2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
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 javax.swing.SwingUtilities.invokeLater(new Runnable() {
554 public void run() { BuildWebServiceMenu();}
558 public void setGUINucleotide(boolean nucleotide)
560 showTranslation.setVisible(nucleotide);
561 conservationMenuItem.setEnabled(!nucleotide);
562 modifyConservation.setEnabled(!nucleotide);
563 showGroupConservation.setEnabled(!nucleotide);
564 // Remember AlignFrame always starts as protein
567 calculateMenu.remove(calculateMenu.getItemCount() - 2);
572 * set up menus for the currently viewport. This may be called after any
573 * operation that affects the data in the current view (selection changed,
574 * etc) to update the menus to reflect the new state.
576 public void setMenusForViewport()
578 setMenusFromViewport(viewport);
582 * Need to call this method when tabs are selected for multiple views, or when
583 * loading from Jalview2XML.java
588 void setMenusFromViewport(AlignViewport av)
590 padGapsMenuitem.setSelected(av.padGaps);
591 colourTextMenuItem.setSelected(av.showColourText);
592 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
593 conservationMenuItem.setSelected(av.getConservationSelected());
594 seqLimits.setSelected(av.getShowJVSuffix());
595 idRightAlign.setSelected(av.rightAlignIds);
596 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
597 renderGapsMenuItem.setSelected(av.renderGaps);
598 wrapMenuItem.setSelected(av.wrapAlignment);
599 scaleAbove.setVisible(av.wrapAlignment);
600 scaleLeft.setVisible(av.wrapAlignment);
601 scaleRight.setVisible(av.wrapAlignment);
602 annotationPanelMenuItem.setState(av.showAnnotation);
603 viewBoxesMenuItem.setSelected(av.showBoxes);
604 viewTextMenuItem.setSelected(av.showText);
605 showNonconservedMenuItem.setSelected(av.showUnconserved);
606 showGroupConsensus.setSelected(av.showGroupConsensus);
607 showGroupConservation.setSelected(av.showGroupConservation);
608 showConsensusHistogram.setSelected(av.showConsensusHistogram);
609 showSequenceLogo.setSelected(av.showSequenceLogo);
610 setColourSelected(ColourSchemeProperty.getColourName(av
611 .getGlobalColourScheme()));
613 showSeqFeatures.setSelected(av.showSequenceFeatures);
614 hiddenMarkers.setState(av.showHiddenMarkers);
615 applyToAllGroups.setState(av.colourAppliesToAllGroups);
616 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
617 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
619 setShowProductsEnabled();
624 Hashtable progressBars, progressBarHandlers;
629 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
631 public void setProgressBar(String message, long id)
633 if (progressBars == null)
635 progressBars = new Hashtable();
636 progressBarHandlers = new Hashtable();
639 JPanel progressPanel;
640 Long lId = new Long(id);
641 GridLayout layout = (GridLayout) statusPanel.getLayout();
642 if (progressBars.get(lId) != null)
644 progressPanel = (JPanel) progressBars.get(new Long(id));
645 statusPanel.remove(progressPanel);
646 progressBars.remove(lId);
647 progressPanel = null;
650 statusBar.setText(message);
652 if (progressBarHandlers.contains(lId))
654 progressBarHandlers.remove(lId);
656 layout.setRows(layout.getRows() - 1);
660 progressPanel = new JPanel(new BorderLayout(10, 5));
662 JProgressBar progressBar = new JProgressBar();
663 progressBar.setIndeterminate(true);
665 progressPanel.add(new JLabel(message), BorderLayout.WEST);
666 progressPanel.add(progressBar, BorderLayout.CENTER);
668 layout.setRows(layout.getRows() + 1);
669 statusPanel.add(progressPanel);
671 progressBars.put(lId, progressPanel);
674 setMenusForViewport();
678 public void registerHandler(final long id,
679 final IProgressIndicatorHandler handler)
681 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
684 "call setProgressBar before registering the progress bar's handler.");
686 progressBarHandlers.put(new Long(id), handler);
687 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
688 if (handler.canCancel())
690 JButton cancel = new JButton("Cancel");
691 final IProgressIndicator us = this;
692 cancel.addActionListener(new ActionListener()
695 public void actionPerformed(ActionEvent e)
697 handler.cancelActivity(id);
698 us.setProgressBar("Cancelled "
699 + ((JLabel) progressPanel.getComponent(0)).getText(), id);
702 progressPanel.add(cancel, BorderLayout.EAST);
708 * @return true if any progress bars are still active
710 public boolean operationInProgress()
712 if (progressBars != null && progressBars.size() > 0)
720 * Added so Castor Mapping file can obtain Jalview Version
722 public String getVersion()
724 return jalview.bin.Cache.getProperty("VERSION");
727 public FeatureRenderer getFeatureRenderer()
729 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
732 public void fetchSequence_actionPerformed(ActionEvent e)
734 new SequenceFetcher(this);
737 public void addFromFile_actionPerformed(ActionEvent e)
739 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
742 public void reload_actionPerformed(ActionEvent e)
744 if (fileName != null)
746 // TODO: work out how to recover feature settings for correct view(s) when
748 if (currentFileFormat.equals("Jalview"))
750 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
751 for (int i = 0; i < frames.length; i++)
753 if (frames[i] instanceof AlignFrame && frames[i] != this
754 && ((AlignFrame) frames[i]).fileName.equals(fileName))
758 frames[i].setSelected(true);
759 Desktop.instance.closeAssociatedWindows();
760 } catch (java.beans.PropertyVetoException ex)
766 Desktop.instance.closeAssociatedWindows();
768 FileLoader loader = new FileLoader();
769 String protocol = fileName.startsWith("http:") ? "URL" : "File";
770 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
774 Rectangle bounds = this.getBounds();
776 FileLoader loader = new FileLoader();
777 String protocol = fileName.startsWith("http:") ? "URL" : "File";
778 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
779 protocol, currentFileFormat);
781 newframe.setBounds(bounds);
782 if (featureSettings != null && featureSettings.isShowing())
784 final Rectangle fspos = featureSettings.frame.getBounds();
785 // TODO: need a 'show feature settings' function that takes bounds -
786 // need to refactor Desktop.addFrame
787 newframe.featureSettings_actionPerformed(null);
788 final FeatureSettings nfs = newframe.featureSettings;
789 SwingUtilities.invokeLater(new Runnable()
793 nfs.frame.setBounds(fspos);
796 this.featureSettings.close();
797 this.featureSettings = null;
799 this.closeMenuItem_actionPerformed(true);
804 public void addFromText_actionPerformed(ActionEvent e)
806 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
809 public void addFromURL_actionPerformed(ActionEvent e)
811 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
814 public void save_actionPerformed(ActionEvent e)
817 || (currentFileFormat == null || !jalview.io.FormatAdapter
818 .isValidIOFormat(currentFileFormat, true))
819 || fileName.startsWith("http"))
821 saveAs_actionPerformed(null);
825 saveAlignment(fileName, currentFileFormat);
835 public void saveAs_actionPerformed(ActionEvent e)
837 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
838 .getProperty("LAST_DIRECTORY"),
839 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
840 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
841 currentFileFormat, false);
843 chooser.setFileView(new JalviewFileView());
844 chooser.setDialogTitle("Save Alignment to file");
845 chooser.setToolTipText("Save");
847 int value = chooser.showSaveDialog(this);
849 if (value == JalviewFileChooser.APPROVE_OPTION)
851 currentFileFormat = chooser.getSelectedFormat();
852 if (currentFileFormat == null)
854 JOptionPane.showInternalMessageDialog(Desktop.desktop,
855 "You must select a file format before saving!",
856 "File format not specified", JOptionPane.WARNING_MESSAGE);
857 value = chooser.showSaveDialog(this);
861 fileName = chooser.getSelectedFile().getPath();
863 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
866 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
867 if (currentFileFormat.indexOf(" ") > -1)
869 currentFileFormat = currentFileFormat.substring(0,
870 currentFileFormat.indexOf(" "));
872 saveAlignment(fileName, currentFileFormat);
876 public boolean saveAlignment(String file, String format)
878 boolean success = true;
880 if (format.equalsIgnoreCase("Jalview"))
882 String shortName = title;
884 if (shortName.indexOf(java.io.File.separatorChar) > -1)
886 shortName = shortName.substring(shortName
887 .lastIndexOf(java.io.File.separatorChar) + 1);
890 success = new Jalview2XML().SaveAlignment(this, file, shortName);
892 statusBar.setText("Successfully saved to file: " + fileName + " in "
893 + format + " format.");
898 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
900 warningMessage("Cannot save file " + fileName + " using format "
901 + format, "Alignment output format not supported");
902 saveAs_actionPerformed(null);
903 // JBPNote need to have a raise_gui flag here
907 String[] omitHidden = null;
909 if (viewport.hasHiddenColumns)
911 int reply = JOptionPane
912 .showInternalConfirmDialog(
914 "The Alignment contains hidden columns."
915 + "\nDo you want to save only the visible alignment?",
916 "Save / Omit Hidden Columns",
917 JOptionPane.YES_NO_OPTION,
918 JOptionPane.QUESTION_MESSAGE);
920 if (reply == JOptionPane.YES_OPTION)
922 omitHidden = viewport.getViewAsString(false);
925 FormatAdapter f = new FormatAdapter();
926 String output = f.formatSequences(format,
927 (Alignment) viewport.alignment, // class cast exceptions will
928 // occur in the distant future
929 omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
939 java.io.PrintWriter out = new java.io.PrintWriter(
940 new java.io.FileWriter(file));
945 statusBar.setText("Successfully saved to file: " + fileName
946 + " in " + format + " format.");
947 } catch (Exception ex)
950 ex.printStackTrace();
957 JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
958 + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
964 private void warningMessage(String warning, String title)
966 if (new jalview.util.Platform().isHeadless())
968 System.err.println("Warning: " + title + "\nWarning: " + warning);
973 JOptionPane.showInternalMessageDialog(this, warning, title,
974 JOptionPane.WARNING_MESSAGE);
985 protected void outputText_actionPerformed(ActionEvent e)
987 String[] omitHidden = null;
989 if (viewport.hasHiddenColumns)
991 int reply = JOptionPane
992 .showInternalConfirmDialog(
994 "The Alignment contains hidden columns."
995 + "\nDo you want to output only the visible alignment?",
996 "Save / Omit Hidden Columns",
997 JOptionPane.YES_NO_OPTION,
998 JOptionPane.QUESTION_MESSAGE);
1000 if (reply == JOptionPane.YES_OPTION)
1002 omitHidden = viewport.getViewAsString(false);
1006 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1007 cap.setForInput(null);
1008 Desktop.addInternalFrame(cap, "Alignment output - "
1009 + e.getActionCommand(), 600, 500);
1011 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1012 viewport.alignment, omitHidden, viewport.colSel));
1021 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1023 new HTMLOutput(alignPanel, alignPanel.seqPanel.seqCanvas
1024 .getSequenceRenderer(), alignPanel.seqPanel.seqCanvas
1025 .getFeatureRenderer());
1028 public void createImageMap(File file, String image)
1030 alignPanel.makePNGImageMap(file, image);
1039 public void createPNG(File f)
1041 alignPanel.makePNG(f);
1050 public void createEPS(File f)
1052 alignPanel.makeEPS(f);
1055 public void pageSetup_actionPerformed(ActionEvent e)
1057 PrinterJob printJob = PrinterJob.getPrinterJob();
1058 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1067 public void printMenuItem_actionPerformed(ActionEvent e)
1069 // Putting in a thread avoids Swing painting problems
1070 PrintThread thread = new PrintThread(alignPanel);
1074 public void exportFeatures_actionPerformed(ActionEvent e)
1076 new AnnotationExporter().exportFeatures(alignPanel);
1079 public void exportAnnotations_actionPerformed(ActionEvent e)
1081 new AnnotationExporter().exportAnnotations(alignPanel,
1082 viewport.showAnnotation ? viewport.alignment
1083 .getAlignmentAnnotation() : null, viewport.alignment
1085 ((Alignment) viewport.alignment).alignmentProperties);
1088 public void associatedData_actionPerformed(ActionEvent e)
1090 // Pick the tree file
1091 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
1092 .getProperty("LAST_DIRECTORY"));
1093 chooser.setFileView(new JalviewFileView());
1094 chooser.setDialogTitle("Load Jalview Annotations or Features File");
1095 chooser.setToolTipText("Load Jalview Annotations / Features file");
1097 int value = chooser.showOpenDialog(null);
1099 if (value == JalviewFileChooser.APPROVE_OPTION)
1101 String choice = chooser.getSelectedFile().getPath();
1102 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1103 loadJalviewDataFile(choice);
1109 * Close the current view or all views in the alignment frame. If the frame
1110 * only contains one view then the alignment will be removed from memory.
1112 * @param closeAllTabs
1114 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1116 if (alignPanels != null && alignPanels.size() < 2)
1118 closeAllTabs = true;
1123 if (alignPanels != null)
1127 if (this.isClosed())
1129 // really close all the windows - otherwise wait till
1130 // setClosed(true) is called
1131 for (int i = 0; i < alignPanels.size(); i++)
1133 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1140 closeView(alignPanel);
1146 this.setClosed(true);
1148 } catch (Exception ex)
1150 ex.printStackTrace();
1155 * close alignPanel2 and shuffle tabs appropriately.
1157 * @param alignPanel2
1159 public void closeView(AlignmentPanel alignPanel2)
1161 int index = tabbedPane.getSelectedIndex();
1162 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1163 alignPanels.removeElement(alignPanel2);
1165 // if (viewport == alignPanel2.av)
1169 alignPanel2.closePanel();
1172 tabbedPane.removeTabAt(closedindex);
1173 tabbedPane.validate();
1175 if (index > closedindex || index == tabbedPane.getTabCount())
1177 // modify currently selected tab index if necessary.
1181 this.tabSelectionChanged(index);
1187 void updateEditMenuBar()
1190 if (viewport.historyList.size() > 0)
1192 undoMenuItem.setEnabled(true);
1193 CommandI command = (CommandI) viewport.historyList.peek();
1194 undoMenuItem.setText("Undo " + command.getDescription());
1198 undoMenuItem.setEnabled(false);
1199 undoMenuItem.setText("Undo");
1202 if (viewport.redoList.size() > 0)
1204 redoMenuItem.setEnabled(true);
1206 CommandI command = (CommandI) viewport.redoList.peek();
1207 redoMenuItem.setText("Redo " + command.getDescription());
1211 redoMenuItem.setEnabled(false);
1212 redoMenuItem.setText("Redo");
1216 public void addHistoryItem(CommandI command)
1218 if (command.getSize() > 0)
1220 viewport.historyList.push(command);
1221 viewport.redoList.clear();
1222 updateEditMenuBar();
1223 viewport.hasHiddenColumns = (viewport.colSel != null
1224 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1225 .getHiddenColumns().size() > 0);
1231 * @return alignment objects for all views
1233 AlignmentI[] getViewAlignments()
1235 if (alignPanels != null)
1237 Enumeration e = alignPanels.elements();
1238 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1239 for (int i = 0; e.hasMoreElements(); i++)
1241 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1245 if (viewport != null)
1247 return new AlignmentI[]
1248 { viewport.alignment };
1259 protected void undoMenuItem_actionPerformed(ActionEvent e)
1261 if (viewport.historyList.empty())
1263 CommandI command = (CommandI) viewport.historyList.pop();
1264 viewport.redoList.push(command);
1265 command.undoCommand(getViewAlignments());
1267 AlignViewport originalSource = getOriginatingSource(command);
1268 updateEditMenuBar();
1270 if (originalSource != null)
1272 originalSource.hasHiddenColumns = (viewport.colSel != null
1273 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1274 .getHiddenColumns().size() > 0);
1275 originalSource.firePropertyChange("alignment", null,
1276 originalSource.alignment.getSequences());
1286 protected void redoMenuItem_actionPerformed(ActionEvent e)
1288 if (viewport.redoList.size() < 1)
1293 CommandI command = (CommandI) viewport.redoList.pop();
1294 viewport.historyList.push(command);
1295 command.doCommand(getViewAlignments());
1297 AlignViewport originalSource = getOriginatingSource(command);
1298 updateEditMenuBar();
1300 if (originalSource != null)
1302 originalSource.hasHiddenColumns = (viewport.colSel != null
1303 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1304 .getHiddenColumns().size() > 0);
1305 originalSource.firePropertyChange("alignment", null,
1306 originalSource.alignment.getSequences());
1310 AlignViewport getOriginatingSource(CommandI command)
1312 AlignViewport originalSource = null;
1313 // For sequence removal and addition, we need to fire
1314 // the property change event FROM the viewport where the
1315 // original alignment was altered
1316 AlignmentI al = null;
1317 if (command instanceof EditCommand)
1319 EditCommand editCommand = (EditCommand) command;
1320 al = editCommand.getAlignment();
1321 Vector comps = (Vector) PaintRefresher.components.get(viewport
1322 .getSequenceSetId());
1324 for (int i = 0; i < comps.size(); i++)
1326 if (comps.elementAt(i) instanceof AlignmentPanel)
1328 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
1330 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1337 if (originalSource == null)
1339 // The original view is closed, we must validate
1340 // the current view against the closed view first
1343 PaintRefresher.validateSequences(al, viewport.alignment);
1346 originalSource = viewport;
1349 return originalSource;
1358 public void moveSelectedSequences(boolean up)
1360 SequenceGroup sg = viewport.getSelectionGroup();
1369 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1371 SequenceI seq = viewport.alignment.getSequenceAt(i);
1373 if (!sg.getSequences(null).contains(seq))
1378 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1380 if (sg.getSequences(null).contains(temp))
1385 viewport.alignment.getSequences().setElementAt(temp, i);
1386 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1391 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1393 SequenceI seq = viewport.alignment.getSequenceAt(i);
1395 if (!sg.getSequences(null).contains(seq))
1400 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1402 if (sg.getSequences(null).contains(temp))
1407 viewport.alignment.getSequences().setElementAt(temp, i);
1408 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1412 alignPanel.paintAlignment(true);
1415 synchronized void slideSequences(boolean right, int size)
1417 Vector sg = new Vector();
1418 if (viewport.cursorMode)
1420 sg.addElement(viewport.alignment
1421 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1423 else if (viewport.getSelectionGroup() != null
1424 && viewport.getSelectionGroup().getSize() != viewport.alignment
1427 sg = viewport.getSelectionGroup().getSequences(
1428 viewport.hiddenRepSequences);
1436 Vector invertGroup = new Vector();
1438 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1440 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
1441 invertGroup.add(viewport.alignment.getSequenceAt(i));
1444 SequenceI[] seqs1 = new SequenceI[sg.size()];
1445 for (int i = 0; i < sg.size(); i++)
1446 seqs1[i] = (SequenceI) sg.elementAt(i);
1448 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1449 for (int i = 0; i < invertGroup.size(); i++)
1450 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1452 SlideSequencesCommand ssc;
1454 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1455 size, viewport.getGapCharacter());
1457 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1458 size, viewport.getGapCharacter());
1460 int groupAdjustment = 0;
1461 if (ssc.getGapsInsertedBegin() && right)
1463 if (viewport.cursorMode)
1464 alignPanel.seqPanel.moveCursor(size, 0);
1466 groupAdjustment = size;
1468 else if (!ssc.getGapsInsertedBegin() && !right)
1470 if (viewport.cursorMode)
1471 alignPanel.seqPanel.moveCursor(-size, 0);
1473 groupAdjustment = -size;
1476 if (groupAdjustment != 0)
1478 viewport.getSelectionGroup().setStartRes(
1479 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1480 viewport.getSelectionGroup().setEndRes(
1481 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1484 boolean appendHistoryItem = false;
1485 if (viewport.historyList != null && viewport.historyList.size() > 0
1486 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1488 appendHistoryItem = ssc
1489 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1493 if (!appendHistoryItem)
1494 addHistoryItem(ssc);
1505 protected void copy_actionPerformed(ActionEvent e)
1508 if (viewport.getSelectionGroup() == null)
1512 // TODO: preserve the ordering of displayed alignment annotation in any
1513 // internal paste (particularly sequence associated annotation)
1514 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1515 String[] omitHidden = null;
1517 if (viewport.hasHiddenColumns)
1519 omitHidden = viewport.getViewAsString(true);
1522 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1525 StringSelection ss = new StringSelection(output);
1529 jalview.gui.Desktop.internalCopy = true;
1530 // Its really worth setting the clipboard contents
1531 // to empty before setting the large StringSelection!!
1532 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
1533 new StringSelection(""), null);
1535 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1537 } catch (OutOfMemoryError er)
1539 new OOMWarning("copying region", er);
1543 Vector hiddenColumns = null;
1544 if (viewport.hasHiddenColumns)
1546 hiddenColumns = new Vector();
1547 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1548 .getSelectionGroup().getEndRes();
1549 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1552 int[] region = (int[]) viewport.getColumnSelection()
1553 .getHiddenColumns().elementAt(i);
1554 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1556 hiddenColumns.addElement(new int[]
1557 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1562 Desktop.jalviewClipboard = new Object[]
1563 { seqs, viewport.alignment.getDataset(), hiddenColumns };
1564 statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
1573 protected void pasteNew_actionPerformed(ActionEvent e)
1584 protected void pasteThis_actionPerformed(ActionEvent e)
1590 * Paste contents of Jalview clipboard
1592 * @param newAlignment
1593 * true to paste to a new alignment, otherwise add to this.
1595 void paste(boolean newAlignment)
1597 boolean externalPaste = true;
1600 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1601 Transferable contents = c.getContents(this);
1603 if (contents == null)
1611 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1612 if (str.length() < 1)
1617 format = new IdentifyFile().Identify(str, "Paste");
1619 } catch (OutOfMemoryError er)
1621 new OOMWarning("Out of memory pasting sequences!!", er);
1625 SequenceI[] sequences;
1626 boolean annotationAdded = false;
1627 AlignmentI alignment = null;
1629 if (Desktop.jalviewClipboard != null)
1631 // The clipboard was filled from within Jalview, we must use the
1633 // And dataset from the copied alignment
1634 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1635 // be doubly sure that we create *new* sequence objects.
1636 sequences = new SequenceI[newseq.length];
1637 for (int i = 0; i < newseq.length; i++)
1639 sequences[i] = new Sequence(newseq[i]);
1641 alignment = new Alignment(sequences);
1642 externalPaste = false;
1646 // parse the clipboard as an alignment.
1647 alignment = new FormatAdapter().readFile(str, "Paste", format);
1648 sequences = alignment.getSequencesArray();
1656 if (Desktop.jalviewClipboard != null)
1658 // dataset is inherited
1659 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1663 // new dataset is constructed
1664 alignment.setDataset(null);
1666 alwidth = alignment.getWidth() + 1;
1670 AlignmentI pastedal = alignment; // preserve pasted alignment object
1671 // Add pasted sequences and dataset into existing alignment.
1672 alignment = viewport.getAlignment();
1673 alwidth = alignment.getWidth() + 1;
1674 // decide if we need to import sequences from an existing dataset
1675 boolean importDs = Desktop.jalviewClipboard != null
1676 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1677 // importDs==true instructs us to copy over new dataset sequences from
1678 // an existing alignment
1679 Vector newDs = (importDs) ? new Vector() : null; // used to create
1680 // minimum dataset set
1682 for (int i = 0; i < sequences.length; i++)
1686 newDs.addElement(null);
1688 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1690 if (importDs && ds != null)
1692 if (!newDs.contains(ds))
1694 newDs.setElementAt(ds, i);
1695 ds = new Sequence(ds);
1696 // update with new dataset sequence
1697 sequences[i].setDatasetSequence(ds);
1701 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1706 // copy and derive new dataset sequence
1707 sequences[i] = sequences[i].deriveSequence();
1708 alignment.getDataset().addSequence(
1709 sequences[i].getDatasetSequence());
1710 // TODO: avoid creation of duplicate dataset sequences with a
1711 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1713 alignment.addSequence(sequences[i]); // merges dataset
1717 newDs.clear(); // tidy up
1719 if (pastedal.getAlignmentAnnotation() != null)
1721 // Add any annotation attached to alignment.
1722 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1723 for (int i = 0; i < alann.length; i++)
1725 annotationAdded = true;
1726 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1728 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1729 newann.padAnnotation(alwidth);
1730 alignment.addAnnotation(newann);
1740 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1741 sequences, 0, alignment.getWidth(), alignment));
1743 // Add any annotations attached to sequences
1744 for (int i = 0; i < sequences.length; i++)
1746 if (sequences[i].getAnnotation() != null)
1748 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1750 annotationAdded = true;
1751 sequences[i].getAnnotation()[a].adjustForAlignment();
1752 sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1753 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1758 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1765 // propagate alignment changed.
1766 viewport.setEndSeq(alignment.getHeight());
1767 if (annotationAdded)
1769 // Duplicate sequence annotation in all views.
1770 AlignmentI[] alview = this.getViewAlignments();
1771 for (int i = 0; i < sequences.length; i++)
1773 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1776 for (int avnum = 0; avnum < alview.length; avnum++)
1778 if (alview[avnum] != alignment)
1780 // duplicate in a view other than the one with input focus
1781 int avwidth = alview[avnum].getWidth() + 1;
1782 // this relies on sann being preserved after we
1783 // modify the sequence's annotation array for each duplication
1784 for (int a = 0; a < sann.length; a++)
1786 AlignmentAnnotation newann = new AlignmentAnnotation(
1788 sequences[i].addAlignmentAnnotation(newann);
1789 newann.padAnnotation(avwidth);
1790 alview[avnum].addAnnotation(newann); // annotation was
1791 // duplicated earlier
1792 alview[avnum].setAnnotationIndex(newann, a);
1797 buildSortByAnnotationScoresMenu();
1799 viewport.firePropertyChange("alignment", null, alignment
1805 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
1807 String newtitle = new String("Copied sequences");
1809 if (Desktop.jalviewClipboard != null
1810 && Desktop.jalviewClipboard[2] != null)
1812 Vector hc = (Vector) Desktop.jalviewClipboard[2];
1813 for (int i = 0; i < hc.size(); i++)
1815 int[] region = (int[]) hc.elementAt(i);
1816 af.viewport.hideColumns(region[0], region[1]);
1820 // >>>This is a fix for the moment, until a better solution is
1822 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
1824 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1826 // TODO: maintain provenance of an alignment, rather than just make the
1827 // title a concatenation of operations.
1830 if (title.startsWith("Copied sequences"))
1836 newtitle = newtitle.concat("- from " + title);
1841 newtitle = new String("Pasted sequences");
1844 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1849 } catch (Exception ex)
1851 ex.printStackTrace();
1852 System.out.println("Exception whilst pasting: " + ex);
1853 // could be anything being pasted in here
1864 protected void cut_actionPerformed(ActionEvent e)
1866 copy_actionPerformed(null);
1867 delete_actionPerformed(null);
1876 protected void delete_actionPerformed(ActionEvent evt)
1879 SequenceGroup sg = viewport.getSelectionGroup();
1885 Vector seqs = new Vector();
1887 for (int i = 0; i < sg.getSize(); i++)
1889 seq = sg.getSequenceAt(i);
1890 seqs.addElement(seq);
1893 // If the cut affects all sequences, remove highlighted columns
1894 if (sg.getSize() == viewport.alignment.getHeight())
1896 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1897 sg.getEndRes() + 1);
1900 SequenceI[] cut = new SequenceI[seqs.size()];
1901 for (int i = 0; i < seqs.size(); i++)
1903 cut[i] = (SequenceI) seqs.elementAt(i);
1907 * //ADD HISTORY ITEM
1909 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1910 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1911 viewport.alignment));
1913 viewport.setSelectionGroup(null);
1914 viewport.sendSelection();
1915 viewport.alignment.deleteGroup(sg);
1917 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1919 if (viewport.getAlignment().getHeight() < 1)
1923 this.setClosed(true);
1924 } catch (Exception ex)
1936 protected void deleteGroups_actionPerformed(ActionEvent e)
1938 viewport.alignment.deleteAllGroups();
1939 viewport.sequenceColours = null;
1940 viewport.setSelectionGroup(null);
1941 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1942 alignPanel.updateAnnotation();
1943 alignPanel.paintAlignment(true);
1952 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1954 SequenceGroup sg = new SequenceGroup();
1956 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1958 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1961 sg.setEndRes(viewport.alignment.getWidth() - 1);
1962 viewport.setSelectionGroup(sg);
1963 viewport.sendSelection();
1964 alignPanel.paintAlignment(true);
1965 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1974 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1976 if (viewport.cursorMode)
1978 alignPanel.seqPanel.keyboardNo1 = null;
1979 alignPanel.seqPanel.keyboardNo2 = null;
1981 viewport.setSelectionGroup(null);
1982 viewport.getColumnSelection().clear();
1983 viewport.setSelectionGroup(null);
1984 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1985 alignPanel.idPanel.idCanvas.searchResults = null;
1986 alignPanel.paintAlignment(true);
1987 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1996 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1998 SequenceGroup sg = viewport.getSelectionGroup();
2002 selectAllSequenceMenuItem_actionPerformed(null);
2007 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2009 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2012 alignPanel.paintAlignment(true);
2013 viewport.sendSelection();
2014 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2017 public void invertColSel_actionPerformed(ActionEvent e)
2019 viewport.invertColumnSelection();
2020 alignPanel.paintAlignment(true);
2029 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2031 trimAlignment(true);
2040 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2042 trimAlignment(false);
2045 void trimAlignment(boolean trimLeft)
2047 ColumnSelection colSel = viewport.getColumnSelection();
2050 if (colSel.size() > 0)
2054 column = colSel.getMin();
2058 column = colSel.getMax();
2062 if (viewport.getSelectionGroup() != null)
2064 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2065 viewport.hiddenRepSequences);
2069 seqs = viewport.alignment.getSequencesArray();
2072 TrimRegionCommand trimRegion;
2075 trimRegion = new TrimRegionCommand("Remove Left",
2076 TrimRegionCommand.TRIM_LEFT, seqs, column,
2077 viewport.alignment, viewport.colSel,
2078 viewport.selectionGroup);
2079 viewport.setStartRes(0);
2083 trimRegion = new TrimRegionCommand("Remove Right",
2084 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2085 viewport.alignment, viewport.colSel,
2086 viewport.selectionGroup);
2089 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2091 addHistoryItem(trimRegion);
2093 Vector groups = viewport.alignment.getGroups();
2095 for (int i = 0; i < groups.size(); i++)
2097 SequenceGroup sg = (SequenceGroup) groups.get(i);
2099 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2100 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2102 viewport.alignment.deleteGroup(sg);
2106 viewport.firePropertyChange("alignment", null, viewport
2107 .getAlignment().getSequences());
2117 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2119 int start = 0, end = viewport.alignment.getWidth() - 1;
2122 if (viewport.getSelectionGroup() != null)
2124 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2125 viewport.hiddenRepSequences);
2126 start = viewport.getSelectionGroup().getStartRes();
2127 end = viewport.getSelectionGroup().getEndRes();
2131 seqs = viewport.alignment.getSequencesArray();
2134 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2135 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
2137 addHistoryItem(removeGapCols);
2139 statusBar.setText("Removed " + removeGapCols.getSize()
2140 + " empty columns.");
2142 // This is to maintain viewport position on first residue
2143 // of first sequence
2144 SequenceI seq = viewport.alignment.getSequenceAt(0);
2145 int startRes = seq.findPosition(viewport.startRes);
2146 // ShiftList shifts;
2147 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2148 // edit.alColumnChanges=shifts.getInverse();
2149 // if (viewport.hasHiddenColumns)
2150 // viewport.getColumnSelection().compensateForEdits(shifts);
2151 viewport.setStartRes(seq.findIndex(startRes) - 1);
2152 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2163 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2165 int start = 0, end = viewport.alignment.getWidth() - 1;
2168 if (viewport.getSelectionGroup() != null)
2170 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2171 viewport.hiddenRepSequences);
2172 start = viewport.getSelectionGroup().getStartRes();
2173 end = viewport.getSelectionGroup().getEndRes();
2177 seqs = viewport.alignment.getSequencesArray();
2180 // This is to maintain viewport position on first residue
2181 // of first sequence
2182 SequenceI seq = viewport.alignment.getSequenceAt(0);
2183 int startRes = seq.findPosition(viewport.startRes);
2185 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2186 viewport.alignment));
2188 viewport.setStartRes(seq.findIndex(startRes) - 1);
2190 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2201 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2203 viewport.padGaps = padGapsMenuitem.isSelected();
2204 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2210 // if (justifySeqs>0)
2212 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2224 public void findMenuItem_actionPerformed(ActionEvent e)
2229 public void newView_actionPerformed(ActionEvent e)
2231 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2234 newap.av.gatherViewsHere = false;
2236 if (viewport.viewName == null)
2238 viewport.viewName = "Original";
2241 newap.av.historyList = viewport.historyList;
2242 newap.av.redoList = viewport.redoList;
2244 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2245 String newViewName = "View " + index;
2247 Vector comps = (Vector) PaintRefresher.components.get(viewport
2248 .getSequenceSetId());
2249 Vector existingNames = new Vector();
2250 for (int i = 0; i < comps.size(); i++)
2252 if (comps.elementAt(i) instanceof AlignmentPanel)
2254 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2255 if (!existingNames.contains(ap.av.viewName))
2257 existingNames.addElement(ap.av.viewName);
2262 while (existingNames.contains(newViewName))
2264 newViewName = "View " + (++index);
2267 newap.av.viewName = newViewName;
2269 addAlignmentPanel(newap, true);
2271 if (alignPanels.size() == 2)
2273 viewport.gatherViewsHere = true;
2275 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2278 public void expandViews_actionPerformed(ActionEvent e)
2280 Desktop.instance.explodeViews(this);
2283 public void gatherViews_actionPerformed(ActionEvent e)
2285 Desktop.instance.gatherViews(this);
2294 public void font_actionPerformed(ActionEvent e)
2296 new FontChooser(alignPanel);
2305 protected void seqLimit_actionPerformed(ActionEvent e)
2307 viewport.setShowJVSuffix(seqLimits.isSelected());
2309 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2310 .calculateIdWidth());
2311 alignPanel.paintAlignment(true);
2314 public void idRightAlign_actionPerformed(ActionEvent e)
2316 viewport.rightAlignIds = idRightAlign.isSelected();
2317 alignPanel.paintAlignment(true);
2320 public void centreColumnLabels_actionPerformed(ActionEvent e)
2322 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2323 alignPanel.paintAlignment(true);
2329 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2331 protected void followHighlight_actionPerformed()
2333 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2335 alignPanel.scrollToPosition(
2336 alignPanel.seqPanel.seqCanvas.searchResults, false);
2346 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2348 viewport.setColourText(colourTextMenuItem.isSelected());
2349 alignPanel.paintAlignment(true);
2358 public void wrapMenuItem_actionPerformed(ActionEvent e)
2360 scaleAbove.setVisible(wrapMenuItem.isSelected());
2361 scaleLeft.setVisible(wrapMenuItem.isSelected());
2362 scaleRight.setVisible(wrapMenuItem.isSelected());
2363 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2364 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2367 public void showAllSeqs_actionPerformed(ActionEvent e)
2369 viewport.showAllHiddenSeqs();
2372 public void showAllColumns_actionPerformed(ActionEvent e)
2374 viewport.showAllHiddenColumns();
2378 public void hideSelSequences_actionPerformed(ActionEvent e)
2380 viewport.hideAllSelectedSeqs();
2381 alignPanel.paintAlignment(true);
2385 * called by key handler and the hide all/show all menu items
2390 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2393 boolean hide = false;
2394 SequenceGroup sg = viewport.getSelectionGroup();
2395 if (!toggleSeqs && !toggleCols)
2397 // Hide everything by the current selection - this is a hack - we do the
2398 // invert and then hide
2399 // first check that there will be visible columns after the invert.
2400 if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
2401 .getSelected().size() > 0)
2402 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2405 // now invert the sequence set, if required - empty selection implies
2406 // that no hiding is required.
2409 invertSequenceMenuItem_actionPerformed(null);
2410 sg = viewport.getSelectionGroup();
2414 viewport.expandColSelection(sg, true);
2415 // finally invert the column selection and get the new sequence
2417 invertColSel_actionPerformed(null);
2424 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
2426 hideSelSequences_actionPerformed(null);
2429 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
2431 showAllSeqs_actionPerformed(null);
2437 if (viewport.colSel.getSelected().size() > 0)
2439 hideSelColumns_actionPerformed(null);
2442 viewport.selectionGroup = sg;
2447 showAllColumns_actionPerformed(null);
2456 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2457 * event.ActionEvent)
2459 public void hideAllButSelection_actionPerformed(ActionEvent e)
2461 toggleHiddenRegions(false, false);
2468 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2471 public void hideAllSelection_actionPerformed(ActionEvent e)
2473 SequenceGroup sg = viewport.getSelectionGroup();
2474 viewport.expandColSelection(sg, false);
2475 viewport.hideAllSelectedSeqs();
2476 viewport.hideSelectedColumns();
2477 alignPanel.paintAlignment(true);
2484 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2487 public void showAllhidden_actionPerformed(ActionEvent e)
2489 viewport.showAllHiddenColumns();
2490 viewport.showAllHiddenSeqs();
2491 alignPanel.paintAlignment(true);
2494 public void hideSelColumns_actionPerformed(ActionEvent e)
2496 viewport.hideSelectedColumns();
2497 alignPanel.paintAlignment(true);
2500 public void hiddenMarkers_actionPerformed(ActionEvent e)
2502 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2512 protected void scaleAbove_actionPerformed(ActionEvent e)
2514 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2515 alignPanel.paintAlignment(true);
2524 protected void scaleLeft_actionPerformed(ActionEvent e)
2526 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2527 alignPanel.paintAlignment(true);
2536 protected void scaleRight_actionPerformed(ActionEvent e)
2538 viewport.setScaleRightWrapped(scaleRight.isSelected());
2539 alignPanel.paintAlignment(true);
2548 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2550 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2551 alignPanel.paintAlignment(true);
2560 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2562 viewport.setShowText(viewTextMenuItem.isSelected());
2563 alignPanel.paintAlignment(true);
2572 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2574 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2575 alignPanel.paintAlignment(true);
2578 public FeatureSettings featureSettings;
2580 public void featureSettings_actionPerformed(ActionEvent e)
2582 if (featureSettings != null)
2584 featureSettings.close();
2585 featureSettings = null;
2587 if (!showSeqFeatures.isSelected())
2589 // make sure features are actually displayed
2590 showSeqFeatures.setSelected(true);
2591 showSeqFeatures_actionPerformed(null);
2593 featureSettings = new FeatureSettings(this);
2597 * Set or clear 'Show Sequence Features'
2602 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2604 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2605 alignPanel.paintAlignment(true);
2606 if (alignPanel.getOverviewPanel() != null)
2608 alignPanel.getOverviewPanel().updateOverviewImage();
2613 * Set or clear 'Show Sequence Features'
2618 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2620 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2622 if (viewport.getShowSequenceFeaturesHeight())
2624 // ensure we're actually displaying features
2625 viewport.setShowSequenceFeatures(true);
2626 showSeqFeatures.setSelected(true);
2628 alignPanel.paintAlignment(true);
2629 if (alignPanel.getOverviewPanel() != null)
2631 alignPanel.getOverviewPanel().updateOverviewImage();
2641 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2643 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2644 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2647 public void alignmentProperties()
2649 JEditorPane editPane = new JEditorPane("text/html", "");
2650 editPane.setEditable(false);
2651 StringBuffer contents = new StringBuffer("<html>");
2654 int min = Integer.MAX_VALUE, max = 0;
2655 for (int i = 0; i < viewport.alignment.getHeight(); i++)
2657 int size = viewport.alignment.getSequenceAt(i).getEnd()
2658 - viewport.alignment.getSequenceAt(i).getStart();
2665 avg = avg / (float) viewport.alignment.getHeight();
2667 contents.append("<br>Sequences: " + viewport.alignment.getHeight());
2668 contents.append("<br>Minimum Sequence Length: " + min);
2669 contents.append("<br>Maximum Sequence Length: " + max);
2670 contents.append("<br>Average Length: " + (int) avg);
2672 if (((Alignment) viewport.alignment).getProperties() != null)
2674 Hashtable props = ((Alignment) viewport.alignment).getProperties();
2675 Enumeration en = props.keys();
2676 contents.append("<br><br><table border=\"1\">");
2677 while (en.hasMoreElements())
2679 String key = en.nextElement().toString();
2680 StringBuffer val = new StringBuffer();
2681 String vals = props.get(key).toString();
2685 npos = vals.indexOf("\n", pos);
2688 val.append(vals.substring(pos));
2692 val.append(vals.substring(pos, npos));
2696 } while (npos != -1);
2698 .append("<tr><td>" + key + "</td><td>" + val + "</td></tr>");
2700 contents.append("</table>");
2702 editPane.setText(contents.toString() + "</html>");
2703 JInternalFrame frame = new JInternalFrame();
2704 frame.getContentPane().add(new JScrollPane(editPane));
2706 Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
2707 + getTitle(), 500, 400);
2716 public void overviewMenuItem_actionPerformed(ActionEvent e)
2718 if (alignPanel.overviewPanel != null)
2723 JInternalFrame frame = new JInternalFrame();
2724 OverviewPanel overview = new OverviewPanel(alignPanel);
2725 frame.setContentPane(overview);
2726 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(), frame
2727 .getWidth(), frame.getHeight());
2729 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2731 .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2733 public void internalFrameClosed(
2734 javax.swing.event.InternalFrameEvent evt)
2736 alignPanel.setOverviewPanel(null);
2740 alignPanel.setOverviewPanel(overview);
2743 public void textColour_actionPerformed(ActionEvent e)
2745 new TextColourChooser().chooseColour(alignPanel, null);
2754 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2765 public void clustalColour_actionPerformed(ActionEvent e)
2767 changeColour(new ClustalxColourScheme(
2768 viewport.alignment.getSequences(), viewport.alignment
2778 public void zappoColour_actionPerformed(ActionEvent e)
2780 changeColour(new ZappoColourScheme());
2789 public void taylorColour_actionPerformed(ActionEvent e)
2791 changeColour(new TaylorColourScheme());
2800 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2802 changeColour(new HydrophobicColourScheme());
2811 public void helixColour_actionPerformed(ActionEvent e)
2813 changeColour(new HelixColourScheme());
2822 public void strandColour_actionPerformed(ActionEvent e)
2824 changeColour(new StrandColourScheme());
2833 public void turnColour_actionPerformed(ActionEvent e)
2835 changeColour(new TurnColourScheme());
2844 public void buriedColour_actionPerformed(ActionEvent e)
2846 changeColour(new BuriedColourScheme());
2855 public void nucleotideColour_actionPerformed(ActionEvent e)
2857 changeColour(new NucleotideColourScheme());
2860 public void annotationColour_actionPerformed(ActionEvent e)
2862 new AnnotationColourChooser(viewport, alignPanel);
2871 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2873 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2882 public void changeColour(ColourSchemeI cs)
2888 if (viewport.getAbovePIDThreshold())
2890 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2893 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2895 viewport.setGlobalColourScheme(cs);
2899 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2902 if (viewport.getConservationSelected())
2905 Alignment al = (Alignment) viewport.alignment;
2906 Conservation c = new Conservation("All",
2907 ResidueProperties.propHash, 3, al.getSequences(), 0, al
2911 c.verdict(false, viewport.ConsPercGaps);
2913 cs.setConservation(c);
2915 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
2920 cs.setConservation(null);
2923 cs.setConsensus(viewport.hconsensus);
2926 viewport.setGlobalColourScheme(cs);
2928 if (viewport.getColourAppliesToAllGroups())
2930 Vector groups = viewport.alignment.getGroups();
2932 for (int i = 0; i < groups.size(); i++)
2934 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2942 if (cs instanceof ClustalxColourScheme)
2944 sg.cs = new ClustalxColourScheme(sg
2945 .getSequences(viewport.hiddenRepSequences), sg.getWidth());
2947 else if (cs instanceof UserColourScheme)
2949 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
2955 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2956 } catch (Exception ex)
2961 if (viewport.getAbovePIDThreshold()
2962 || cs instanceof PIDColourScheme
2963 || cs instanceof Blosum62ColourScheme)
2965 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2967 sg.cs.setConsensus(AAFrequency.calculate(sg
2968 .getSequences(viewport.hiddenRepSequences), sg
2969 .getStartRes(), sg.getEndRes() + 1));
2973 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2976 if (viewport.getConservationSelected())
2978 Conservation c = new Conservation("Group",
2979 ResidueProperties.propHash, 3, sg
2980 .getSequences(viewport.hiddenRepSequences), sg
2981 .getStartRes(), sg.getEndRes() + 1);
2983 c.verdict(false, viewport.ConsPercGaps);
2984 sg.cs.setConservation(c);
2988 sg.cs.setConservation(null);
2993 if (alignPanel.getOverviewPanel() != null)
2995 alignPanel.getOverviewPanel().updateOverviewImage();
2998 alignPanel.paintAlignment(true);
3007 protected void modifyPID_actionPerformed(ActionEvent e)
3009 if (viewport.getAbovePIDThreshold()
3010 && viewport.globalColourScheme != null)
3012 SliderPanel.setPIDSliderSource(alignPanel, viewport
3013 .getGlobalColourScheme(), "Background");
3014 SliderPanel.showPIDSlider();
3024 protected void modifyConservation_actionPerformed(ActionEvent e)
3026 if (viewport.getConservationSelected()
3027 && viewport.globalColourScheme != null)
3029 SliderPanel.setConservationSlider(alignPanel,
3030 viewport.globalColourScheme, "Background");
3031 SliderPanel.showConservationSlider();
3041 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3043 viewport.setConservationSelected(conservationMenuItem.isSelected());
3045 viewport.setAbovePIDThreshold(false);
3046 abovePIDThreshold.setSelected(false);
3048 changeColour(viewport.getGlobalColourScheme());
3050 modifyConservation_actionPerformed(null);
3059 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3061 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3063 conservationMenuItem.setSelected(false);
3064 viewport.setConservationSelected(false);
3066 changeColour(viewport.getGlobalColourScheme());
3068 modifyPID_actionPerformed(null);
3077 public void userDefinedColour_actionPerformed(ActionEvent e)
3079 if (e.getActionCommand().equals("User Defined..."))
3081 new UserDefinedColours(alignPanel, null);
3085 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3086 .getUserColourSchemes().get(e.getActionCommand());
3092 public void updateUserColourMenu()
3095 Component[] menuItems = colourMenu.getMenuComponents();
3096 int i, iSize = menuItems.length;
3097 for (i = 0; i < iSize; i++)
3099 if (menuItems[i].getName() != null
3100 && menuItems[i].getName().equals("USER_DEFINED"))
3102 colourMenu.remove(menuItems[i]);
3106 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3108 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3109 .getUserColourSchemes().keys();
3111 while (userColours.hasMoreElements())
3113 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3114 userColours.nextElement().toString());
3115 radioItem.setName("USER_DEFINED");
3116 radioItem.addMouseListener(new MouseAdapter()
3118 public void mousePressed(MouseEvent evt)
3120 if (evt.isControlDown()
3121 || SwingUtilities.isRightMouseButton(evt))
3124 .removeActionListener(radioItem.getActionListeners()[0]);
3126 int option = JOptionPane.showInternalConfirmDialog(
3127 jalview.gui.Desktop.desktop,
3128 "Remove from default list?",
3129 "Remove user defined colour",
3130 JOptionPane.YES_NO_OPTION);
3131 if (option == JOptionPane.YES_OPTION)
3133 jalview.gui.UserDefinedColours
3134 .removeColourFromDefaults(radioItem.getText());
3135 colourMenu.remove(radioItem);
3139 radioItem.addActionListener(new ActionListener()
3141 public void actionPerformed(ActionEvent evt)
3143 userDefinedColour_actionPerformed(evt);
3150 radioItem.addActionListener(new ActionListener()
3152 public void actionPerformed(ActionEvent evt)
3154 userDefinedColour_actionPerformed(evt);
3158 colourMenu.insert(radioItem, 15);
3159 colours.add(radioItem);
3170 public void PIDColour_actionPerformed(ActionEvent e)
3172 changeColour(new PIDColourScheme());
3181 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3183 changeColour(new Blosum62ColourScheme());
3192 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3194 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3195 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3196 .getAlignment().getSequenceAt(0), null);
3197 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3198 viewport.alignment));
3199 alignPanel.paintAlignment(true);
3208 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3210 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3211 AlignmentSorter.sortByID(viewport.getAlignment());
3212 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
3213 alignPanel.paintAlignment(true);
3222 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3224 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3225 AlignmentSorter.sortByLength(viewport.getAlignment());
3226 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3227 viewport.alignment));
3228 alignPanel.paintAlignment(true);
3237 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3239 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3240 AlignmentSorter.sortByGroup(viewport.getAlignment());
3241 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3242 viewport.alignment));
3244 alignPanel.paintAlignment(true);
3253 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3255 new RedundancyPanel(alignPanel, this);
3264 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3266 if ((viewport.getSelectionGroup() == null)
3267 || (viewport.getSelectionGroup().getSize() < 2))
3269 JOptionPane.showInternalMessageDialog(this,
3270 "You must select at least 2 sequences.", "Invalid Selection",
3271 JOptionPane.WARNING_MESSAGE);
3275 JInternalFrame frame = new JInternalFrame();
3276 frame.setContentPane(new PairwiseAlignPanel(viewport));
3277 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
3287 public void PCAMenuItem_actionPerformed(ActionEvent e)
3289 if (((viewport.getSelectionGroup() != null)
3290 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3291 .getSelectionGroup().getSize() > 0))
3292 || (viewport.getAlignment().getHeight() < 4))
3294 JOptionPane.showInternalMessageDialog(this,
3295 "Principal component analysis must take\n"
3296 + "at least 4 input sequences.",
3297 "Sequence selection insufficient",
3298 JOptionPane.WARNING_MESSAGE);
3303 new PCAPanel(alignPanel);
3306 public void autoCalculate_actionPerformed(ActionEvent e)
3308 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3309 if (viewport.autoCalculateConsensus)
3311 viewport.firePropertyChange("alignment", null, viewport
3312 .getAlignment().getSequences());
3322 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3324 NewTreePanel("AV", "PID", "Average distance tree using PID");
3333 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3335 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3344 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3346 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3355 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3357 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3370 void NewTreePanel(String type, String pwType, String title)
3374 if (viewport.getSelectionGroup() != null)
3376 if (viewport.getSelectionGroup().getSize() < 3)
3381 "You need to have more than two sequences selected to build a tree!",
3382 "Not enough sequences", JOptionPane.WARNING_MESSAGE);
3387 SequenceGroup sg = viewport.getSelectionGroup();
3389 /* Decide if the selection is a column region */
3390 while (s < sg.getSize())
3392 if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
3398 "The selected region to create a tree may\nonly contain residues or gaps.\n"
3399 + "Try using the Pad function in the edit menu,\n"
3400 + "or one of the multiple sequence alignment web services.",
3401 "Sequences in selection are not aligned",
3402 JOptionPane.WARNING_MESSAGE);
3408 title = title + " on region";
3409 tp = new TreePanel(alignPanel, type, pwType);
3413 // are the visible sequences aligned?
3414 if (!viewport.alignment.isAligned(false))
3419 "The sequences must be aligned before creating a tree.\n"
3420 + "Try using the Pad function in the edit menu,\n"
3421 + "or one of the multiple sequence alignment web services.",
3422 "Sequences not aligned",
3423 JOptionPane.WARNING_MESSAGE);
3428 if (viewport.alignment.getHeight() < 2)
3433 tp = new TreePanel(alignPanel, type, pwType);
3438 if (viewport.viewName != null)
3440 title += viewport.viewName + " of ";
3443 title += this.title;
3445 Desktop.addInternalFrame(tp, title, 600, 500);
3456 public void addSortByOrderMenuItem(String title,
3457 final AlignmentOrder order)
3459 final JMenuItem item = new JMenuItem("by " + title);
3461 item.addActionListener(new java.awt.event.ActionListener()
3463 public void actionPerformed(ActionEvent e)
3465 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3467 // TODO: JBPNote - have to map order entries to curent SequenceI
3469 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3471 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3472 viewport.alignment));
3474 alignPanel.paintAlignment(true);
3480 * Add a new sort by annotation score menu item
3483 * the menu to add the option to
3485 * the label used to retrieve scores for each sequence on the
3488 public void addSortByAnnotScoreMenuItem(JMenu sort,
3489 final String scoreLabel)
3491 final JMenuItem item = new JMenuItem(scoreLabel);
3493 item.addActionListener(new java.awt.event.ActionListener()
3495 public void actionPerformed(ActionEvent e)
3497 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3498 AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport
3499 .getAlignment());// ,viewport.getSelectionGroup());
3500 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3501 viewport.alignment));
3502 alignPanel.paintAlignment(true);
3508 * last hash for alignment's annotation array - used to minimise cost of
3511 protected int _annotationScoreVectorHash;
3514 * search the alignment and rebuild the sort by annotation score submenu the
3515 * last alignment annotation vector hash is stored to minimize cost of
3516 * rebuilding in subsequence calls.
3519 public void buildSortByAnnotationScoresMenu()
3521 if (viewport.alignment.getAlignmentAnnotation() == null)
3526 if (viewport.alignment.getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3528 sortByAnnotScore.removeAll();
3529 // almost certainly a quicker way to do this - but we keep it simple
3530 Hashtable scoreSorts = new Hashtable();
3531 AlignmentAnnotation aann[];
3532 Enumeration sq = viewport.alignment.getSequences().elements();
3533 while (sq.hasMoreElements())
3535 aann = ((SequenceI) sq.nextElement()).getAnnotation();
3536 for (int i = 0; aann != null && i < aann.length; i++)
3538 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3540 scoreSorts.put(aann[i].label, aann[i].label);
3544 Enumeration labels = scoreSorts.keys();
3545 while (labels.hasMoreElements())
3547 addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels
3550 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3553 _annotationScoreVectorHash = viewport.alignment
3554 .getAlignmentAnnotation().hashCode();
3559 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3560 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3561 * call. Listeners are added to remove the menu item when the treePanel is
3562 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3566 * Displayed tree window.
3568 * SortBy menu item title.
3570 public void buildTreeMenu()
3572 sortByTreeMenu.removeAll();
3574 Vector comps = (Vector) PaintRefresher.components.get(viewport
3575 .getSequenceSetId());
3576 Vector treePanels = new Vector();
3577 int i, iSize = comps.size();
3578 for (i = 0; i < iSize; i++)
3580 if (comps.elementAt(i) instanceof TreePanel)
3582 treePanels.add(comps.elementAt(i));
3586 iSize = treePanels.size();
3590 sortByTreeMenu.setVisible(false);
3594 sortByTreeMenu.setVisible(true);
3596 for (i = 0; i < treePanels.size(); i++)
3598 TreePanel tp = (TreePanel) treePanels.elementAt(i);
3599 final JMenuItem item = new JMenuItem(tp.getTitle());
3600 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3601 item.addActionListener(new java.awt.event.ActionListener()
3603 public void actionPerformed(ActionEvent e)
3605 SequenceI[] oldOrder = viewport.getAlignment()
3606 .getSequencesArray();
3607 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
3609 addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
3610 viewport.alignment));
3612 alignPanel.paintAlignment(true);
3616 sortByTreeMenu.add(item);
3621 * Work out whether the whole set of sequences or just the selected set will
3622 * be submitted for multiple alignment.
3625 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3627 // Now, check we have enough sequences
3628 AlignmentView msa = null;
3630 if ((viewport.getSelectionGroup() != null)
3631 && (viewport.getSelectionGroup().getSize() > 1))
3633 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3634 // some common interface!
3636 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3637 * SequenceI[sz = seqs.getSize(false)];
3639 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3640 * seqs.getSequenceAt(i); }
3642 msa = viewport.getAlignmentView(true);
3647 * Vector seqs = viewport.getAlignment().getSequences();
3649 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3651 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3652 * seqs.elementAt(i); } }
3654 msa = viewport.getAlignmentView(false);
3660 * Decides what is submitted to a secondary structure prediction service: the
3661 * first sequence in the alignment, or in the current selection, or, if the
3662 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3663 * region or the whole alignment. (where the first sequence in the set is the
3664 * one that the prediction will be for).
3666 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3668 AlignmentView seqs = null;
3670 if ((viewport.getSelectionGroup() != null)
3671 && (viewport.getSelectionGroup().getSize() > 0))
3673 seqs = viewport.getAlignmentView(true);
3677 seqs = viewport.getAlignmentView(false);
3679 // limit sequences - JBPNote in future - could spawn multiple prediction
3681 // TODO: viewport.alignment.isAligned is a global state - the local
3682 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3683 if (!viewport.alignment.isAligned(false))
3685 seqs.setSequences(new SeqCigar[]
3686 { seqs.getSequences()[0] });
3687 // TODO: if seqs.getSequences().length>1 then should really have warned
3700 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3702 // Pick the tree file
3703 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
3704 .getProperty("LAST_DIRECTORY"));
3705 chooser.setFileView(new JalviewFileView());
3706 chooser.setDialogTitle("Select a newick-like tree file");
3707 chooser.setToolTipText("Load a tree file");
3709 int value = chooser.showOpenDialog(null);
3711 if (value == JalviewFileChooser.APPROVE_OPTION)
3713 String choice = chooser.getSelectedFile().getPath();
3714 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3715 jalview.io.NewickFile fin = null;
3718 fin = new jalview.io.NewickFile(choice, "File");
3719 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3720 } catch (Exception ex)
3722 JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3723 "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
3724 ex.printStackTrace();
3726 if (fin != null && fin.hasWarningMessage())
3728 JOptionPane.showMessageDialog(Desktop.desktop, fin
3729 .getWarningMessage(), "Possible problem with tree file",
3730 JOptionPane.WARNING_MESSAGE);
3735 public TreePanel ShowNewickTree(NewickFile nf, String title)
3737 return ShowNewickTree(nf, title, 600, 500, 4, 5);
3740 public TreePanel ShowNewickTree(NewickFile nf, String title,
3741 AlignmentView input)
3743 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
3746 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
3747 int h, int x, int y)
3749 return ShowNewickTree(nf, title, null, w, h, x, y);
3753 * Add a treeviewer for the tree extracted from a newick file object to the
3754 * current alignment view
3761 * Associated alignment input data (or null)
3770 * @return TreePanel handle
3772 public TreePanel ShowNewickTree(NewickFile nf, String title,
3773 AlignmentView input, int w, int h, int x, int y)
3775 TreePanel tp = null;
3781 if (nf.getTree() != null)
3783 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
3789 tp.setLocation(x, y);
3792 Desktop.addInternalFrame(tp, title, w, h);
3794 } catch (Exception ex)
3796 ex.printStackTrace();
3802 private boolean buildingMenu = false;
3805 * Generates menu items and listener event actions for web service clients
3808 public void BuildWebServiceMenu()
3810 while (buildingMenu)
3814 System.err.println("Waiting for building menu to finish.");
3816 } catch (Exception e)
3821 buildingMenu = true;
3825 .println("Building ws menu again " + Thread.currentThread());
3826 // TODO: add support for context dependent disabling of services based on
3827 // alignment and current selection
3828 // TODO: add additional serviceHandle parameter to specify abstract
3830 // class independently of AbstractName
3831 // TODO: add in rediscovery GUI function to restart discoverer
3832 // TODO: group services by location as well as function and/or introduce
3833 // object broker mechanism.
3834 Vector wsmenu = new Vector();
3835 final IProgressIndicator af = this;
3836 if (Cache.getDefault("SHOW_JWS1_SERVICES", true)
3837 && Discoverer.services != null
3838 && (Discoverer.services.size() > 0))
3840 // TODO: refactor to allow list of AbstractName/Handler bindings to be
3841 // stored or retrieved from elsewhere
3842 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
3843 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
3844 Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
3845 // TODO: move GUI generation code onto service implementation - so a
3846 // client instance attaches itself to the GUI with method call like
3847 // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
3851 // Add any Multiple Sequence Alignment Services
3852 final JMenu msawsmenu = new JMenu("Alignment");
3853 for (int i = 0, j = msaws.size(); i < j; i++)
3855 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
3857 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
3858 .getServiceClient(sh);
3859 impl.attachWSMenuEntry(msawsmenu, this);
3862 wsmenu.add(msawsmenu);
3864 if (secstrpr != null)
3866 // Add any secondary structure prediction services
3867 final JMenu secstrmenu = new JMenu(
3868 "Secondary Structure Prediction");
3869 for (int i = 0, j = secstrpr.size(); i < j; i++)
3871 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
3873 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
3874 .getServiceClient(sh);
3875 impl.attachWSMenuEntry(secstrmenu, this);
3877 wsmenu.add(secstrmenu);
3879 if (seqsrch != null)
3881 // Add any sequence search services
3882 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
3883 for (int i = 0, j = seqsrch.size(); i < j; i++)
3885 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
3887 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
3888 .getServiceClient(sh);
3889 impl.attachWSMenuEntry(seqsrchmenu, this);
3891 wsmenu.add(seqsrchmenu);
3895 // TODO: move into separate menu builder class.
3896 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
3898 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
3899 if (jws2servs != null)
3901 if (jws2servs.hasServices())
3903 JMenu jws2men = new JMenu("Jalview 2 Services");
3904 jws2servs.attachWSMenuEntry(jws2men, this);
3905 for (int i = 0, iSize = jws2men.getMenuComponentCount(); i < iSize; i++)
3907 wsmenu.add(jws2men.getMenuComponent(i));
3912 resetWebServiceMenu();
3913 // finally, add the whole shebang onto the webservices menu
3914 if (wsmenu.size() > 0)
3916 for (int i = 0, j = wsmenu.size(); i < j; i++)
3918 webService.add((JMenu) wsmenu.get(i));
3923 this.webService.add(this.webServiceNoServices);
3925 } catch (Exception e)
3929 buildingMenu = false;
3933 * empty the web service menu and add any ad-hoc functions not dynamically
3937 private void resetWebServiceMenu()
3939 webService.removeAll();
3940 build_fetchdbmenu(webService);
3941 build_urlServiceMenu(webService);
3945 * construct any groupURL type service menu entries.
3949 private void build_urlServiceMenu(JMenu webService)
3951 if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
3953 jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
3959 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
3960 * chooser = new JalviewFileChooser(jalview.bin.Cache.
3961 * getProperty("LAST_DIRECTORY"));
3963 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
3964 * to Vamsas file"); chooser.setToolTipText("Export");
3966 * int value = chooser.showSaveDialog(this);
3968 * if (value == JalviewFileChooser.APPROVE_OPTION) {
3969 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
3970 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
3971 * chooser.getSelectedFile().getAbsolutePath(), this); } }
3974 * prototype of an automatically enabled/disabled analysis function
3977 protected void setShowProductsEnabled()
3979 SequenceI[] selection = viewport.getSequenceSelection();
3980 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
3981 viewport.getAlignment().getDataset()))
3983 showProducts.setEnabled(true);
3988 showProducts.setEnabled(false);
3993 * search selection for sequence xRef products and build the show products
3998 * @return true if showProducts menu should be enabled.
4000 public boolean canShowProducts(SequenceI[] selection,
4001 boolean isRegionSelection, Alignment dataset)
4003 boolean showp = false;
4006 showProducts.removeAll();
4007 final boolean dna = viewport.getAlignment().isNucleotide();
4008 final Alignment ds = dataset;
4009 String[] ptypes = (selection == null || selection.length == 0) ? null
4010 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4012 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4013 // selection, dataset, true);
4014 final SequenceI[] sel = selection;
4015 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4018 final boolean isRegSel = isRegionSelection;
4019 final AlignFrame af = this;
4020 final String source = ptypes[t];
4021 JMenuItem xtype = new JMenuItem(ptypes[t]);
4022 xtype.addActionListener(new ActionListener()
4025 public void actionPerformed(ActionEvent e)
4027 // TODO: new thread for this call with vis-delay
4028 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4029 isRegSel, dna, source);
4033 showProducts.add(xtype);
4035 showProducts.setVisible(showp);
4036 showProducts.setEnabled(showp);
4037 } catch (Exception e)
4039 jalview.bin.Cache.log
4041 "canTranslate threw an exception - please report to help@jalview.org",
4048 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4049 boolean isRegSel, boolean dna, String source)
4051 final boolean fisRegSel = isRegSel;
4052 final boolean fdna = dna;
4053 final String fsrc = source;
4054 final AlignFrame ths = this;
4055 final SequenceI[] fsel = sel;
4056 Runnable foo = new Runnable()
4061 final long sttime = System.currentTimeMillis();
4062 ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4065 Alignment ds = ths.getViewport().alignment.getDataset(); // update
4069 Alignment prods = CrossRef
4070 .findXrefSequences(fsel, fdna, fsrc, ds);
4073 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4074 for (int s = 0; s < sprods.length; s++)
4076 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4077 if (ds.getSequences() == null
4078 || !ds.getSequences().contains(
4079 sprods[s].getDatasetSequence()))
4080 ds.addSequence(sprods[s].getDatasetSequence());
4081 sprods[s].updatePDBIds();
4083 Alignment al = new Alignment(sprods);
4084 AlignedCodonFrame[] cf = prods.getCodonFrames();
4086 for (int s = 0; cf != null && s < cf.length; s++)
4088 al.addCodonFrame(cf[s]);
4091 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4093 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4094 + " for " + ((fisRegSel) ? "selected region of " : "")
4096 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4101 System.err.println("No Sequences generated for xRef type "
4104 } catch (Exception e)
4106 jalview.bin.Cache.log.error(
4107 "Exception when finding crossreferences", e);
4108 } catch (OutOfMemoryError e)
4110 new OOMWarning("whilst fetching crossreferences", e);
4113 jalview.bin.Cache.log.error("Error when finding crossreferences",
4116 ths.setProgressBar("Finished searching for sequences from " + fsrc,
4121 Thread frunner = new Thread(foo);
4125 public boolean canShowTranslationProducts(SequenceI[] selection,
4126 AlignmentI alignment)
4131 return (jalview.analysis.Dna.canTranslate(selection, viewport
4132 .getViewAsVisibleContigs(true)));
4133 } catch (Exception e)
4135 jalview.bin.Cache.log
4137 "canTranslate threw an exception - please report to help@jalview.org",
4143 public void showProducts_actionPerformed(ActionEvent e)
4145 // /////////////////////////////
4146 // Collect Data to be translated/transferred
4148 SequenceI[] selection = viewport.getSequenceSelection();
4149 AlignmentI al = null;
4152 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4153 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4154 viewport.getAlignment().getDataset());
4155 } catch (Exception ex)
4158 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4165 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4166 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4170 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4171 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4172 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4176 public void showTranslation_actionPerformed(ActionEvent e)
4178 // /////////////////////////////
4179 // Collect Data to be translated/transferred
4181 SequenceI[] selection = viewport.getSequenceSelection();
4182 String[] seqstring = viewport.getViewAsString(true);
4183 AlignmentI al = null;
4186 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4187 viewport.getViewAsVisibleContigs(true), viewport
4188 .getGapCharacter(), viewport.alignment
4189 .getAlignmentAnnotation(), viewport.alignment
4190 .getWidth(), viewport.getAlignment().getDataset());
4191 } catch (Exception ex)
4194 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4201 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4202 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4206 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4207 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4208 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4213 * Try to load a features file onto the alignment.
4216 * contents or path to retrieve file
4218 * access mode of file (see jalview.io.AlignFile)
4219 * @return true if features file was parsed corectly.
4221 public boolean parseFeaturesFile(String file, String type)
4223 boolean featuresFile = false;
4226 featuresFile = new FeaturesFile(file, type).parse(viewport.alignment
4227 .getDataset(), alignPanel.seqPanel.seqCanvas
4228 .getFeatureRenderer().featureColours, false);
4229 } catch (Exception ex)
4231 ex.printStackTrace();
4236 viewport.showSequenceFeatures = true;
4237 showSeqFeatures.setSelected(true);
4238 if (alignPanel.seqPanel.seqCanvas.fr != null)
4240 // update the min/max ranges where necessary
4241 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4243 if (featureSettings != null)
4245 featureSettings.setTableData();
4247 alignPanel.paintAlignment(true);
4250 return featuresFile;
4253 public void dragEnter(DropTargetDragEvent evt)
4257 public void dragExit(DropTargetEvent evt)
4261 public void dragOver(DropTargetDragEvent evt)
4265 public void dropActionChanged(DropTargetDragEvent evt)
4269 public void drop(DropTargetDropEvent evt)
4271 Transferable t = evt.getTransferable();
4272 java.util.List files = null;
4276 DataFlavor uriListFlavor = new DataFlavor(
4277 "text/uri-list;class=java.lang.String");
4278 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4280 // Works on Windows and MacOSX
4281 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4282 files = (java.util.List) t
4283 .getTransferData(DataFlavor.javaFileListFlavor);
4285 else if (t.isDataFlavorSupported(uriListFlavor))
4287 // This is used by Unix drag system
4288 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4289 String data = (String) t.getTransferData(uriListFlavor);
4290 files = new java.util.ArrayList(1);
4291 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4292 data, "\r\n"); st.hasMoreTokens();)
4294 String s = st.nextToken();
4295 if (s.startsWith("#"))
4297 // the line is a comment (as per the RFC 2483)
4301 java.net.URI uri = new java.net.URI(s);
4302 // check to see if we can handle this kind of URI
4303 if (uri.getScheme().toLowerCase().startsWith("http"))
4305 files.add(uri.toString());
4309 // otherwise preserve old behaviour: catch all for file objects
4310 java.io.File file = new java.io.File(uri);
4311 files.add(file.toString());
4315 } catch (Exception e)
4317 e.printStackTrace();
4324 for (int i = 0; i < files.size(); i++)
4326 loadJalviewDataFile(files.get(i).toString());
4328 } catch (Exception ex)
4330 ex.printStackTrace();
4336 * Attempt to load a "dropped" file or URL string: First by testing whether
4337 * it's and Annotation file, then a JNet file, and finally a features file. If
4338 * all are false then the user may have dropped an alignment file onto this
4342 * either a filename or a URL string.
4344 public void loadJalviewDataFile(String file)
4348 String protocol = jalview.io.FormatAdapter.FILE;
4349 String f = file.toLowerCase();
4350 if (f.indexOf("http:") == 0 || f.indexOf("https:") == 0
4351 || f.indexOf("file:") == 0)
4353 protocol = jalview.io.FormatAdapter.URL;
4356 boolean isAnnotation = new AnnotationFile().readAnnotationFile(
4357 viewport.alignment, file, protocol);
4361 // try to see if its a JNet 'concise' style annotation file *before* we
4362 // try to parse it as a features file
4363 String format = new IdentifyFile().Identify(file, protocol);
4364 if (format.equalsIgnoreCase("JnetFile"))
4366 jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
4368 new JnetAnnotationMaker().add_annotation(predictions, viewport
4369 .getAlignment(), 0, false);
4370 isAnnotation = true;
4374 // try to parse it as a features file
4375 boolean isGroupsFile = parseFeaturesFile(file, protocol);
4376 // if it wasn't a features file then we just treat it as a general
4377 // alignment file to load into the current view.
4380 new FileLoader().LoadFile(viewport, file, protocol, format);
4384 alignPanel.paintAlignment(true);
4391 alignPanel.adjustAnnotationHeight();
4392 viewport.updateSequenceIdColours();
4393 buildSortByAnnotationScoresMenu();
4394 alignPanel.paintAlignment(true);
4396 } catch (Exception ex)
4398 ex.printStackTrace();
4402 public void tabSelectionChanged(int index)
4406 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
4407 viewport = alignPanel.av;
4408 setMenusFromViewport(viewport);
4412 public void tabbedPane_mousePressed(MouseEvent e)
4414 if (SwingUtilities.isRightMouseButton(e))
4416 String reply = JOptionPane.showInternalInputDialog(this,
4417 "Enter View Name", "Edit View Name",
4418 JOptionPane.QUESTION_MESSAGE);
4422 viewport.viewName = reply;
4423 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4428 public AlignViewport getCurrentView()
4434 * Open the dialog for regex description parsing.
4436 protected void extractScores_actionPerformed(ActionEvent e)
4438 ParseProperties pp = new jalview.analysis.ParseProperties(
4439 viewport.alignment);
4440 // TODO: verify regex and introduce GUI dialog for version 2.5
4441 // if (pp.getScoresFromDescription("col", "score column ",
4442 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4444 if (pp.getScoresFromDescription("description column",
4445 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4447 buildSortByAnnotationScoresMenu();
4455 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4458 protected void showDbRefs_actionPerformed(ActionEvent e)
4460 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
4466 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4469 protected void showNpFeats_actionPerformed(ActionEvent e)
4471 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
4475 * find the viewport amongst the tabs in this alignment frame and close that
4480 public boolean closeView(AlignViewport av)
4484 this.closeMenuItem_actionPerformed(false);
4487 Component[] comp = tabbedPane.getComponents();
4488 for (int i = 0; comp != null && i < comp.length; i++)
4490 if (comp[i] instanceof AlignmentPanel)
4492 if (((AlignmentPanel) comp[i]).av == av)
4495 closeView((AlignmentPanel) comp[i]);
4503 protected void build_fetchdbmenu(JMenu webService)
4505 // Temporary hack - DBRef Fetcher always top level ws entry.
4506 // TODO We probably want to store a sequence database checklist in
4507 // preferences and have checkboxes.. rather than individual sources selected
4509 JMenu rfetch = new JMenu("Fetch DB References");
4511 .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
4512 webService.add(rfetch);
4514 JMenuItem fetchr = new JMenuItem("Standard Databases");
4516 .setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
4517 fetchr.addActionListener(new ActionListener()
4520 public void actionPerformed(ActionEvent e)
4522 new Thread(new Runnable()
4527 new jalview.ws.DBRefFetcher(alignPanel.av
4528 .getSequenceSelection(), alignPanel.alignFrame)
4529 .fetchDBRefs(false);
4537 JMenu dfetch = new JMenu();
4539 jalview.ws.SequenceFetcher sf = SequenceFetcher
4540 .getSequenceFetcherSingleton(this);
4541 String[] otherdb = sf.getOrderedSupportedSources();
4542 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4543 // jalview.util.QuickSort.sort(otherdb, otherdb);
4544 int comp = 0, mcomp = 15;
4545 String mname = null;
4546 if (otherdb != null && otherdb.length > 0)
4548 for (int i = 0; i < otherdb.length; i++)
4550 String dbname = sf.getSourceProxy(otherdb[i]).getDbName();
4553 mname = "from '" + dbname + "'";
4555 fetchr = new JMenuItem(otherdb[i]);
4556 final String[] dassource = new String[]
4558 fetchr.addActionListener(new ActionListener()
4561 public void actionPerformed(ActionEvent e)
4563 new Thread(new Runnable()
4568 new jalview.ws.DBRefFetcher(alignPanel.av
4569 .getSequenceSelection(), alignPanel.alignFrame,
4570 dassource).fetchDBRefs(false);
4576 fetchr.setToolTipText("Retrieve from " + dbname);
4578 if (comp++ == mcomp || i == (otherdb.length - 1))
4580 dfetch.setText(mname + " to '" + dbname + "'");
4582 dfetch = new JMenu();
4591 * Left justify the whole alignment.
4593 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
4595 AlignmentI al = viewport.getAlignment();
4597 viewport.firePropertyChange("alignment", null, al);
4601 * Right justify the whole alignment.
4603 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
4605 AlignmentI al = viewport.getAlignment();
4607 viewport.firePropertyChange("alignment", null, al);
4610 public void setShowSeqFeatures(boolean b)
4612 showSeqFeatures.setSelected(true);
4613 viewport.setShowSequenceFeatures(true);
4620 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
4621 * awt.event.ActionEvent)
4623 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
4625 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
4626 alignPanel.paintAlignment(true);
4633 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
4636 protected void showGroupConsensus_actionPerformed(ActionEvent e)
4638 viewport.setShowGroupConsensus(showGroupConsensus.getState());
4639 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4647 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
4648 * .event.ActionEvent)
4650 protected void showGroupConservation_actionPerformed(ActionEvent e)
4652 viewport.setShowGroupConservation(showGroupConservation.getState());
4653 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4660 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
4661 * .event.ActionEvent)
4663 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
4665 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
4666 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4673 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
4674 * .event.ActionEvent)
4676 protected void showSequenceLogo_actionPerformed(ActionEvent e)
4678 viewport.setShowSequenceLogo(showSequenceLogo.getState());
4679 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4682 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
4684 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4691 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
4692 * .event.ActionEvent)
4694 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
4696 if (viewport.getSelectionGroup() != null)
4698 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
4699 viewport.getSequenceSelection(), viewport.getAlignmentView(
4700 true).getSequenceStrings(viewport.getGapCharacter()),
4701 viewport.alignment.getGroups());
4702 viewport.alignment.deleteAllGroups();
4703 viewport.sequenceColours = null;
4704 viewport.setSelectionGroup(null);
4705 // set view properties for each group
4706 for (int g = 0; g < gps.length; g++)
4708 gps[g].setShowNonconserved(viewport.getShowUnconserved());
4709 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
4710 viewport.alignment.addGroup(gps[g]);
4711 Color col = new Color((int) (Math.random() * 255), (int) (Math
4712 .random() * 255), (int) (Math.random() * 255));
4713 col = col.brighter();
4714 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
4715 .hasMoreElements(); viewport.setSequenceColour(
4716 (SequenceI) sq.nextElement(), col))
4719 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
4720 alignPanel.updateAnnotation();
4721 alignPanel.paintAlignment(true);
4726 class PrintThread extends Thread
4730 public PrintThread(AlignmentPanel ap)
4735 static PageFormat pf;
4739 PrinterJob printJob = PrinterJob.getPrinterJob();
4743 printJob.setPrintable(ap, pf);
4747 printJob.setPrintable(ap);
4750 if (printJob.printDialog())
4755 } catch (Exception PrintException)
4757 PrintException.printStackTrace();