viewport.setSelectionGroup(sg);
1978 viewport.sendSelection();
1979 alignPanel.paintAlignment(true);
1980 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1989 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1991 if (viewport.cursorMode)
1993 alignPanel.seqPanel.keyboardNo1 = null;
1994 alignPanel.seqPanel.keyboardNo2 = null;
1996 viewport.setSelectionGroup(null);
1997 viewport.getColumnSelection().clear();
1998 viewport.setSelectionGroup(null);
1999 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2000 alignPanel.idPanel.idCanvas.searchResults = null;
2001 alignPanel.paintAlignment(true);
2002 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2011 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2013 SequenceGroup sg = viewport.getSelectionGroup();
2017 selectAllSequenceMenuItem_actionPerformed(null);
2022 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2024 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2027 alignPanel.paintAlignment(true);
2028 viewport.sendSelection();
2029 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2032 public void invertColSel_actionPerformed(ActionEvent e)
2034 viewport.invertColumnSelection();
2035 alignPanel.paintAlignment(true);
2044 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2046 trimAlignment(true);
2055 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2057 trimAlignment(false);
2060 void trimAlignment(boolean trimLeft)
2062 ColumnSelection colSel = viewport.getColumnSelection();
2065 if (colSel.size() > 0)
2069 column = colSel.getMin();
2073 column = colSel.getMax();
2077 if (viewport.getSelectionGroup() != null)
2079 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2080 viewport.hiddenRepSequences);
2084 seqs = viewport.alignment.getSequencesArray();
2087 TrimRegionCommand trimRegion;
2090 trimRegion = new TrimRegionCommand("Remove Left",
2091 TrimRegionCommand.TRIM_LEFT, seqs, column,
2092 viewport.alignment, viewport.colSel,
2093 viewport.selectionGroup);
2094 viewport.setStartRes(0);
2098 trimRegion = new TrimRegionCommand("Remove Right",
2099 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2100 viewport.alignment, viewport.colSel,
2101 viewport.selectionGroup);
2104 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2106 addHistoryItem(trimRegion);
2108 Vector groups = viewport.alignment.getGroups();
2110 for (int i = 0; i < groups.size(); i++)
2112 SequenceGroup sg = (SequenceGroup) groups.get(i);
2114 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2115 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2117 viewport.alignment.deleteGroup(sg);
2121 viewport.firePropertyChange("alignment", null, viewport
2122 .getAlignment().getSequences());
2132 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2134 int start = 0, end = viewport.alignment.getWidth() - 1;
2137 if (viewport.getSelectionGroup() != null)
2139 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2140 viewport.hiddenRepSequences);
2141 start = viewport.getSelectionGroup().getStartRes();
2142 end = viewport.getSelectionGroup().getEndRes();
2146 seqs = viewport.alignment.getSequencesArray();
2149 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2150 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
2152 addHistoryItem(removeGapCols);
2154 statusBar.setText("Removed " + removeGapCols.getSize()
2155 + " empty columns.");
2157 // This is to maintain viewport position on first residue
2158 // of first sequence
2159 SequenceI seq = viewport.alignment.getSequenceAt(0);
2160 int startRes = seq.findPosition(viewport.startRes);
2161 // ShiftList shifts;
2162 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2163 // edit.alColumnChanges=shifts.getInverse();
2164 // if (viewport.hasHiddenColumns)
2165 // viewport.getColumnSelection().compensateForEdits(shifts);
2166 viewport.setStartRes(seq.findIndex(startRes) - 1);
2167 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2178 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2180 int start = 0, end = viewport.alignment.getWidth() - 1;
2183 if (viewport.getSelectionGroup() != null)
2185 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2186 viewport.hiddenRepSequences);
2187 start = viewport.getSelectionGroup().getStartRes();
2188 end = viewport.getSelectionGroup().getEndRes();
2192 seqs = viewport.alignment.getSequencesArray();
2195 // This is to maintain viewport position on first residue
2196 // of first sequence
2197 SequenceI seq = viewport.alignment.getSequenceAt(0);
2198 int startRes = seq.findPosition(viewport.startRes);
2200 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2201 viewport.alignment));
2203 viewport.setStartRes(seq.findIndex(startRes) - 1);
2205 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2216 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2218 viewport.padGaps = padGapsMenuitem.isSelected();
2219 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2225 // if (justifySeqs>0)
2227 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2239 public void findMenuItem_actionPerformed(ActionEvent e)
2244 public void newView_actionPerformed(ActionEvent e)
2246 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2249 newap.av.gatherViewsHere = false;
2251 if (viewport.viewName == null)
2253 viewport.viewName = "Original";
2256 newap.av.historyList = viewport.historyList;
2257 newap.av.redoList = viewport.redoList;
2259 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2260 String newViewName = "View " + index;
2262 Vector comps = (Vector) PaintRefresher.components.get(viewport
2263 .getSequenceSetId());
2264 Vector existingNames = new Vector();
2265 for (int i = 0; i < comps.size(); i++)
2267 if (comps.elementAt(i) instanceof AlignmentPanel)
2269 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2270 if (!existingNames.contains(ap.av.viewName))
2272 existingNames.addElement(ap.av.viewName);
2277 while (existingNames.contains(newViewName))
2279 newViewName = "View " + (++index);
2282 newap.av.viewName = newViewName;
2284 addAlignmentPanel(newap, true);
2286 if (alignPanels.size() == 2)
2288 viewport.gatherViewsHere = true;
2290 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2293 public void expandViews_actionPerformed(ActionEvent e)
2295 Desktop.instance.explodeViews(this);
2298 public void gatherViews_actionPerformed(ActionEvent e)
2300 Desktop.instance.gatherViews(this);
2309 public void font_actionPerformed(ActionEvent e)
2311 new FontChooser(alignPanel);
2320 protected void seqLimit_actionPerformed(ActionEvent e)
2322 viewport.setShowJVSuffix(seqLimits.isSelected());
2324 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2325 .calculateIdWidth());
2326 alignPanel.paintAlignment(true);
2329 public void idRightAlign_actionPerformed(ActionEvent e)
2331 viewport.rightAlignIds = idRightAlign.isSelected();
2332 alignPanel.paintAlignment(true);
2335 public void centreColumnLabels_actionPerformed(ActionEvent e)
2337 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2338 alignPanel.paintAlignment(true);
2344 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2346 protected void followHighlight_actionPerformed()
2348 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2350 alignPanel.scrollToPosition(
2351 alignPanel.seqPanel.seqCanvas.searchResults, false);
2361 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2363 viewport.setColourText(colourTextMenuItem.isSelected());
2364 alignPanel.paintAlignment(true);
2373 public void wrapMenuItem_actionPerformed(ActionEvent e)
2375 scaleAbove.setVisible(wrapMenuItem.isSelected());
2376 scaleLeft.setVisible(wrapMenuItem.isSelected());
2377 scaleRight.setVisible(wrapMenuItem.isSelected());
2378 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2379 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2382 public void showAllSeqs_actionPerformed(ActionEvent e)
2384 viewport.showAllHiddenSeqs();
2387 public void showAllColumns_actionPerformed(ActionEvent e)
2389 viewport.showAllHiddenColumns();
2393 public void hideSelSequences_actionPerformed(ActionEvent e)
2395 viewport.hideAllSelectedSeqs();
2396 alignPanel.paintAlignment(true);
2400 * called by key handler and the hide all/show all menu items
2405 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2408 boolean hide = false;
2409 SequenceGroup sg = viewport.getSelectionGroup();
2410 if (!toggleSeqs && !toggleCols)
2412 // Hide everything by the current selection - this is a hack - we do the
2413 // invert and then hide
2414 // first check that there will be visible columns after the invert.
2415 if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
2416 .getSelected().size() > 0)
2417 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2420 // now invert the sequence set, if required - empty selection implies
2421 // that no hiding is required.
2424 invertSequenceMenuItem_actionPerformed(null);
2425 sg = viewport.getSelectionGroup();
2429 viewport.expandColSelection(sg, true);
2430 // finally invert the column selection and get the new sequence
2432 invertColSel_actionPerformed(null);
2439 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
2441 hideSelSequences_actionPerformed(null);
2444 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
2446 showAllSeqs_actionPerformed(null);
2452 if (viewport.colSel.getSelected().size() > 0)
2454 hideSelColumns_actionPerformed(null);
2457 viewport.selectionGroup = sg;
2462 showAllColumns_actionPerformed(null);
2471 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2472 * event.ActionEvent)
2474 public void hideAllButSelection_actionPerformed(ActionEvent e)
2476 toggleHiddenRegions(false, false);
2483 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2486 public void hideAllSelection_actionPerformed(ActionEvent e)
2488 SequenceGroup sg = viewport.getSelectionGroup();
2489 viewport.expandColSelection(sg, false);
2490 viewport.hideAllSelectedSeqs();
2491 viewport.hideSelectedColumns();
2492 alignPanel.paintAlignment(true);
2499 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2502 public void showAllhidden_actionPerformed(ActionEvent e)
2504 viewport.showAllHiddenColumns();
2505 viewport.showAllHiddenSeqs();
2506 alignPanel.paintAlignment(true);
2509 public void hideSelColumns_actionPerformed(ActionEvent e)
2511 viewport.hideSelectedColumns();
2512 alignPanel.paintAlignment(true);
2515 public void hiddenMarkers_actionPerformed(ActionEvent e)
2517 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2527 protected void scaleAbove_actionPerformed(ActionEvent e)
2529 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2530 alignPanel.paintAlignment(true);
2539 protected void scaleLeft_actionPerformed(ActionEvent e)
2541 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2542 alignPanel.paintAlignment(true);
2551 protected void scaleRight_actionPerformed(ActionEvent e)
2553 viewport.setScaleRightWrapped(scaleRight.isSelected());
2554 alignPanel.paintAlignment(true);
2563 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2565 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2566 alignPanel.paintAlignment(true);
2575 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2577 viewport.setShowText(viewTextMenuItem.isSelected());
2578 alignPanel.paintAlignment(true);
2587 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2589 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2590 alignPanel.paintAlignment(true);
2593 public FeatureSettings featureSettings;
2595 public void featureSettings_actionPerformed(ActionEvent e)
2597 if (featureSettings != null)
2599 featureSettings.close();
2600 featureSettings = null;
2602 if (!showSeqFeatures.isSelected())
2604 // make sure features are actually displayed
2605 showSeqFeatures.setSelected(true);
2606 showSeqFeatures_actionPerformed(null);
2608 featureSettings = new FeatureSettings(this);
2612 * Set or clear 'Show Sequence Features'
2617 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2619 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2620 alignPanel.paintAlignment(true);
2621 if (alignPanel.getOverviewPanel() != null)
2623 alignPanel.getOverviewPanel().updateOverviewImage();
2628 * Set or clear 'Show Sequence Features'
2633 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2635 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2637 if (viewport.getShowSequenceFeaturesHeight())
2639 // ensure we're actually displaying features
2640 viewport.setShowSequenceFeatures(true);
2641 showSeqFeatures.setSelected(true);
2643 alignPanel.paintAlignment(true);
2644 if (alignPanel.getOverviewPanel() != null)
2646 alignPanel.getOverviewPanel().updateOverviewImage();
2656 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2658 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2659 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2662 public void alignmentProperties()
2664 JEditorPane editPane = new JEditorPane("text/html", "");
2665 editPane.setEditable(false);
2666 StringBuffer contents = new StringBuffer("<html>");
2669 int min = Integer.MAX_VALUE, max = 0;
2670 for (int i = 0; i < viewport.alignment.getHeight(); i++)
2672 int size = viewport.alignment.getSequenceAt(i).getEnd()
2673 - viewport.alignment.getSequenceAt(i).getStart();
2680 avg = avg / (float) viewport.alignment.getHeight();
2682 contents.append("<br>Sequences: " + viewport.alignment.getHeight());
2683 contents.append("<br>Minimum Sequence Length: " + min);
2684 contents.append("<br>Maximum Sequence Length: " + max);
2685 contents.append("<br>Average Length: " + (int) avg);
2687 if (((Alignment) viewport.alignment).getProperties() != null)
2689 Hashtable props = ((Alignment) viewport.alignment).getProperties();
2690 Enumeration en = props.keys();
2691 contents.append("<br><br><table border=\"1\">");
2692 while (en.hasMoreElements())
2694 String key = en.nextElement().toString();
2695 StringBuffer val = new StringBuffer();
2696 String vals = props.get(key).toString();
2700 npos = vals.indexOf("\n", pos);
2703 val.append(vals.substring(pos));
2707 val.append(vals.substring(pos, npos));
2711 } while (npos != -1);
2712 contents.append("<tr><td>" + key + "</td><td>" + val + "</td></tr>");
2714 contents.append("</table>");
2716 editPane.setText(contents.toString() + "</html>");
2717 JInternalFrame frame = new JInternalFrame();
2718 frame.getContentPane().add(new JScrollPane(editPane));
2720 Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
2721 + getTitle(), 500, 400);
2730 public void overviewMenuItem_actionPerformed(ActionEvent e)
2732 if (alignPanel.overviewPanel != null)
2737 JInternalFrame frame = new JInternalFrame();
2738 OverviewPanel overview = new OverviewPanel(alignPanel);
2739 frame.setContentPane(overview);
2740 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2741 frame.getWidth(), frame.getHeight());
2743 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2744 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2746 public void internalFrameClosed(
2747 javax.swing.event.InternalFrameEvent evt)
2749 alignPanel.setOverviewPanel(null);
2753 alignPanel.setOverviewPanel(overview);
2756 public void textColour_actionPerformed(ActionEvent e)
2758 new TextColourChooser().chooseColour(alignPanel, null);
2767 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2778 public void clustalColour_actionPerformed(ActionEvent e)
2780 changeColour(new ClustalxColourScheme(
2781 viewport.alignment.getSequences(),
2782 viewport.alignment.getWidth()));
2791 public void zappoColour_actionPerformed(ActionEvent e)
2793 changeColour(new ZappoColourScheme());
2802 public void taylorColour_actionPerformed(ActionEvent e)
2804 changeColour(new TaylorColourScheme());
2813 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2815 changeColour(new HydrophobicColourScheme());
2824 public void helixColour_actionPerformed(ActionEvent e)
2826 changeColour(new HelixColourScheme());
2835 public void strandColour_actionPerformed(ActionEvent e)
2837 changeColour(new StrandColourScheme());
2846 public void turnColour_actionPerformed(ActionEvent e)
2848 changeColour(new TurnColourScheme());
2857 public void buriedColour_actionPerformed(ActionEvent e)
2859 changeColour(new BuriedColourScheme());
2868 public void nucleotideColour_actionPerformed(ActionEvent e)
2870 changeColour(new NucleotideColourScheme());
2873 public void annotationColour_actionPerformed(ActionEvent e)
2875 new AnnotationColourChooser(viewport, alignPanel);
2884 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2886 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2895 public void changeColour(ColourSchemeI cs)
2901 if (viewport.getAbovePIDThreshold())
2903 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2906 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2908 viewport.setGlobalColourScheme(cs);
2912 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2915 if (viewport.getConservationSelected())
2918 Alignment al = (Alignment) viewport.alignment;
2919 Conservation c = new Conservation("All",
2920 ResidueProperties.propHash, 3, al.getSequences(), 0,
2924 c.verdict(false, viewport.ConsPercGaps);
2926 cs.setConservation(c);
2928 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
2933 cs.setConservation(null);
2936 cs.setConsensus(viewport.hconsensus);
2939 viewport.setGlobalColourScheme(cs);
2941 if (viewport.getColourAppliesToAllGroups())
2943 Vector groups = viewport.alignment.getGroups();
2945 for (int i = 0; i < groups.size(); i++)
2947 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2955 if (cs instanceof ClustalxColourScheme)
2957 sg.cs = new ClustalxColourScheme(
2958 sg.getSequences(viewport.hiddenRepSequences),
2961 else if (cs instanceof UserColourScheme)
2963 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
2969 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2970 } catch (Exception ex)
2975 if (viewport.getAbovePIDThreshold()
2976 || cs instanceof PIDColourScheme
2977 || cs instanceof Blosum62ColourScheme)
2979 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2981 sg.cs.setConsensus(AAFrequency.calculate(
2982 sg.getSequences(viewport.hiddenRepSequences),
2983 sg.getStartRes(), sg.getEndRes() + 1));
2987 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2990 if (viewport.getConservationSelected())
2992 Conservation c = new Conservation("Group",
2993 ResidueProperties.propHash, 3,
2994 sg.getSequences(viewport.hiddenRepSequences),
2995 sg.getStartRes(), sg.getEndRes() + 1);
2997 c.verdict(false, viewport.ConsPercGaps);
2998 sg.cs.setConservation(c);
3002 sg.cs.setConservation(null);
3007 if (alignPanel.getOverviewPanel() != null)
3009 alignPanel.getOverviewPanel().updateOverviewImage();
3012 alignPanel.paintAlignment(true);
3021 protected void modifyPID_actionPerformed(ActionEvent e)
3023 if (viewport.getAbovePIDThreshold()
3024 && viewport.globalColourScheme != null)
3026 SliderPanel.setPIDSliderSource(alignPanel,
3027 viewport.getGlobalColourScheme(), "Background");
3028 SliderPanel.showPIDSlider();
3038 protected void modifyConservation_actionPerformed(ActionEvent e)
3040 if (viewport.getConservationSelected()
3041 && viewport.globalColourScheme != null)
3043 SliderPanel.setConservationSlider(alignPanel,
3044 viewport.globalColourScheme, "Background");
3045 SliderPanel.showConservationSlider();
3055 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3057 viewport.setConservationSelected(conservationMenuItem.isSelected());
3059 viewport.setAbovePIDThreshold(false);
3060 abovePIDThreshold.setSelected(false);
3062 changeColour(viewport.getGlobalColourScheme());
3064 modifyConservation_actionPerformed(null);
3073 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3075 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3077 conservationMenuItem.setSelected(false);
3078 viewport.setConservationSelected(false);
3080 changeColour(viewport.getGlobalColourScheme());
3082 modifyPID_actionPerformed(null);
3091 public void userDefinedColour_actionPerformed(ActionEvent e)
3093 if (e.getActionCommand().equals("User Defined..."))
3095 new UserDefinedColours(alignPanel, null);
3099 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3100 .getUserColourSchemes().get(e.getActionCommand());
3106 public void updateUserColourMenu()
3109 Component[] menuItems = colourMenu.getMenuComponents();
3110 int i, iSize = menuItems.length;
3111 for (i = 0; i < iSize; i++)
3113 if (menuItems[i].getName() != null
3114 && menuItems[i].getName().equals("USER_DEFINED"))
3116 colourMenu.remove(menuItems[i]);
3120 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3122 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3123 .getUserColourSchemes().keys();
3125 while (userColours.hasMoreElements())
3127 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3128 userColours.nextElement().toString());
3129 radioItem.setName("USER_DEFINED");
3130 radioItem.addMouseListener(new MouseAdapter()
3132 public void mousePressed(MouseEvent evt)
3134 if (evt.isControlDown()
3135 || SwingUtilities.isRightMouseButton(evt))
3137 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3139 int option = JOptionPane.showInternalConfirmDialog(
3140 jalview.gui.Desktop.desktop,
3141 "Remove from default list?",
3142 "Remove user defined colour",
3143 JOptionPane.YES_NO_OPTION);
3144 if (option == JOptionPane.YES_OPTION)
3146 jalview.gui.UserDefinedColours
3147 .removeColourFromDefaults(radioItem.getText());
3148 colourMenu.remove(radioItem);
3152 radioItem.addActionListener(new ActionListener()
3154 public void actionPerformed(ActionEvent evt)
3156 userDefinedColour_actionPerformed(evt);
3163 radioItem.addActionListener(new ActionListener()
3165 public void actionPerformed(ActionEvent evt)
3167 userDefinedColour_actionPerformed(evt);
3171 colourMenu.insert(radioItem, 15);
3172 colours.add(radioItem);
3183 public void PIDColour_actionPerformed(ActionEvent e)
3185 changeColour(new PIDColourScheme());
3194 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3196 changeColour(new Blosum62ColourScheme());
3205 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3207 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3208 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3209 .getAlignment().getSequenceAt(0), null);
3210 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3211 viewport.alignment));
3212 alignPanel.paintAlignment(true);
3221 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3223 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3224 AlignmentSorter.sortByID(viewport.getAlignment());
3225 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
3226 alignPanel.paintAlignment(true);
3235 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3237 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3238 AlignmentSorter.sortByLength(viewport.getAlignment());
3239 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3240 viewport.alignment));
3241 alignPanel.paintAlignment(true);
3250 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3252 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3253 AlignmentSorter.sortByGroup(viewport.getAlignment());
3254 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3255 viewport.alignment));
3257 alignPanel.paintAlignment(true);
3266 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3268 new RedundancyPanel(alignPanel, this);
3277 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3279 if ((viewport.getSelectionGroup() == null)
3280 || (viewport.getSelectionGroup().getSize() < 2))
3282 JOptionPane.showInternalMessageDialog(this,
3283 "You must select at least 2 sequences.", "Invalid Selection",
3284 JOptionPane.WARNING_MESSAGE);
3288 JInternalFrame frame = new JInternalFrame();
3289 frame.setContentPane(new PairwiseAlignPanel(viewport));
3290 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
3300 public void PCAMenuItem_actionPerformed(ActionEvent e)
3302 if (((viewport.getSelectionGroup() != null)
3303 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3304 .getSelectionGroup().getSize() > 0))
3305 || (viewport.getAlignment().getHeight() < 4))
3307 JOptionPane.showInternalMessageDialog(this,
3308 "Principal component analysis must take\n"
3309 + "at least 4 input sequences.",
3310 "Sequence selection insufficient",
3311 JOptionPane.WARNING_MESSAGE);
3316 new PCAPanel(alignPanel);
3319 public void autoCalculate_actionPerformed(ActionEvent e)
3321 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3322 if (viewport.autoCalculateConsensus)
3324 viewport.firePropertyChange("alignment", null, viewport
3325 .getAlignment().getSequences());
3335 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3337 NewTreePanel("AV", "PID", "Average distance tree using PID");
3346 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3348 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3357 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3359 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3368 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3370 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3383 void NewTreePanel(String type, String pwType, String title)
3387 if (viewport.getSelectionGroup() != null)
3389 if (viewport.getSelectionGroup().getSize() < 3)
3394 "You need to have more than two sequences selected to build a tree!",
3395 "Not enough sequences", JOptionPane.WARNING_MESSAGE);
3400 SequenceGroup sg = viewport.getSelectionGroup();
3402 /* Decide if the selection is a column region */
3403 while (s < sg.getSize())
3405 if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
3411 "The selected region to create a tree may\nonly contain residues or gaps.\n"
3412 + "Try using the Pad function in the edit menu,\n"
3413 + "or one of the multiple sequence alignment web services.",
3414 "Sequences in selection are not aligned",
3415 JOptionPane.WARNING_MESSAGE);
3421 title = title + " on region";
3422 tp = new TreePanel(alignPanel, type, pwType);
3426 // are the visible sequences aligned?
3427 if (!viewport.alignment.isAligned(false))
3432 "The sequences must be aligned before creating a tree.\n"
3433 + "Try using the Pad function in the edit menu,\n"
3434 + "or one of the multiple sequence alignment web services.",
3435 "Sequences not aligned",
3436 JOptionPane.WARNING_MESSAGE);
3441 if (viewport.alignment.getHeight() < 2)
3446 tp = new TreePanel(alignPanel, type, pwType);
3451 if (viewport.viewName != null)
3453 title += viewport.viewName + " of ";
3456 title += this.title;
3458 Desktop.addInternalFrame(tp, title, 600, 500);
3469 public void addSortByOrderMenuItem(String title,
3470 final AlignmentOrder order)
3472 final JMenuItem item = new JMenuItem("by " + title);
3474 item.addActionListener(new java.awt.event.ActionListener()
3476 public void actionPerformed(ActionEvent e)
3478 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3480 // TODO: JBPNote - have to map order entries to curent SequenceI
3482 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3484 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3485 viewport.alignment));
3487 alignPanel.paintAlignment(true);
3493 * Add a new sort by annotation score menu item
3496 * the menu to add the option to
3498 * the label used to retrieve scores for each sequence on the
3501 public void addSortByAnnotScoreMenuItem(JMenu sort,
3502 final String scoreLabel)
3504 final JMenuItem item = new JMenuItem(scoreLabel);
3506 item.addActionListener(new java.awt.event.ActionListener()
3508 public void actionPerformed(ActionEvent e)
3510 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3511 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3512 viewport.getAlignment());// ,viewport.getSelectionGroup());
3513 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3514 viewport.alignment));
3515 alignPanel.paintAlignment(true);
3521 * last hash for alignment's annotation array - used to minimise cost of
3524 protected int _annotationScoreVectorHash;
3527 * search the alignment and rebuild the sort by annotation score submenu the
3528 * last alignment annotation vector hash is stored to minimize cost of
3529 * rebuilding in subsequence calls.
3532 public void buildSortByAnnotationScoresMenu()
3534 if (viewport.alignment.getAlignmentAnnotation() == null)
3539 if (viewport.alignment.getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3541 sortByAnnotScore.removeAll();
3542 // almost certainly a quicker way to do this - but we keep it simple
3543 Hashtable scoreSorts = new Hashtable();
3544 AlignmentAnnotation aann[];
3545 Enumeration sq = viewport.alignment.getSequences().elements();
3546 while (sq.hasMoreElements())
3548 aann = ((SequenceI) sq.nextElement()).getAnnotation();
3549 for (int i = 0; aann != null && i < aann.length; i++)
3551 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3553 scoreSorts.put(aann[i].label, aann[i].label);
3557 Enumeration labels = scoreSorts.keys();
3558 while (labels.hasMoreElements())
3560 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3561 (String) labels.nextElement());
3563 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3566 _annotationScoreVectorHash = viewport.alignment
3567 .getAlignmentAnnotation().hashCode();
3572 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3573 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3574 * call. Listeners are added to remove the menu item when the treePanel is
3575 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3579 * Displayed tree window.
3581 * SortBy menu item title.
3583 public void buildTreeMenu()
3585 sortByTreeMenu.removeAll();
3587 Vector comps = (Vector) PaintRefresher.components.get(viewport
3588 .getSequenceSetId());
3589 Vector treePanels = new Vector();
3590 int i, iSize = comps.size();
3591 for (i = 0; i < iSize; i++)
3593 if (comps.elementAt(i) instanceof TreePanel)
3595 treePanels.add(comps.elementAt(i));
3599 iSize = treePanels.size();
3603 sortByTreeMenu.setVisible(false);
3607 sortByTreeMenu.setVisible(true);
3609 for (i = 0; i < treePanels.size(); i++)
3611 TreePanel tp = (TreePanel) treePanels.elementAt(i);
3612 final JMenuItem item = new JMenuItem(tp.getTitle());
3613 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3614 item.addActionListener(new java.awt.event.ActionListener()
3616 public void actionPerformed(ActionEvent e)
3618 SequenceI[] oldOrder = viewport.getAlignment()
3619 .getSequencesArray();
3620 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
3622 addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
3623 viewport.alignment));
3625 alignPanel.paintAlignment(true);
3629 sortByTreeMenu.add(item);
3634 * Work out whether the whole set of sequences or just the selected set will
3635 * be submitted for multiple alignment.
3638 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3640 // Now, check we have enough sequences
3641 AlignmentView msa = null;
3643 if ((viewport.getSelectionGroup() != null)
3644 && (viewport.getSelectionGroup().getSize() > 1))
3646 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3647 // some common interface!
3649 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3650 * SequenceI[sz = seqs.getSize(false)];
3652 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3653 * seqs.getSequenceAt(i); }
3655 msa = viewport.getAlignmentView(true);
3660 * Vector seqs = viewport.getAlignment().getSequences();
3662 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3664 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3665 * seqs.elementAt(i); } }
3667 msa = viewport.getAlignmentView(false);
3673 * Decides what is submitted to a secondary structure prediction service: the
3674 * first sequence in the alignment, or in the current selection, or, if the
3675 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3676 * region or the whole alignment. (where the first sequence in the set is the
3677 * one that the prediction will be for).
3679 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3681 AlignmentView seqs = null;
3683 if ((viewport.getSelectionGroup() != null)
3684 && (viewport.getSelectionGroup().getSize() > 0))
3686 seqs = viewport.getAlignmentView(true);
3690 seqs = viewport.getAlignmentView(false);
3692 // limit sequences - JBPNote in future - could spawn multiple prediction
3694 // TODO: viewport.alignment.isAligned is a global state - the local
3695 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3696 if (!viewport.alignment.isAligned(false))
3698 seqs.setSequences(new SeqCigar[]
3699 { seqs.getSequences()[0] });
3700 // TODO: if seqs.getSequences().length>1 then should really have warned
3713 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3715 // Pick the tree file
3716 JalviewFileChooser chooser = new JalviewFileChooser(
3717 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3718 chooser.setFileView(new JalviewFileView());
3719 chooser.setDialogTitle("Select a newick-like tree file");
3720 chooser.setToolTipText("Load a tree file");
3722 int value = chooser.showOpenDialog(null);
3724 if (value == JalviewFileChooser.APPROVE_OPTION)
3726 String choice = chooser.getSelectedFile().getPath();
3727 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3728 jalview.io.NewickFile fin = null;
3731 fin = new jalview.io.NewickFile(choice, "File");
3732 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3733 } catch (Exception ex)
3735 JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3736 "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
3737 ex.printStackTrace();
3739 if (fin != null && fin.hasWarningMessage())
3741 JOptionPane.showMessageDialog(Desktop.desktop,
3742 fin.getWarningMessage(), "Possible problem with tree file",
3743 JOptionPane.WARNING_MESSAGE);
3748 public TreePanel ShowNewickTree(NewickFile nf, String title)
3750 return ShowNewickTree(nf, title, 600, 500, 4, 5);
3753 public TreePanel ShowNewickTree(NewickFile nf, String title,
3754 AlignmentView input)
3756 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
3759 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
3760 int h, int x, int y)
3762 return ShowNewickTree(nf, title, null, w, h, x, y);
3766 * Add a treeviewer for the tree extracted from a newick file object to the
3767 * current alignment view
3774 * Associated alignment input data (or null)
3783 * @return TreePanel handle
3785 public TreePanel ShowNewickTree(NewickFile nf, String title,
3786 AlignmentView input, int w, int h, int x, int y)
3788 TreePanel tp = null;
3794 if (nf.getTree() != null)
3796 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
3802 tp.setLocation(x, y);
3805 Desktop.addInternalFrame(tp, title, w, h);
3807 } catch (Exception ex)
3809 ex.printStackTrace();
3815 private boolean buildingMenu = false;
3818 * Generates menu items and listener event actions for web service clients
3821 public void BuildWebServiceMenu()
3823 while (buildingMenu)
3827 System.err.println("Waiting for building menu to finish.");
3829 } catch (Exception e)
3834 final AlignFrame me = this;
3835 buildingMenu = true;
3836 new Thread(new Runnable()
3842 System.err.println("Building ws menu again "
3843 + Thread.currentThread());
3844 // TODO: add support for context dependent disabling of services based
3846 // alignment and current selection
3847 // TODO: add additional serviceHandle parameter to specify abstract
3849 // class independently of AbstractName
3850 // TODO: add in rediscovery GUI function to restart discoverer
3851 // TODO: group services by location as well as function and/or
3853 // object broker mechanism.
3854 final Vector wsmenu = new Vector();
3855 final IProgressIndicator af = me;
3856 if (Cache.getDefault("SHOW_JWS1_SERVICES", true)
3857 && Discoverer.services != null
3858 && (Discoverer.services.size() > 0))
3860 // TODO: refactor to allow list of AbstractName/Handler bindings to
3862 // stored or retrieved from elsewhere
3863 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
3864 Vector secstrpr = (Vector) Discoverer.services
3866 Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
3867 // TODO: move GUI generation code onto service implementation - so a
3868 // client instance attaches itself to the GUI with method call like
3869 // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
3873 // Add any Multiple Sequence Alignment Services
3874 final JMenu msawsmenu = new JMenu("Alignment");
3875 for (int i = 0, j = msaws.size(); i < j; i++)
3877 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
3879 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
3880 .getServiceClient(sh);
3881 impl.attachWSMenuEntry(msawsmenu, me);
3884 wsmenu.add(msawsmenu);
3886 if (secstrpr != null)
3888 // Add any secondary structure prediction services
3889 final JMenu secstrmenu = new JMenu(
3890 "Secondary Structure Prediction");
3891 for (int i = 0, j = secstrpr.size(); i < j; i++)
3893 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
3895 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
3896 .getServiceClient(sh);
3897 impl.attachWSMenuEntry(secstrmenu, me);
3899 wsmenu.add(secstrmenu);
3901 if (seqsrch != null)
3903 // Add any sequence search services
3904 final JMenu seqsrchmenu = new JMenu(
3905 "Sequence Database Search");
3906 for (int i = 0, j = seqsrch.size(); i < j; i++)
3908 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
3910 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
3911 .getServiceClient(sh);
3912 impl.attachWSMenuEntry(seqsrchmenu, me);
3914 wsmenu.add(seqsrchmenu);
3918 // TODO: move into separate menu builder class.
3919 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
3921 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
3922 if (jws2servs != null)
3924 if (jws2servs.hasServices())
3926 JMenu jws2men = new JMenu("Jaba Web Services");
3927 jws2servs.attachWSMenuEntry(jws2men, me);
3928 for (int i = 0, iSize = jws2men.getMenuComponentCount(); i < iSize; i++)
3930 wsmenu.add(jws2men.getMenuComponent(i));
3936 javax.swing.SwingUtilities.invokeLater(new Runnable()
3943 resetWebServiceMenu();
3944 // finally, add the whole shebang onto the webservices menu
3945 if (wsmenu.size() > 0)
3947 for (int i = 0, j = wsmenu.size(); i < j; i++)
3949 webService.add((JMenu) wsmenu.get(i));
3954 me.webService.add(me.webServiceNoServices);
3956 } catch (Exception e)
3962 } catch (Exception e)
3967 buildingMenu = false;
3974 * empty the web service menu and add any ad-hoc functions not dynamically
3978 private void resetWebServiceMenu()
3980 webService.removeAll();
3981 build_fetchdbmenu(webService);
3982 build_urlServiceMenu(webService);
3986 * construct any groupURL type service menu entries.
3990 private void build_urlServiceMenu(JMenu webService)
3992 if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
3994 jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
4000 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4001 * chooser = new JalviewFileChooser(jalview.bin.Cache.
4002 * getProperty("LAST_DIRECTORY"));
4004 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4005 * to Vamsas file"); chooser.setToolTipText("Export");
4007 * int value = chooser.showSaveDialog(this);
4009 * if (value == JalviewFileChooser.APPROVE_OPTION) {
4010 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4011 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4012 * chooser.getSelectedFile().getAbsolutePath(), this); } }
4015 * prototype of an automatically enabled/disabled analysis function
4018 protected void setShowProductsEnabled()
4020 SequenceI[] selection = viewport.getSequenceSelection();
4021 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4022 viewport.getAlignment().getDataset()))
4024 showProducts.setEnabled(true);
4029 showProducts.setEnabled(false);
4034 * search selection for sequence xRef products and build the show products
4039 * @return true if showProducts menu should be enabled.
4041 public boolean canShowProducts(SequenceI[] selection,
4042 boolean isRegionSelection, Alignment dataset)
4044 boolean showp = false;
4047 showProducts.removeAll();
4048 final boolean dna = viewport.getAlignment().isNucleotide();
4049 final Alignment ds = dataset;
4050 String[] ptypes = (selection == null || selection.length == 0) ? null
4051 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4053 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4054 // selection, dataset, true);
4055 final SequenceI[] sel = selection;
4056 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4059 final boolean isRegSel = isRegionSelection;
4060 final AlignFrame af = this;
4061 final String source = ptypes[t];
4062 JMenuItem xtype = new JMenuItem(ptypes[t]);
4063 xtype.addActionListener(new ActionListener()
4066 public void actionPerformed(ActionEvent e)
4068 // TODO: new thread for this call with vis-delay
4069 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4070 isRegSel, dna, source);
4074 showProducts.add(xtype);
4076 showProducts.setVisible(showp);
4077 showProducts.setEnabled(showp);
4078 } catch (Exception e)
4080 jalview.bin.Cache.log
4081 .warn("canTranslate threw an exception - please report to help@jalview.org",
4088 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4089 boolean isRegSel, boolean dna, String source)
4091 final boolean fisRegSel = isRegSel;
4092 final boolean fdna = dna;
4093 final String fsrc = source;
4094 final AlignFrame ths = this;
4095 final SequenceI[] fsel = sel;
4096 Runnable foo = new Runnable()
4101 final long sttime = System.currentTimeMillis();
4102 ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4105 Alignment ds = ths.getViewport().alignment.getDataset(); // update
4109 Alignment prods = CrossRef
4110 .findXrefSequences(fsel, fdna, fsrc, ds);
4113 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4114 for (int s = 0; s < sprods.length; s++)
4116 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4117 if (ds.getSequences() == null
4118 || !ds.getSequences().contains(
4119 sprods[s].getDatasetSequence()))
4120 ds.addSequence(sprods[s].getDatasetSequence());
4121 sprods[s].updatePDBIds();
4123 Alignment al = new Alignment(sprods);
4124 AlignedCodonFrame[] cf = prods.getCodonFrames();
4126 for (int s = 0; cf != null && s < cf.length; s++)
4128 al.addCodonFrame(cf[s]);
4131 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4133 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4134 + " for " + ((fisRegSel) ? "selected region of " : "")
4136 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4141 System.err.println("No Sequences generated for xRef type "
4144 } catch (Exception e)
4146 jalview.bin.Cache.log.error(
4147 "Exception when finding crossreferences", e);
4148 } catch (OutOfMemoryError e)
4150 new OOMWarning("whilst fetching crossreferences", e);
4153 jalview.bin.Cache.log.error("Error when finding crossreferences",
4156 ths.setProgressBar("Finished searching for sequences from " + fsrc,
4161 Thread frunner = new Thread(foo);
4165 public boolean canShowTranslationProducts(SequenceI[] selection,
4166 AlignmentI alignment)
4171 return (jalview.analysis.Dna.canTranslate(selection,
4172 viewport.getViewAsVisibleContigs(true)));
4173 } catch (Exception e)
4175 jalview.bin.Cache.log
4176 .warn("canTranslate threw an exception - please report to help@jalview.org",
4182 public void showProducts_actionPerformed(ActionEvent e)
4184 // /////////////////////////////
4185 // Collect Data to be translated/transferred
4187 SequenceI[] selection = viewport.getSequenceSelection();
4188 AlignmentI al = null;
4191 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4192 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4193 viewport.getAlignment().getDataset());
4194 } catch (Exception ex)
4197 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4204 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4205 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4209 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4210 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4211 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4215 public void showTranslation_actionPerformed(ActionEvent e)
4217 // /////////////////////////////
4218 // Collect Data to be translated/transferred
4220 SequenceI[] selection = viewport.getSequenceSelection();
4221 String[] seqstring = viewport.getViewAsString(true);
4222 AlignmentI al = null;
4225 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4226 viewport.getViewAsVisibleContigs(true), viewport
4227 .getGapCharacter(), viewport.alignment
4228 .getAlignmentAnnotation(), viewport.alignment
4229 .getWidth(), viewport.getAlignment().getDataset());
4230 } catch (Exception ex)
4233 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4240 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4241 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4245 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4246 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4247 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4252 * Try to load a features file onto the alignment.
4255 * contents or path to retrieve file
4257 * access mode of file (see jalview.io.AlignFile)
4258 * @return true if features file was parsed corectly.
4260 public boolean parseFeaturesFile(String file, String type)
4262 boolean featuresFile = false;
4265 featuresFile = new FeaturesFile(file, type)
4266 .parse(viewport.alignment.getDataset(),
4267 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
4269 } catch (Exception ex)
4271 ex.printStackTrace();
4276 viewport.showSequenceFeatures = true;
4277 showSeqFeatures.setSelected(true);
4278 if (alignPanel.seqPanel.seqCanvas.fr != null)
4280 // update the min/max ranges where necessary
4281 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4283 if (featureSettings != null)
4285 featureSettings.setTableData();
4287 alignPanel.paintAlignment(true);
4290 return featuresFile;
4293 public void dragEnter(DropTargetDragEvent evt)
4297 public void dragExit(DropTargetEvent evt)
4301 public void dragOver(DropTargetDragEvent evt)
4305 public void dropActionChanged(DropTargetDragEvent evt)
4309 public void drop(DropTargetDropEvent evt)
4311 Transferable t = evt.getTransferable();
4312 java.util.List files = null;
4316 DataFlavor uriListFlavor = new DataFlavor(
4317 "text/uri-list;class=java.lang.String");
4318 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4320 // Works on Windows and MacOSX
4321 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4322 files = (java.util.List) t
4323 .getTransferData(DataFlavor.javaFileListFlavor);
4325 else if (t.isDataFlavorSupported(uriListFlavor))
4327 // This is used by Unix drag system
4328 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4329 String data = (String) t.getTransferData(uriListFlavor);
4330 files = new java.util.ArrayList(1);
4331 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4332 data, "\r\n"); st.hasMoreTokens();)
4334 String s = st.nextToken();
4335 if (s.startsWith("#"))
4337 // the line is a comment (as per the RFC 2483)
4341 java.net.URI uri = new java.net.URI(s);
4342 // check to see if we can handle this kind of URI
4343 if (uri.getScheme().toLowerCase().startsWith("http"))
4345 files.add(uri.toString());
4349 // otherwise preserve old behaviour: catch all for file objects
4350 java.io.File file = new java.io.File(uri);
4351 files.add(file.toString());
4355 } catch (Exception e)
4357 e.printStackTrace();
4364 for (int i = 0; i < files.size(); i++)
4366 loadJalviewDataFile(files.get(i).toString());
4368 } catch (Exception ex)
4370 ex.printStackTrace();
4376 * Attempt to load a "dropped" file or URL string: First by testing whether
4377 * it's and Annotation file, then a JNet file, and finally a features file. If
4378 * all are false then the user may have dropped an alignment file onto this
4382 * either a filename or a URL string.
4384 public void loadJalviewDataFile(String file)
4388 String protocol = jalview.io.FormatAdapter.FILE;
4389 String f = file.toLowerCase();
4390 if (f.indexOf("http:") == 0 || f.indexOf("https:") == 0
4391 || f.indexOf("file:") == 0)
4393 protocol = jalview.io.FormatAdapter.URL;
4396 boolean isAnnotation = new AnnotationFile().readAnnotationFile(
4397 viewport.alignment, file, protocol);
4401 // try to see if its a JNet 'concise' style annotation file *before* we
4402 // try to parse it as a features file
4403 String format = new IdentifyFile().Identify(file, protocol);
4404 if (format.equalsIgnoreCase("JnetFile"))
4406 jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
4408 new JnetAnnotationMaker().add_annotation(predictions,
4409 viewport.getAlignment(), 0, false);
4410 isAnnotation = true;
4414 // try to parse it as a features file
4415 boolean isGroupsFile = parseFeaturesFile(file, protocol);
4416 // if it wasn't a features file then we just treat it as a general
4417 // alignment file to load into the current view.
4420 new FileLoader().LoadFile(viewport, file, protocol, format);
4424 alignPanel.paintAlignment(true);
4431 alignPanel.adjustAnnotationHeight();
4432 viewport.updateSequenceIdColours();
4433 buildSortByAnnotationScoresMenu();
4434 alignPanel.paintAlignment(true);
4436 } catch (Exception ex)
4438 ex.printStackTrace();
4442 public void tabSelectionChanged(int index)
4446 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
4447 viewport = alignPanel.av;
4448 setMenusFromViewport(viewport);
4452 public void tabbedPane_mousePressed(MouseEvent e)
4454 if (SwingUtilities.isRightMouseButton(e))
4456 String reply = JOptionPane.showInternalInputDialog(this,
4457 "Enter View Name", "Edit View Name",
4458 JOptionPane.QUESTION_MESSAGE);
4462 viewport.viewName = reply;
4463 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4468 public AlignViewport getCurrentView()
4474 * Open the dialog for regex description parsing.
4476 protected void extractScores_actionPerformed(ActionEvent e)
4478 ParseProperties pp = new jalview.analysis.ParseProperties(
4479 viewport.alignment);
4480 // TODO: verify regex and introduce GUI dialog for version 2.5
4481 // if (pp.getScoresFromDescription("col", "score column ",
4482 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4484 if (pp.getScoresFromDescription("description column",
4485 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4487 buildSortByAnnotationScoresMenu();
4495 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4498 protected void showDbRefs_actionPerformed(ActionEvent e)
4500 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
4506 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4509 protected void showNpFeats_actionPerformed(ActionEvent e)
4511 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
4515 * find the viewport amongst the tabs in this alignment frame and close that
4520 public boolean closeView(AlignViewport av)
4524 this.closeMenuItem_actionPerformed(false);
4527 Component[] comp = tabbedPane.getComponents();
4528 for (int i = 0; comp != null && i < comp.length; i++)
4530 if (comp[i] instanceof AlignmentPanel)
4532 if (((AlignmentPanel) comp[i]).av == av)
4535 closeView((AlignmentPanel) comp[i]);
4543 protected void build_fetchdbmenu(JMenu webService)
4545 // Temporary hack - DBRef Fetcher always top level ws entry.
4546 // TODO We probably want to store a sequence database checklist in
4547 // preferences and have checkboxes.. rather than individual sources selected
4549 final JMenu rfetch = new JMenu("Fetch DB References");
4550 rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
4551 webService.add(rfetch);
4553 JMenuItem fetchr = new JMenuItem("Standard Databases");
4554 fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
4555 fetchr.addActionListener(new ActionListener()
4558 public void actionPerformed(ActionEvent e)
4560 new Thread(new Runnable()
4565 new jalview.ws.DBRefFetcher(alignPanel.av
4566 .getSequenceSelection(), alignPanel.alignFrame)
4567 .fetchDBRefs(false);
4575 final AlignFrame me = this;
4576 new Thread(new Runnable()
4580 final jalview.ws.SequenceFetcher sf = SequenceFetcher
4581 .getSequenceFetcherSingleton(me);
4582 final String[] otherdb = sf.getOrderedSupportedSources();
4583 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4584 // jalview.util.QuickSort.sort(otherdb, otherdb);
4585 javax.swing.SwingUtilities.invokeLater(new Runnable()
4590 JMenu dfetch = new JMenu();
4593 int comp = 0, mcomp = 15;
4594 String mname = null;
4595 if (otherdb != null && otherdb.length > 0)
4597 for (int i = 0; i < otherdb.length; i++)
4599 String dbname = sf.getSourceProxy(otherdb[i]).getDbName();
4602 mname = "from '" + dbname + "'";
4604 fetchr = new JMenuItem(otherdb[i]);
4605 final String[] dassource = new String[]
4607 fetchr.addActionListener(new ActionListener()
4610 public void actionPerformed(ActionEvent e)
4612 new Thread(new Runnable()
4617 new jalview.ws.DBRefFetcher(alignPanel.av
4618 .getSequenceSelection(),
4619 alignPanel.alignFrame, dassource)
4620 .fetchDBRefs(false);
4626 fetchr.setToolTipText("Retrieve from " + dbname);
4628 if (comp++ == mcomp || i == (otherdb.length - 1))
4630 dfetch.setText(mname + " to '" + dbname + "'");
4632 dfetch = new JMenu();
4646 * Left justify the whole alignment.
4648 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
4650 AlignmentI al = viewport.getAlignment();
4652 viewport.firePropertyChange("alignment", null, al);
4656 * Right justify the whole alignment.
4658 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
4660 AlignmentI al = viewport.getAlignment();
4662 viewport.firePropertyChange("alignment", null, al);
4665 public void setShowSeqFeatures(boolean b)
4667 showSeqFeatures.setSelected(true);
4668 viewport.setShowSequenceFeatures(true);
4675 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
4676 * awt.event.ActionEvent)
4678 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
4680 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
4681 alignPanel.paintAlignment(true);
4688 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
4691 protected void showGroupConsensus_actionPerformed(ActionEvent e)
4693 viewport.setShowGroupConsensus(showGroupConsensus.getState());
4694 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4702 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
4703 * .event.ActionEvent)
4705 protected void showGroupConservation_actionPerformed(ActionEvent e)
4707 viewport.setShowGroupConservation(showGroupConservation.getState());
4708 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4715 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
4716 * .event.ActionEvent)
4718 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
4720 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
4721 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4728 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
4729 * .event.ActionEvent)
4731 protected void showSequenceLogo_actionPerformed(ActionEvent e)
4733 viewport.setShowSequenceLogo(showSequenceLogo.getState());
4734 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4737 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
4739 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4746 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
4747 * .event.ActionEvent)
4749 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
4751 if (viewport.getSelectionGroup() != null)
4753 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
4754 viewport.getSequenceSelection(),
4755 viewport.getAlignmentView(true).getSequenceStrings(
4756 viewport.getGapCharacter()),
4757 viewport.alignment.getGroups());
4758 viewport.alignment.deleteAllGroups();
4759 viewport.sequenceColours = null;
4760 viewport.setSelectionGroup(null);
4761 // set view properties for each group
4762 for (int g = 0; g < gps.length; g++)
4764 gps[g].setShowNonconserved(viewport.getShowUnconserved());
4765 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
4766 viewport.alignment.addGroup(gps[g]);
4767 Color col = new Color((int) (Math.random() * 255),
4768 (int) (Math.random() * 255), (int) (Math.random() * 255));
4769 col = col.brighter();
4770 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
4771 .hasMoreElements(); viewport.setSequenceColour(
4772 (SequenceI) sq.nextElement(), col))
4775 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
4776 alignPanel.updateAnnotation();
4777 alignPanel.paintAlignment(true);
4782 class PrintThread extends Thread
4786 public PrintThread(AlignmentPanel ap)
4791 static PageFormat pf;
4795 PrinterJob printJob = PrinterJob.getPrinterJob();
4799 printJob.setPrintable(ap, pf);
4803 printJob.setPrintable(ap);
4806 if (printJob.printDialog())
4811 } catch (Exception PrintException)
4813 PrintException.printStackTrace();