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.commands.*;
34 import jalview.datamodel.*;
36 import jalview.jbgui.*;
37 import jalview.schemes.*;
39 import jalview.ws.jws2.Jws2Discoverer;
47 public class AlignFrame extends GAlignFrame implements DropTargetListener,
52 public static final int DEFAULT_WIDTH = 700;
55 public static final int DEFAULT_HEIGHT = 500;
57 public AlignmentPanel alignPanel;
59 AlignViewport viewport;
61 Vector alignPanels = new Vector();
64 * Last format used to load or save alignments in this window
66 String currentFileFormat = null;
69 * Current filename for this alignment
71 String fileName = null;
74 * Creates a new AlignFrame object with specific width and height.
80 public AlignFrame(AlignmentI al, int width, int height)
82 this(al, null, width, height);
86 * Creates a new AlignFrame object with specific width, height and
92 * @param sequenceSetId
94 public AlignFrame(AlignmentI al, int width, int height,
97 this(al, null, width, height, sequenceSetId);
101 * Creates a new AlignFrame object with specific width, height and
107 * @param sequenceSetId
110 public AlignFrame(AlignmentI al, int width, int height,
111 String sequenceSetId, String viewId)
113 this(al, null, width, height, sequenceSetId, viewId);
117 * new alignment window with hidden columns
121 * @param hiddenColumns
122 * ColumnSelection or null
124 * Width of alignment frame
128 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
129 int width, int height)
131 this(al, hiddenColumns, width, height, null);
135 * Create alignment frame for al with hiddenColumns, a specific width and
136 * height, and specific sequenceId
139 * @param hiddenColumns
142 * @param sequenceSetId
145 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
146 int width, int height, String sequenceSetId)
148 this(al, hiddenColumns, width, height, sequenceSetId, null);
152 * Create alignment frame for al with hiddenColumns, a specific width and
153 * height, and specific sequenceId
156 * @param hiddenColumns
159 * @param sequenceSetId
164 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
165 int width, int height, String sequenceSetId, String viewId)
167 setSize(width, height);
168 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
170 alignPanel = new AlignmentPanel(this, viewport);
172 if (al.getDataset() == null)
177 addAlignmentPanel(alignPanel, true);
182 * Make a new AlignFrame from exisiting alignmentPanels
189 public AlignFrame(AlignmentPanel ap)
193 addAlignmentPanel(ap, false);
198 * initalise the alignframe from the underlying viewport data and the
203 if (viewport.conservation == null)
205 BLOSUM62Colour.setEnabled(false);
206 conservationMenuItem.setEnabled(false);
207 modifyConservation.setEnabled(false);
208 // PIDColour.setEnabled(false);
209 // abovePIDThreshold.setEnabled(false);
210 // modifyPID.setEnabled(false);
213 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
216 if (sortby.equals("Id"))
218 sortIDMenuItem_actionPerformed(null);
220 else if (sortby.equals("Pairwise Identity"))
222 sortPairwiseMenuItem_actionPerformed(null);
225 if (Desktop.desktop != null)
227 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
228 addServiceListeners();
229 setGUINucleotide(viewport.alignment.isNucleotide());
232 setMenusFromViewport(viewport);
233 buildSortByAnnotationScoresMenu();
234 if (viewport.wrapAlignment)
236 wrapMenuItem_actionPerformed(null);
239 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
241 this.overviewMenuItem_actionPerformed(null);
249 * Change the filename and format for the alignment, and enable the 'reload'
250 * button functionality.
257 public void setFileName(String file, String format)
260 currentFileFormat = format;
261 reload.setEnabled(true);
264 void addKeyListener()
266 addKeyListener(new KeyAdapter()
268 public void keyPressed(KeyEvent evt)
270 if (viewport.cursorMode
271 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
272 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
273 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
274 && Character.isDigit(evt.getKeyChar()))
275 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
277 switch (evt.getKeyCode())
280 case 27: // escape key
281 deselectAllSequenceMenuItem_actionPerformed(null);
285 case KeyEvent.VK_DOWN:
286 if (evt.isAltDown() || !viewport.cursorMode)
287 moveSelectedSequences(false);
288 if (viewport.cursorMode)
289 alignPanel.seqPanel.moveCursor(0, 1);
293 if (evt.isAltDown() || !viewport.cursorMode)
294 moveSelectedSequences(true);
295 if (viewport.cursorMode)
296 alignPanel.seqPanel.moveCursor(0, -1);
300 case KeyEvent.VK_LEFT:
301 if (evt.isAltDown() || !viewport.cursorMode)
302 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
304 alignPanel.seqPanel.moveCursor(-1, 0);
308 case KeyEvent.VK_RIGHT:
309 if (evt.isAltDown() || !viewport.cursorMode)
310 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
312 alignPanel.seqPanel.moveCursor(1, 0);
315 case KeyEvent.VK_SPACE:
316 if (viewport.cursorMode)
318 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
319 || evt.isShiftDown() || evt.isAltDown());
323 case KeyEvent.VK_DELETE:
324 case KeyEvent.VK_BACK_SPACE:
325 if (!viewport.cursorMode)
327 cut_actionPerformed(null);
331 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
332 || evt.isShiftDown() || evt.isAltDown());
338 if (viewport.cursorMode)
340 alignPanel.seqPanel.setCursorRow();
344 if (viewport.cursorMode && !evt.isControlDown())
346 alignPanel.seqPanel.setCursorColumn();
350 if (viewport.cursorMode)
352 alignPanel.seqPanel.setCursorPosition();
356 case KeyEvent.VK_ENTER:
357 case KeyEvent.VK_COMMA:
358 if (viewport.cursorMode)
360 alignPanel.seqPanel.setCursorRowAndColumn();
365 if (viewport.cursorMode)
367 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
371 if (viewport.cursorMode)
373 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
378 viewport.cursorMode = !viewport.cursorMode;
379 statusBar.setText("Keyboard editing mode is "
380 + (viewport.cursorMode ? "on" : "off"));
381 if (viewport.cursorMode)
383 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
384 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
386 alignPanel.seqPanel.seqCanvas.repaint();
392 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
393 java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
395 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
397 javax.help.HelpBroker hb = hs.createHelpBroker();
398 hb.setCurrentID("home");
399 hb.setDisplayed(true);
400 } catch (Exception ex)
402 ex.printStackTrace();
407 boolean toggleSeqs = !evt.isControlDown();
408 boolean toggleCols = !evt.isShiftDown();
409 toggleHiddenRegions(toggleSeqs, toggleCols);
412 case KeyEvent.VK_PAGE_UP:
413 if (viewport.wrapAlignment)
415 alignPanel.scrollUp(true);
419 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
420 - viewport.endSeq + viewport.startSeq);
423 case KeyEvent.VK_PAGE_DOWN:
424 if (viewport.wrapAlignment)
426 alignPanel.scrollUp(false);
430 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
431 + viewport.endSeq - viewport.startSeq);
437 public void keyReleased(KeyEvent evt)
439 switch (evt.getKeyCode())
441 case KeyEvent.VK_LEFT:
442 if (evt.isAltDown() || !viewport.cursorMode)
443 viewport.firePropertyChange("alignment", null, viewport
444 .getAlignment().getSequences());
447 case KeyEvent.VK_RIGHT:
448 if (evt.isAltDown() || !viewport.cursorMode)
449 viewport.firePropertyChange("alignment", null, viewport
450 .getAlignment().getSequences());
457 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
459 ap.alignFrame = this;
461 alignPanels.addElement(ap);
463 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
465 int aSize = alignPanels.size();
467 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
469 if (aSize == 1 && ap.av.viewName == null)
471 this.getContentPane().add(ap, BorderLayout.CENTER);
477 setInitialTabVisible();
480 expandViews.setEnabled(true);
481 gatherViews.setEnabled(true);
482 tabbedPane.addTab(ap.av.viewName, ap);
484 ap.setVisible(false);
491 ap.av.alignment.padGaps();
493 ap.av.updateConservation(ap);
494 ap.av.updateConsensus(ap);
498 public void setInitialTabVisible()
500 expandViews.setEnabled(true);
501 gatherViews.setEnabled(true);
502 tabbedPane.setVisible(true);
503 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
504 tabbedPane.addTab(first.av.viewName, first);
505 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
508 public AlignViewport getViewport()
513 /* Set up intrinsic listeners for dynamically generated GUI bits. */
514 private void addServiceListeners()
516 final java.beans.PropertyChangeListener thisListener;
517 // Do this once to get current state
518 BuildWebServiceMenu();
520 .addPropertyChangeListener(thisListener = new java.beans.PropertyChangeListener()
522 public void propertyChange(PropertyChangeEvent evt)
524 // System.out.println("Discoverer property change.");
525 if (evt.getPropertyName().equals("services"))
527 // System.out.println("Rebuilding web service menu");
528 BuildWebServiceMenu();
533 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
535 public void internalFrameClosed(
536 javax.swing.event.InternalFrameEvent evt)
538 // System.out.println("deregistering discoverer listener");
539 Desktop.discoverer.removePropertyChangeListener(thisListener);
540 closeMenuItem_actionPerformed(true);
545 public void setGUINucleotide(boolean nucleotide)
547 showTranslation.setVisible(nucleotide);
548 conservationMenuItem.setEnabled(!nucleotide);
549 modifyConservation.setEnabled(!nucleotide);
550 showGroupConservation.setEnabled(!nucleotide);
551 // Remember AlignFrame always starts as protein
554 calculateMenu.remove(calculateMenu.getItemCount() - 2);
559 * set up menus for the currently viewport. This may be called after any
560 * operation that affects the data in the current view (selection changed,
561 * etc) to update the menus to reflect the new state.
563 public void setMenusForViewport()
565 setMenusFromViewport(viewport);
569 * Need to call this method when tabs are selected for multiple views, or when
570 * loading from Jalview2XML.java
575 void setMenusFromViewport(AlignViewport av)
577 padGapsMenuitem.setSelected(av.padGaps);
578 colourTextMenuItem.setSelected(av.showColourText);
579 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
580 conservationMenuItem.setSelected(av.getConservationSelected());
581 seqLimits.setSelected(av.getShowJVSuffix());
582 idRightAlign.setSelected(av.rightAlignIds);
583 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
584 renderGapsMenuItem.setSelected(av.renderGaps);
585 wrapMenuItem.setSelected(av.wrapAlignment);
586 scaleAbove.setVisible(av.wrapAlignment);
587 scaleLeft.setVisible(av.wrapAlignment);
588 scaleRight.setVisible(av.wrapAlignment);
589 annotationPanelMenuItem.setState(av.showAnnotation);
590 viewBoxesMenuItem.setSelected(av.showBoxes);
591 viewTextMenuItem.setSelected(av.showText);
592 showUnconservedMenuItem.setSelected(av.showUnconserved);
593 showGroupConsensus.setSelected(av.showGroupConsensus);
594 showGroupConservation.setSelected(av.showGroupConservation);
595 showConsensusHistogram.setSelected(av.showConsensusHistogram);
596 showSequenceLogo.setSelected(av.showSequenceLogo);
597 setColourSelected(ColourSchemeProperty.getColourName(av
598 .getGlobalColourScheme()));
600 showSeqFeatures.setSelected(av.showSequenceFeatures);
601 hiddenMarkers.setState(av.showHiddenMarkers);
602 applyToAllGroups.setState(av.colourAppliesToAllGroups);
603 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
604 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
606 setShowProductsEnabled();
611 Hashtable progressBars, progressBarHandlers;
616 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
618 public void setProgressBar(String message, long id)
620 if (progressBars == null)
622 progressBars = new Hashtable();
623 progressBarHandlers = new Hashtable();
626 JPanel progressPanel;
627 Long lId = new Long(id);
628 GridLayout layout = (GridLayout) statusPanel.getLayout();
629 if (progressBars.get(lId) != null)
631 progressPanel = (JPanel) progressBars.get(new Long(id));
632 statusPanel.remove(progressPanel);
633 progressBars.remove(lId);
634 progressPanel = null;
637 statusBar.setText(message);
639 if (progressBarHandlers.contains(lId))
641 progressBarHandlers.remove(lId);
643 layout.setRows(layout.getRows() - 1);
647 progressPanel = new JPanel(new BorderLayout(10, 5));
649 JProgressBar progressBar = new JProgressBar();
650 progressBar.setIndeterminate(true);
652 progressPanel.add(new JLabel(message), BorderLayout.WEST);
653 progressPanel.add(progressBar, BorderLayout.CENTER);
655 layout.setRows(layout.getRows() + 1);
656 statusPanel.add(progressPanel);
658 progressBars.put(lId, progressPanel);
661 setMenusForViewport();
665 public void registerHandler(final long id,
666 final IProgressIndicatorHandler handler)
668 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
671 "call setProgressBar before registering the progress bar's handler.");
673 progressBarHandlers.put(new Long(id), handler);
674 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
675 if (handler.canCancel())
677 JButton cancel = new JButton("Cancel");
678 final IProgressIndicator us = this;
679 cancel.addActionListener(new ActionListener()
682 public void actionPerformed(ActionEvent e)
684 handler.cancelActivity(id);
685 us.setProgressBar("Cancelled "
686 + ((JLabel) progressPanel.getComponent(0)).getText(), id);
689 progressPanel.add(cancel, BorderLayout.EAST);
695 * @return true if any progress bars are still active
697 public boolean operationInProgress()
699 if (progressBars != null && progressBars.size() > 0)
707 * Added so Castor Mapping file can obtain Jalview Version
709 public String getVersion()
711 return jalview.bin.Cache.getProperty("VERSION");
714 public FeatureRenderer getFeatureRenderer()
716 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
719 public void fetchSequence_actionPerformed(ActionEvent e)
721 new SequenceFetcher(this);
724 public void addFromFile_actionPerformed(ActionEvent e)
726 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
729 public void reload_actionPerformed(ActionEvent e)
731 if (fileName != null)
733 // TODO: work out how to recover feature settings for correct view(s) when
735 if (currentFileFormat.equals("Jalview"))
737 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
738 for (int i = 0; i < frames.length; i++)
740 if (frames[i] instanceof AlignFrame && frames[i] != this
741 && ((AlignFrame) frames[i]).fileName.equals(fileName))
745 frames[i].setSelected(true);
746 Desktop.instance.closeAssociatedWindows();
747 } catch (java.beans.PropertyVetoException ex)
753 Desktop.instance.closeAssociatedWindows();
755 FileLoader loader = new FileLoader();
756 String protocol = fileName.startsWith("http:") ? "URL" : "File";
757 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
761 Rectangle bounds = this.getBounds();
763 FileLoader loader = new FileLoader();
764 String protocol = fileName.startsWith("http:") ? "URL" : "File";
765 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
766 protocol, currentFileFormat);
768 newframe.setBounds(bounds);
769 if (featureSettings != null && featureSettings.isShowing())
771 final Rectangle fspos = featureSettings.frame.getBounds();
772 // TODO: need a 'show feature settings' function that takes bounds -
773 // need to refactor Desktop.addFrame
774 newframe.featureSettings_actionPerformed(null);
775 final FeatureSettings nfs = newframe.featureSettings;
776 SwingUtilities.invokeLater(new Runnable()
780 nfs.frame.setBounds(fspos);
783 this.featureSettings.close();
784 this.featureSettings = null;
786 this.closeMenuItem_actionPerformed(true);
791 public void addFromText_actionPerformed(ActionEvent e)
793 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
796 public void addFromURL_actionPerformed(ActionEvent e)
798 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
801 public void save_actionPerformed(ActionEvent e)
804 || (currentFileFormat == null || !jalview.io.FormatAdapter
805 .isValidIOFormat(currentFileFormat, true))
806 || fileName.startsWith("http"))
808 saveAs_actionPerformed(null);
812 saveAlignment(fileName, currentFileFormat);
822 public void saveAs_actionPerformed(ActionEvent e)
824 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
825 .getProperty("LAST_DIRECTORY"),
826 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
827 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
828 currentFileFormat, false);
830 chooser.setFileView(new JalviewFileView());
831 chooser.setDialogTitle("Save Alignment to file");
832 chooser.setToolTipText("Save");
834 int value = chooser.showSaveDialog(this);
836 if (value == JalviewFileChooser.APPROVE_OPTION)
838 currentFileFormat = chooser.getSelectedFormat();
839 if (currentFileFormat == null)
841 JOptionPane.showInternalMessageDialog(Desktop.desktop,
842 "You must select a file format before saving!",
843 "File format not specified", JOptionPane.WARNING_MESSAGE);
844 value = chooser.showSaveDialog(this);
848 fileName = chooser.getSelectedFile().getPath();
850 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
853 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
854 if (currentFileFormat.indexOf(" ") > -1)
856 currentFileFormat = currentFileFormat.substring(0,
857 currentFileFormat.indexOf(" "));
859 saveAlignment(fileName, currentFileFormat);
863 public boolean saveAlignment(String file, String format)
865 boolean success = true;
867 if (format.equalsIgnoreCase("Jalview"))
869 String shortName = title;
871 if (shortName.indexOf(java.io.File.separatorChar) > -1)
873 shortName = shortName.substring(shortName
874 .lastIndexOf(java.io.File.separatorChar) + 1);
877 success = new Jalview2XML().SaveAlignment(this, file, shortName);
879 statusBar.setText("Successfully saved to file: " + fileName + " in "
880 + format + " format.");
885 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
887 warningMessage("Cannot save file " + fileName + " using format "
888 + format, "Alignment output format not supported");
889 saveAs_actionPerformed(null);
890 // JBPNote need to have a raise_gui flag here
894 String[] omitHidden = null;
896 if (viewport.hasHiddenColumns)
898 int reply = JOptionPane
899 .showInternalConfirmDialog(
901 "The Alignment contains hidden columns."
902 + "\nDo you want to save only the visible alignment?",
903 "Save / Omit Hidden Columns",
904 JOptionPane.YES_NO_OPTION,
905 JOptionPane.QUESTION_MESSAGE);
907 if (reply == JOptionPane.YES_OPTION)
909 omitHidden = viewport.getViewAsString(false);
912 FormatAdapter f = new FormatAdapter();
913 String output = f.formatSequences(format,
914 (Alignment) viewport.alignment, // class cast exceptions will
915 // occur in the distant future
916 omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
926 java.io.PrintWriter out = new java.io.PrintWriter(
927 new java.io.FileWriter(file));
932 statusBar.setText("Successfully saved to file: " + fileName
933 + " in " + format + " format.");
934 } catch (Exception ex)
937 ex.printStackTrace();
944 JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
945 + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
951 private void warningMessage(String warning, String title)
953 if (new jalview.util.Platform().isHeadless())
955 System.err.println("Warning: " + title + "\nWarning: " + warning);
960 JOptionPane.showInternalMessageDialog(this, warning, title,
961 JOptionPane.WARNING_MESSAGE);
972 protected void outputText_actionPerformed(ActionEvent e)
974 String[] omitHidden = null;
976 if (viewport.hasHiddenColumns)
978 int reply = JOptionPane
979 .showInternalConfirmDialog(
981 "The Alignment contains hidden columns."
982 + "\nDo you want to output only the visible alignment?",
983 "Save / Omit Hidden Columns",
984 JOptionPane.YES_NO_OPTION,
985 JOptionPane.QUESTION_MESSAGE);
987 if (reply == JOptionPane.YES_OPTION)
989 omitHidden = viewport.getViewAsString(false);
993 CutAndPasteTransfer cap = new CutAndPasteTransfer();
994 cap.setForInput(null);
995 Desktop.addInternalFrame(cap, "Alignment output - "
996 + e.getActionCommand(), 600, 500);
998 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
999 viewport.alignment, omitHidden, viewport.colSel));
1008 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1010 new HTMLOutput(alignPanel, alignPanel.seqPanel.seqCanvas
1011 .getSequenceRenderer(), alignPanel.seqPanel.seqCanvas
1012 .getFeatureRenderer());
1015 public void createImageMap(File file, String image)
1017 alignPanel.makePNGImageMap(file, image);
1026 public void createPNG(File f)
1028 alignPanel.makePNG(f);
1037 public void createEPS(File f)
1039 alignPanel.makeEPS(f);
1042 public void pageSetup_actionPerformed(ActionEvent e)
1044 PrinterJob printJob = PrinterJob.getPrinterJob();
1045 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1054 public void printMenuItem_actionPerformed(ActionEvent e)
1056 // Putting in a thread avoids Swing painting problems
1057 PrintThread thread = new PrintThread(alignPanel);
1061 public void exportFeatures_actionPerformed(ActionEvent e)
1063 new AnnotationExporter().exportFeatures(alignPanel);
1066 public void exportAnnotations_actionPerformed(ActionEvent e)
1068 new AnnotationExporter().exportAnnotations(alignPanel,
1069 viewport.showAnnotation ? viewport.alignment
1070 .getAlignmentAnnotation() : null, viewport.alignment
1072 ((Alignment) viewport.alignment).alignmentProperties);
1075 public void associatedData_actionPerformed(ActionEvent e)
1077 // Pick the tree file
1078 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
1079 .getProperty("LAST_DIRECTORY"));
1080 chooser.setFileView(new JalviewFileView());
1081 chooser.setDialogTitle("Load Jalview Annotations or Features File");
1082 chooser.setToolTipText("Load Jalview Annotations / Features file");
1084 int value = chooser.showOpenDialog(null);
1086 if (value == JalviewFileChooser.APPROVE_OPTION)
1088 String choice = chooser.getSelectedFile().getPath();
1089 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1090 loadJalviewDataFile(choice);
1096 * Close the current view or all views in the alignment frame. If the frame
1097 * only contains one view then the alignment will be removed from memory.
1099 * @param closeAllTabs
1101 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1103 if (alignPanels != null && alignPanels.size() < 2)
1105 closeAllTabs = true;
1110 if (alignPanels != null)
1114 if (this.isClosed())
1116 // really close all the windows - otherwise wait till
1117 // setClosed(true) is called
1118 for (int i = 0; i < alignPanels.size(); i++)
1120 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1127 closeView(alignPanel);
1133 this.setClosed(true);
1135 } catch (Exception ex)
1137 ex.printStackTrace();
1142 * close alignPanel2 and shuffle tabs appropriately.
1144 * @param alignPanel2
1146 public void closeView(AlignmentPanel alignPanel2)
1148 int index = tabbedPane.getSelectedIndex();
1149 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1150 alignPanels.removeElement(alignPanel2);
1152 // if (viewport == alignPanel2.av)
1156 alignPanel2.closePanel();
1159 tabbedPane.removeTabAt(closedindex);
1160 tabbedPane.validate();
1162 if (index > closedindex || index == tabbedPane.getTabCount())
1164 // modify currently selected tab index if necessary.
1168 this.tabSelectionChanged(index);
1174 void updateEditMenuBar()
1177 if (viewport.historyList.size() > 0)
1179 undoMenuItem.setEnabled(true);
1180 CommandI command = (CommandI) viewport.historyList.peek();
1181 undoMenuItem.setText("Undo " + command.getDescription());
1185 undoMenuItem.setEnabled(false);
1186 undoMenuItem.setText("Undo");
1189 if (viewport.redoList.size() > 0)
1191 redoMenuItem.setEnabled(true);
1193 CommandI command = (CommandI) viewport.redoList.peek();
1194 redoMenuItem.setText("Redo " + command.getDescription());
1198 redoMenuItem.setEnabled(false);
1199 redoMenuItem.setText("Redo");
1203 public void addHistoryItem(CommandI command)
1205 if (command.getSize() > 0)
1207 viewport.historyList.push(command);
1208 viewport.redoList.clear();
1209 updateEditMenuBar();
1210 viewport.hasHiddenColumns = (viewport.colSel != null
1211 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1212 .getHiddenColumns().size() > 0);
1218 * @return alignment objects for all views
1220 AlignmentI[] getViewAlignments()
1222 if (alignPanels != null)
1224 Enumeration e = alignPanels.elements();
1225 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1226 for (int i = 0; e.hasMoreElements(); i++)
1228 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1232 if (viewport != null)
1234 return new AlignmentI[]
1235 { viewport.alignment };
1246 protected void undoMenuItem_actionPerformed(ActionEvent e)
1248 if (viewport.historyList.empty())
1250 CommandI command = (CommandI) viewport.historyList.pop();
1251 viewport.redoList.push(command);
1252 command.undoCommand(getViewAlignments());
1254 AlignViewport originalSource = getOriginatingSource(command);
1255 updateEditMenuBar();
1257 if (originalSource != null)
1259 originalSource.hasHiddenColumns = (viewport.colSel != null
1260 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1261 .getHiddenColumns().size() > 0);
1262 originalSource.firePropertyChange("alignment", null,
1263 originalSource.alignment.getSequences());
1273 protected void redoMenuItem_actionPerformed(ActionEvent e)
1275 if (viewport.redoList.size() < 1)
1280 CommandI command = (CommandI) viewport.redoList.pop();
1281 viewport.historyList.push(command);
1282 command.doCommand(getViewAlignments());
1284 AlignViewport originalSource = getOriginatingSource(command);
1285 updateEditMenuBar();
1287 if (originalSource != null)
1289 originalSource.hasHiddenColumns = (viewport.colSel != null
1290 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1291 .getHiddenColumns().size() > 0);
1292 originalSource.firePropertyChange("alignment", null,
1293 originalSource.alignment.getSequences());
1297 AlignViewport getOriginatingSource(CommandI command)
1299 AlignViewport originalSource = null;
1300 // For sequence removal and addition, we need to fire
1301 // the property change event FROM the viewport where the
1302 // original alignment was altered
1303 AlignmentI al = null;
1304 if (command instanceof EditCommand)
1306 EditCommand editCommand = (EditCommand) command;
1307 al = editCommand.getAlignment();
1308 Vector comps = (Vector) PaintRefresher.components.get(viewport
1309 .getSequenceSetId());
1311 for (int i = 0; i < comps.size(); i++)
1313 if (comps.elementAt(i) instanceof AlignmentPanel)
1315 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
1317 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1324 if (originalSource == null)
1326 // The original view is closed, we must validate
1327 // the current view against the closed view first
1330 PaintRefresher.validateSequences(al, viewport.alignment);
1333 originalSource = viewport;
1336 return originalSource;
1345 public void moveSelectedSequences(boolean up)
1347 SequenceGroup sg = viewport.getSelectionGroup();
1356 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1358 SequenceI seq = viewport.alignment.getSequenceAt(i);
1360 if (!sg.getSequences(null).contains(seq))
1365 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1367 if (sg.getSequences(null).contains(temp))
1372 viewport.alignment.getSequences().setElementAt(temp, i);
1373 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1378 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1380 SequenceI seq = viewport.alignment.getSequenceAt(i);
1382 if (!sg.getSequences(null).contains(seq))
1387 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1389 if (sg.getSequences(null).contains(temp))
1394 viewport.alignment.getSequences().setElementAt(temp, i);
1395 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1399 alignPanel.paintAlignment(true);
1402 synchronized void slideSequences(boolean right, int size)
1404 Vector sg = new Vector();
1405 if (viewport.cursorMode)
1407 sg.addElement(viewport.alignment
1408 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1410 else if (viewport.getSelectionGroup() != null
1411 && viewport.getSelectionGroup().getSize() != viewport.alignment
1414 sg = viewport.getSelectionGroup().getSequences(
1415 viewport.hiddenRepSequences);
1423 Vector invertGroup = new Vector();
1425 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1427 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
1428 invertGroup.add(viewport.alignment.getSequenceAt(i));
1431 SequenceI[] seqs1 = new SequenceI[sg.size()];
1432 for (int i = 0; i < sg.size(); i++)
1433 seqs1[i] = (SequenceI) sg.elementAt(i);
1435 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1436 for (int i = 0; i < invertGroup.size(); i++)
1437 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1439 SlideSequencesCommand ssc;
1441 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1442 size, viewport.getGapCharacter());
1444 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1445 size, viewport.getGapCharacter());
1447 int groupAdjustment = 0;
1448 if (ssc.getGapsInsertedBegin() && right)
1450 if (viewport.cursorMode)
1451 alignPanel.seqPanel.moveCursor(size, 0);
1453 groupAdjustment = size;
1455 else if (!ssc.getGapsInsertedBegin() && !right)
1457 if (viewport.cursorMode)
1458 alignPanel.seqPanel.moveCursor(-size, 0);
1460 groupAdjustment = -size;
1463 if (groupAdjustment != 0)
1465 viewport.getSelectionGroup().setStartRes(
1466 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1467 viewport.getSelectionGroup().setEndRes(
1468 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1471 boolean appendHistoryItem = false;
1472 if (viewport.historyList != null && viewport.historyList.size() > 0
1473 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1475 appendHistoryItem = ssc
1476 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1480 if (!appendHistoryItem)
1481 addHistoryItem(ssc);
1492 protected void copy_actionPerformed(ActionEvent e)
1495 if (viewport.getSelectionGroup() == null)
1499 // TODO: preserve the ordering of displayed alignment annotation in any
1500 // internal paste (particularly sequence associated annotation)
1501 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1502 String[] omitHidden = null;
1504 if (viewport.hasHiddenColumns)
1506 omitHidden = viewport.getViewAsString(true);
1509 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1512 StringSelection ss = new StringSelection(output);
1516 jalview.gui.Desktop.internalCopy = true;
1517 // Its really worth setting the clipboard contents
1518 // to empty before setting the large StringSelection!!
1519 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
1520 new StringSelection(""), null);
1522 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1524 } catch (OutOfMemoryError er)
1526 new OOMWarning("copying region", er);
1530 Vector hiddenColumns = null;
1531 if (viewport.hasHiddenColumns)
1533 hiddenColumns = new Vector();
1534 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1535 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1538 int[] region = (int[]) viewport.getColumnSelection()
1539 .getHiddenColumns().elementAt(i);
1541 hiddenColumns.addElement(new int[]
1542 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1546 Desktop.jalviewClipboard = new Object[]
1547 { seqs, viewport.alignment.getDataset(), hiddenColumns };
1548 statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
1557 protected void pasteNew_actionPerformed(ActionEvent e)
1568 protected void pasteThis_actionPerformed(ActionEvent e)
1574 * Paste contents of Jalview clipboard
1576 * @param newAlignment
1577 * true to paste to a new alignment, otherwise add to this.
1579 void paste(boolean newAlignment)
1581 boolean externalPaste = true;
1584 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1585 Transferable contents = c.getContents(this);
1587 if (contents == null)
1595 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1596 if (str.length() < 1)
1601 format = new IdentifyFile().Identify(str, "Paste");
1603 } catch (OutOfMemoryError er)
1605 new OOMWarning("Out of memory pasting sequences!!", er);
1609 SequenceI[] sequences;
1610 boolean annotationAdded = false;
1611 AlignmentI alignment = null;
1613 if (Desktop.jalviewClipboard != null)
1615 // The clipboard was filled from within Jalview, we must use the
1617 // And dataset from the copied alignment
1618 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1619 // be doubly sure that we create *new* sequence objects.
1620 sequences = new SequenceI[newseq.length];
1621 for (int i = 0; i < newseq.length; i++)
1623 sequences[i] = new Sequence(newseq[i]);
1625 alignment = new Alignment(sequences);
1626 externalPaste = false;
1630 // parse the clipboard as an alignment.
1631 alignment = new FormatAdapter().readFile(str, "Paste", format);
1632 sequences = alignment.getSequencesArray();
1640 if (Desktop.jalviewClipboard != null)
1642 // dataset is inherited
1643 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1647 // new dataset is constructed
1648 alignment.setDataset(null);
1650 alwidth = alignment.getWidth() + 1;
1654 AlignmentI pastedal = alignment; // preserve pasted alignment object
1655 // Add pasted sequences and dataset into existing alignment.
1656 alignment = viewport.getAlignment();
1657 alwidth = alignment.getWidth() + 1;
1658 // decide if we need to import sequences from an existing dataset
1659 boolean importDs = Desktop.jalviewClipboard != null
1660 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1661 // importDs==true instructs us to copy over new dataset sequences from
1662 // an existing alignment
1663 Vector newDs = (importDs) ? new Vector() : null; // used to create
1664 // minimum dataset set
1666 for (int i = 0; i < sequences.length; i++)
1670 newDs.addElement(null);
1672 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1674 if (importDs && ds != null)
1676 if (!newDs.contains(ds))
1678 newDs.setElementAt(ds, i);
1679 ds = new Sequence(ds);
1680 // update with new dataset sequence
1681 sequences[i].setDatasetSequence(ds);
1685 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1690 // copy and derive new dataset sequence
1691 sequences[i] = sequences[i].deriveSequence();
1692 alignment.getDataset().addSequence(
1693 sequences[i].getDatasetSequence());
1694 // TODO: avoid creation of duplicate dataset sequences with a
1695 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1697 alignment.addSequence(sequences[i]); // merges dataset
1701 newDs.clear(); // tidy up
1703 if (pastedal.getAlignmentAnnotation() != null)
1705 // Add any annotation attached to alignment.
1706 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1707 for (int i = 0; i < alann.length; i++)
1709 annotationAdded = true;
1710 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1712 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1713 newann.padAnnotation(alwidth);
1714 alignment.addAnnotation(newann);
1724 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1725 sequences, 0, alignment.getWidth(), alignment));
1727 // Add any annotations attached to sequences
1728 for (int i = 0; i < sequences.length; i++)
1730 if (sequences[i].getAnnotation() != null)
1732 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1734 annotationAdded = true;
1735 sequences[i].getAnnotation()[a].adjustForAlignment();
1736 sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1737 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1742 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1749 // propagate alignment changed.
1750 viewport.setEndSeq(alignment.getHeight());
1751 if (annotationAdded)
1753 // Duplicate sequence annotation in all views.
1754 AlignmentI[] alview = this.getViewAlignments();
1755 for (int i = 0; i < sequences.length; i++)
1757 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1760 for (int avnum = 0; avnum < alview.length; avnum++)
1762 if (alview[avnum] != alignment)
1764 // duplicate in a view other than the one with input focus
1765 int avwidth = alview[avnum].getWidth() + 1;
1766 // this relies on sann being preserved after we
1767 // modify the sequence's annotation array for each duplication
1768 for (int a = 0; a < sann.length; a++)
1770 AlignmentAnnotation newann = new AlignmentAnnotation(
1772 sequences[i].addAlignmentAnnotation(newann);
1773 newann.padAnnotation(avwidth);
1774 alview[avnum].addAnnotation(newann); // annotation was
1775 // duplicated earlier
1776 alview[avnum].setAnnotationIndex(newann, a);
1781 buildSortByAnnotationScoresMenu();
1783 viewport.firePropertyChange("alignment", null, alignment
1789 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
1791 String newtitle = new String("Copied sequences");
1793 if (Desktop.jalviewClipboard != null
1794 && Desktop.jalviewClipboard[2] != null)
1796 Vector hc = (Vector) Desktop.jalviewClipboard[2];
1797 for (int i = 0; i < hc.size(); i++)
1799 int[] region = (int[]) hc.elementAt(i);
1800 af.viewport.hideColumns(region[0], region[1]);
1804 // >>>This is a fix for the moment, until a better solution is
1806 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
1808 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1810 // TODO: maintain provenance of an alignment, rather than just make the
1811 // title a concatenation of operations.
1814 if (title.startsWith("Copied sequences"))
1820 newtitle = newtitle.concat("- from " + title);
1825 newtitle = new String("Pasted sequences");
1828 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1833 } catch (Exception ex)
1835 ex.printStackTrace();
1836 System.out.println("Exception whilst pasting: " + ex);
1837 // could be anything being pasted in here
1848 protected void cut_actionPerformed(ActionEvent e)
1850 copy_actionPerformed(null);
1851 delete_actionPerformed(null);
1860 protected void delete_actionPerformed(ActionEvent evt)
1863 SequenceGroup sg = viewport.getSelectionGroup();
1869 Vector seqs = new Vector();
1871 for (int i = 0; i < sg.getSize(); i++)
1873 seq = sg.getSequenceAt(i);
1874 seqs.addElement(seq);
1877 // If the cut affects all sequences, remove highlighted columns
1878 if (sg.getSize() == viewport.alignment.getHeight())
1880 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1881 sg.getEndRes() + 1);
1884 SequenceI[] cut = new SequenceI[seqs.size()];
1885 for (int i = 0; i < seqs.size(); i++)
1887 cut[i] = (SequenceI) seqs.elementAt(i);
1891 * //ADD HISTORY ITEM
1893 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1894 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1895 viewport.alignment));
1897 viewport.setSelectionGroup(null);
1898 viewport.sendSelection();
1899 viewport.alignment.deleteGroup(sg);
1901 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1903 if (viewport.getAlignment().getHeight() < 1)
1907 this.setClosed(true);
1908 } catch (Exception ex)
1920 protected void deleteGroups_actionPerformed(ActionEvent e)
1922 viewport.alignment.deleteAllGroups();
1923 viewport.sequenceColours = null;
1924 viewport.setSelectionGroup(null);
1925 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1926 alignPanel.updateAnnotation();
1927 alignPanel.paintAlignment(true);
1936 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1938 SequenceGroup sg = new SequenceGroup();
1940 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1942 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1945 sg.setEndRes(viewport.alignment.getWidth() - 1);
1946 viewport.setSelectionGroup(sg);
1947 viewport.sendSelection();
1948 alignPanel.paintAlignment(true);
1949 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1958 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1960 if (viewport.cursorMode)
1962 alignPanel.seqPanel.keyboardNo1 = null;
1963 alignPanel.seqPanel.keyboardNo2 = null;
1965 viewport.setSelectionGroup(null);
1966 viewport.getColumnSelection().clear();
1967 viewport.setSelectionGroup(null);
1968 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1969 alignPanel.idPanel.idCanvas.searchResults = null;
1970 alignPanel.paintAlignment(true);
1971 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1980 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1982 SequenceGroup sg = viewport.getSelectionGroup();
1986 selectAllSequenceMenuItem_actionPerformed(null);
1991 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1993 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1996 alignPanel.paintAlignment(true);
1997 viewport.sendSelection();
1998 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2001 public void invertColSel_actionPerformed(ActionEvent e)
2003 viewport.invertColumnSelection();
2004 alignPanel.paintAlignment(true);
2013 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2015 trimAlignment(true);
2024 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2026 trimAlignment(false);
2029 void trimAlignment(boolean trimLeft)
2031 ColumnSelection colSel = viewport.getColumnSelection();
2034 if (colSel.size() > 0)
2038 column = colSel.getMin();
2042 column = colSel.getMax();
2046 if (viewport.getSelectionGroup() != null)
2048 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2049 viewport.hiddenRepSequences);
2053 seqs = viewport.alignment.getSequencesArray();
2056 TrimRegionCommand trimRegion;
2059 trimRegion = new TrimRegionCommand("Remove Left",
2060 TrimRegionCommand.TRIM_LEFT, seqs, column,
2061 viewport.alignment, viewport.colSel,
2062 viewport.selectionGroup);
2063 viewport.setStartRes(0);
2067 trimRegion = new TrimRegionCommand("Remove Right",
2068 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2069 viewport.alignment, viewport.colSel,
2070 viewport.selectionGroup);
2073 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2075 addHistoryItem(trimRegion);
2077 Vector groups = viewport.alignment.getGroups();
2079 for (int i = 0; i < groups.size(); i++)
2081 SequenceGroup sg = (SequenceGroup) groups.get(i);
2083 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2084 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2086 viewport.alignment.deleteGroup(sg);
2090 viewport.firePropertyChange("alignment", null, viewport
2091 .getAlignment().getSequences());
2101 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2103 int start = 0, end = viewport.alignment.getWidth() - 1;
2106 if (viewport.getSelectionGroup() != null)
2108 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2109 viewport.hiddenRepSequences);
2110 start = viewport.getSelectionGroup().getStartRes();
2111 end = viewport.getSelectionGroup().getEndRes();
2115 seqs = viewport.alignment.getSequencesArray();
2118 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2119 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
2121 addHistoryItem(removeGapCols);
2123 statusBar.setText("Removed " + removeGapCols.getSize()
2124 + " empty columns.");
2126 // This is to maintain viewport position on first residue
2127 // of first sequence
2128 SequenceI seq = viewport.alignment.getSequenceAt(0);
2129 int startRes = seq.findPosition(viewport.startRes);
2130 // ShiftList shifts;
2131 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2132 // edit.alColumnChanges=shifts.getInverse();
2133 // if (viewport.hasHiddenColumns)
2134 // viewport.getColumnSelection().compensateForEdits(shifts);
2135 viewport.setStartRes(seq.findIndex(startRes) - 1);
2136 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2147 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2149 int start = 0, end = viewport.alignment.getWidth() - 1;
2152 if (viewport.getSelectionGroup() != null)
2154 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2155 viewport.hiddenRepSequences);
2156 start = viewport.getSelectionGroup().getStartRes();
2157 end = viewport.getSelectionGroup().getEndRes();
2161 seqs = viewport.alignment.getSequencesArray();
2164 // This is to maintain viewport position on first residue
2165 // of first sequence
2166 SequenceI seq = viewport.alignment.getSequenceAt(0);
2167 int startRes = seq.findPosition(viewport.startRes);
2169 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2170 viewport.alignment));
2172 viewport.setStartRes(seq.findIndex(startRes) - 1);
2174 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2185 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2187 viewport.padGaps = padGapsMenuitem.isSelected();
2188 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2194 // if (justifySeqs>0)
2196 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2208 public void findMenuItem_actionPerformed(ActionEvent e)
2213 public void newView_actionPerformed(ActionEvent e)
2215 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2218 newap.av.gatherViewsHere = false;
2220 if (viewport.viewName == null)
2222 viewport.viewName = "Original";
2225 newap.av.historyList = viewport.historyList;
2226 newap.av.redoList = viewport.redoList;
2228 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2229 String newViewName = "View " + index;
2231 Vector comps = (Vector) PaintRefresher.components.get(viewport
2232 .getSequenceSetId());
2233 Vector existingNames = new Vector();
2234 for (int i = 0; i < comps.size(); i++)
2236 if (comps.elementAt(i) instanceof AlignmentPanel)
2238 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2239 if (!existingNames.contains(ap.av.viewName))
2241 existingNames.addElement(ap.av.viewName);
2246 while (existingNames.contains(newViewName))
2248 newViewName = "View " + (++index);
2251 newap.av.viewName = newViewName;
2253 addAlignmentPanel(newap, true);
2255 if (alignPanels.size() == 2)
2257 viewport.gatherViewsHere = true;
2259 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2262 public void expandViews_actionPerformed(ActionEvent e)
2264 Desktop.instance.explodeViews(this);
2267 public void gatherViews_actionPerformed(ActionEvent e)
2269 Desktop.instance.gatherViews(this);
2278 public void font_actionPerformed(ActionEvent e)
2280 new FontChooser(alignPanel);
2289 protected void seqLimit_actionPerformed(ActionEvent e)
2291 viewport.setShowJVSuffix(seqLimits.isSelected());
2293 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2294 .calculateIdWidth());
2295 alignPanel.paintAlignment(true);
2298 public void idRightAlign_actionPerformed(ActionEvent e)
2300 viewport.rightAlignIds = idRightAlign.isSelected();
2301 alignPanel.paintAlignment(true);
2304 public void centreColumnLabels_actionPerformed(ActionEvent e)
2306 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2307 alignPanel.paintAlignment(true);
2313 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2315 protected void followHighlight_actionPerformed()
2317 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2319 alignPanel.scrollToPosition(
2320 alignPanel.seqPanel.seqCanvas.searchResults, false);
2330 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2332 viewport.setColourText(colourTextMenuItem.isSelected());
2333 alignPanel.paintAlignment(true);
2342 public void wrapMenuItem_actionPerformed(ActionEvent e)
2344 scaleAbove.setVisible(wrapMenuItem.isSelected());
2345 scaleLeft.setVisible(wrapMenuItem.isSelected());
2346 scaleRight.setVisible(wrapMenuItem.isSelected());
2347 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2348 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2351 public void showAllSeqs_actionPerformed(ActionEvent e)
2353 viewport.showAllHiddenSeqs();
2356 public void showAllColumns_actionPerformed(ActionEvent e)
2358 viewport.showAllHiddenColumns();
2362 public void hideSelSequences_actionPerformed(ActionEvent e)
2364 viewport.hideAllSelectedSeqs();
2365 alignPanel.paintAlignment(true);
2369 * called by key handler and the hide all/show all menu items
2374 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2377 boolean hide = false;
2378 SequenceGroup sg = viewport.getSelectionGroup();
2379 if (!toggleSeqs && !toggleCols)
2381 // Hide everything by the current selection - this is a hack - we do the
2382 // invert and then hide
2383 // first check that there will be visible columns after the invert.
2384 if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
2385 .getSelected().size() > 0)
2386 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2389 // now invert the sequence set, if required - empty selection implies
2390 // that no hiding is required.
2393 invertSequenceMenuItem_actionPerformed(null);
2394 sg = viewport.getSelectionGroup();
2398 viewport.expandColSelection(sg, true);
2399 // finally invert the column selection and get the new sequence
2401 invertColSel_actionPerformed(null);
2408 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
2410 hideSelSequences_actionPerformed(null);
2413 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
2415 showAllSeqs_actionPerformed(null);
2421 if (viewport.colSel.getSelected().size() > 0)
2423 hideSelColumns_actionPerformed(null);
2426 viewport.selectionGroup = sg;
2431 showAllColumns_actionPerformed(null);
2440 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2441 * event.ActionEvent)
2443 public void hideAllButSelection_actionPerformed(ActionEvent e)
2445 toggleHiddenRegions(false, false);
2452 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2455 public void hideAllSelection_actionPerformed(ActionEvent e)
2457 SequenceGroup sg = viewport.getSelectionGroup();
2458 viewport.expandColSelection(sg, false);
2459 viewport.hideAllSelectedSeqs();
2460 viewport.hideSelectedColumns();
2461 alignPanel.paintAlignment(true);
2468 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2471 public void showAllhidden_actionPerformed(ActionEvent e)
2473 viewport.showAllHiddenColumns();
2474 viewport.showAllHiddenSeqs();
2475 alignPanel.paintAlignment(true);
2478 public void hideSelColumns_actionPerformed(ActionEvent e)
2480 viewport.hideSelectedColumns();
2481 alignPanel.paintAlignment(true);
2484 public void hiddenMarkers_actionPerformed(ActionEvent e)
2486 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2496 protected void scaleAbove_actionPerformed(ActionEvent e)
2498 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2499 alignPanel.paintAlignment(true);
2508 protected void scaleLeft_actionPerformed(ActionEvent e)
2510 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2511 alignPanel.paintAlignment(true);
2520 protected void scaleRight_actionPerformed(ActionEvent e)
2522 viewport.setScaleRightWrapped(scaleRight.isSelected());
2523 alignPanel.paintAlignment(true);
2532 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2534 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2535 alignPanel.paintAlignment(true);
2544 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2546 viewport.setShowText(viewTextMenuItem.isSelected());
2547 alignPanel.paintAlignment(true);
2556 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2558 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2559 alignPanel.paintAlignment(true);
2562 public FeatureSettings featureSettings;
2564 public void featureSettings_actionPerformed(ActionEvent e)
2566 if (featureSettings != null)
2568 featureSettings.close();
2569 featureSettings = null;
2571 if (!showSeqFeatures.isSelected())
2573 // make sure features are actually displayed
2574 showSeqFeatures.setSelected(true);
2575 showSeqFeatures_actionPerformed(null);
2577 featureSettings = new FeatureSettings(this);
2581 * Set or clear 'Show Sequence Features'
2586 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2588 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2589 alignPanel.paintAlignment(true);
2590 if (alignPanel.getOverviewPanel() != null)
2592 alignPanel.getOverviewPanel().updateOverviewImage();
2597 * Set or clear 'Show Sequence Features'
2602 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2604 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2606 if (viewport.getShowSequenceFeaturesHeight())
2608 // ensure we're actually displaying features
2609 viewport.setShowSequenceFeatures(true);
2610 showSeqFeatures.setSelected(true);
2612 alignPanel.paintAlignment(true);
2613 if (alignPanel.getOverviewPanel() != null)
2615 alignPanel.getOverviewPanel().updateOverviewImage();
2625 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2627 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2628 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2631 public void alignmentProperties()
2633 JEditorPane editPane = new JEditorPane("text/html", "");
2634 editPane.setEditable(false);
2635 StringBuffer contents = new StringBuffer("<html>");
2638 int min = Integer.MAX_VALUE, max = 0;
2639 for (int i = 0; i < viewport.alignment.getHeight(); i++)
2641 int size = viewport.alignment.getSequenceAt(i).getEnd()
2642 - viewport.alignment.getSequenceAt(i).getStart();
2649 avg = avg / (float) viewport.alignment.getHeight();
2651 contents.append("<br>Sequences: " + viewport.alignment.getHeight());
2652 contents.append("<br>Minimum Sequence Length: " + min);
2653 contents.append("<br>Maximum Sequence Length: " + max);
2654 contents.append("<br>Average Length: " + (int) avg);
2656 if (((Alignment) viewport.alignment).getProperties() != null)
2658 Hashtable props = ((Alignment) viewport.alignment).getProperties();
2659 Enumeration en = props.keys();
2660 contents.append("<br><br><table border=\"1\">");
2661 while (en.hasMoreElements())
2663 String key = en.nextElement().toString();
2664 StringBuffer val = new StringBuffer();
2665 String vals = props.get(key).toString();
2669 npos = vals.indexOf("\n", pos);
2672 val.append(vals.substring(pos));
2676 val.append(vals.substring(pos, npos));
2680 } while (npos != -1);
2682 .append("<tr><td>" + key + "</td><td>" + val + "</td></tr>");
2684 contents.append("</table>");
2686 editPane.setText(contents.toString() + "</html>");
2687 JInternalFrame frame = new JInternalFrame();
2688 frame.getContentPane().add(new JScrollPane(editPane));
2690 Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
2691 + getTitle(), 500, 400);
2700 public void overviewMenuItem_actionPerformed(ActionEvent e)
2702 if (alignPanel.overviewPanel != null)
2707 JInternalFrame frame = new JInternalFrame();
2708 OverviewPanel overview = new OverviewPanel(alignPanel);
2709 frame.setContentPane(overview);
2710 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(), frame
2711 .getWidth(), frame.getHeight());
2713 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2715 .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2717 public void internalFrameClosed(
2718 javax.swing.event.InternalFrameEvent evt)
2720 alignPanel.setOverviewPanel(null);
2724 alignPanel.setOverviewPanel(overview);
2727 public void textColour_actionPerformed(ActionEvent e)
2729 new TextColourChooser().chooseColour(alignPanel, null);
2738 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2749 public void clustalColour_actionPerformed(ActionEvent e)
2751 changeColour(new ClustalxColourScheme(
2752 viewport.alignment.getSequences(), viewport.alignment
2762 public void zappoColour_actionPerformed(ActionEvent e)
2764 changeColour(new ZappoColourScheme());
2773 public void taylorColour_actionPerformed(ActionEvent e)
2775 changeColour(new TaylorColourScheme());
2784 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2786 changeColour(new HydrophobicColourScheme());
2795 public void helixColour_actionPerformed(ActionEvent e)
2797 changeColour(new HelixColourScheme());
2806 public void strandColour_actionPerformed(ActionEvent e)
2808 changeColour(new StrandColourScheme());
2817 public void turnColour_actionPerformed(ActionEvent e)
2819 changeColour(new TurnColourScheme());
2828 public void buriedColour_actionPerformed(ActionEvent e)
2830 changeColour(new BuriedColourScheme());
2839 public void nucleotideColour_actionPerformed(ActionEvent e)
2841 changeColour(new NucleotideColourScheme());
2844 public void annotationColour_actionPerformed(ActionEvent e)
2846 new AnnotationColourChooser(viewport, alignPanel);
2855 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2857 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2866 public void changeColour(ColourSchemeI cs)
2872 if (viewport.getAbovePIDThreshold())
2874 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2877 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2879 viewport.setGlobalColourScheme(cs);
2883 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2886 if (viewport.getConservationSelected())
2889 Alignment al = (Alignment) viewport.alignment;
2890 Conservation c = new Conservation("All",
2891 ResidueProperties.propHash, 3, al.getSequences(), 0, al
2895 c.verdict(false, viewport.ConsPercGaps);
2897 cs.setConservation(c);
2899 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
2904 cs.setConservation(null);
2907 cs.setConsensus(viewport.hconsensus);
2910 viewport.setGlobalColourScheme(cs);
2912 if (viewport.getColourAppliesToAllGroups())
2914 Vector groups = viewport.alignment.getGroups();
2916 for (int i = 0; i < groups.size(); i++)
2918 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2926 if (cs instanceof ClustalxColourScheme)
2928 sg.cs = new ClustalxColourScheme(sg
2929 .getSequences(viewport.hiddenRepSequences), sg.getWidth());
2931 else if (cs instanceof UserColourScheme)
2933 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
2939 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2940 } catch (Exception ex)
2945 if (viewport.getAbovePIDThreshold()
2946 || cs instanceof PIDColourScheme
2947 || cs instanceof Blosum62ColourScheme)
2949 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2951 sg.cs.setConsensus(AAFrequency.calculate(sg
2952 .getSequences(viewport.hiddenRepSequences), sg
2953 .getStartRes(), sg.getEndRes() + 1));
2957 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2960 if (viewport.getConservationSelected())
2962 Conservation c = new Conservation("Group",
2963 ResidueProperties.propHash, 3, sg
2964 .getSequences(viewport.hiddenRepSequences), sg
2965 .getStartRes(), sg.getEndRes() + 1);
2967 c.verdict(false, viewport.ConsPercGaps);
2968 sg.cs.setConservation(c);
2972 sg.cs.setConservation(null);
2977 if (alignPanel.getOverviewPanel() != null)
2979 alignPanel.getOverviewPanel().updateOverviewImage();
2982 alignPanel.paintAlignment(true);
2991 protected void modifyPID_actionPerformed(ActionEvent e)
2993 if (viewport.getAbovePIDThreshold()
2994 && viewport.globalColourScheme != null)
2996 SliderPanel.setPIDSliderSource(alignPanel, viewport
2997 .getGlobalColourScheme(), "Background");
2998 SliderPanel.showPIDSlider();
3008 protected void modifyConservation_actionPerformed(ActionEvent e)
3010 if (viewport.getConservationSelected()
3011 && viewport.globalColourScheme != null)
3013 SliderPanel.setConservationSlider(alignPanel,
3014 viewport.globalColourScheme, "Background");
3015 SliderPanel.showConservationSlider();
3025 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3027 viewport.setConservationSelected(conservationMenuItem.isSelected());
3029 viewport.setAbovePIDThreshold(false);
3030 abovePIDThreshold.setSelected(false);
3032 changeColour(viewport.getGlobalColourScheme());
3034 modifyConservation_actionPerformed(null);
3043 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3045 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3047 conservationMenuItem.setSelected(false);
3048 viewport.setConservationSelected(false);
3050 changeColour(viewport.getGlobalColourScheme());
3052 modifyPID_actionPerformed(null);
3061 public void userDefinedColour_actionPerformed(ActionEvent e)
3063 if (e.getActionCommand().equals("User Defined..."))
3065 new UserDefinedColours(alignPanel, null);
3069 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3070 .getUserColourSchemes().get(e.getActionCommand());
3076 public void updateUserColourMenu()
3079 Component[] menuItems = colourMenu.getMenuComponents();
3080 int i, iSize = menuItems.length;
3081 for (i = 0; i < iSize; i++)
3083 if (menuItems[i].getName() != null
3084 && menuItems[i].getName().equals("USER_DEFINED"))
3086 colourMenu.remove(menuItems[i]);
3090 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3092 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3093 .getUserColourSchemes().keys();
3095 while (userColours.hasMoreElements())
3097 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3098 userColours.nextElement().toString());
3099 radioItem.setName("USER_DEFINED");
3100 radioItem.addMouseListener(new MouseAdapter()
3102 public void mousePressed(MouseEvent evt)
3104 if (evt.isControlDown()
3105 || SwingUtilities.isRightMouseButton(evt))
3108 .removeActionListener(radioItem.getActionListeners()[0]);
3110 int option = JOptionPane.showInternalConfirmDialog(
3111 jalview.gui.Desktop.desktop,
3112 "Remove from default list?",
3113 "Remove user defined colour",
3114 JOptionPane.YES_NO_OPTION);
3115 if (option == JOptionPane.YES_OPTION)
3117 jalview.gui.UserDefinedColours
3118 .removeColourFromDefaults(radioItem.getText());
3119 colourMenu.remove(radioItem);
3123 radioItem.addActionListener(new ActionListener()
3125 public void actionPerformed(ActionEvent evt)
3127 userDefinedColour_actionPerformed(evt);
3134 radioItem.addActionListener(new ActionListener()
3136 public void actionPerformed(ActionEvent evt)
3138 userDefinedColour_actionPerformed(evt);
3142 colourMenu.insert(radioItem, 15);
3143 colours.add(radioItem);
3154 public void PIDColour_actionPerformed(ActionEvent e)
3156 changeColour(new PIDColourScheme());
3165 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3167 changeColour(new Blosum62ColourScheme());
3176 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3178 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3179 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3180 .getAlignment().getSequenceAt(0), null);
3181 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3182 viewport.alignment));
3183 alignPanel.paintAlignment(true);
3192 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3194 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3195 AlignmentSorter.sortByID(viewport.getAlignment());
3196 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
3197 alignPanel.paintAlignment(true);
3206 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3208 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3209 AlignmentSorter.sortByLength(viewport.getAlignment());
3210 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3211 viewport.alignment));
3212 alignPanel.paintAlignment(true);
3221 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3223 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3224 AlignmentSorter.sortByGroup(viewport.getAlignment());
3225 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3226 viewport.alignment));
3228 alignPanel.paintAlignment(true);
3237 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3239 new RedundancyPanel(alignPanel, this);
3248 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3250 if ((viewport.getSelectionGroup() == null)
3251 || (viewport.getSelectionGroup().getSize() < 2))
3253 JOptionPane.showInternalMessageDialog(this,
3254 "You must select at least 2 sequences.", "Invalid Selection",
3255 JOptionPane.WARNING_MESSAGE);
3259 JInternalFrame frame = new JInternalFrame();
3260 frame.setContentPane(new PairwiseAlignPanel(viewport));
3261 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
3271 public void PCAMenuItem_actionPerformed(ActionEvent e)
3273 if (((viewport.getSelectionGroup() != null)
3274 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3275 .getSelectionGroup().getSize() > 0))
3276 || (viewport.getAlignment().getHeight() < 4))
3278 JOptionPane.showInternalMessageDialog(this,
3279 "Principal component analysis must take\n"
3280 + "at least 4 input sequences.",
3281 "Sequence selection insufficient",
3282 JOptionPane.WARNING_MESSAGE);
3287 new PCAPanel(alignPanel);
3290 public void autoCalculate_actionPerformed(ActionEvent e)
3292 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3293 if (viewport.autoCalculateConsensus)
3295 viewport.firePropertyChange("alignment", null, viewport
3296 .getAlignment().getSequences());
3306 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3308 NewTreePanel("AV", "PID", "Average distance tree using PID");
3317 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3319 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3328 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3330 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3339 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3341 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3354 void NewTreePanel(String type, String pwType, String title)
3358 if (viewport.getSelectionGroup() != null)
3360 if (viewport.getSelectionGroup().getSize() < 3)
3365 "You need to have more than two sequences selected to build a tree!",
3366 "Not enough sequences", JOptionPane.WARNING_MESSAGE);
3371 SequenceGroup sg = viewport.getSelectionGroup();
3373 /* Decide if the selection is a column region */
3374 while (s < sg.getSize())
3376 if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
3382 "The selected region to create a tree may\nonly contain residues or gaps.\n"
3383 + "Try using the Pad function in the edit menu,\n"
3384 + "or one of the multiple sequence alignment web services.",
3385 "Sequences in selection are not aligned",
3386 JOptionPane.WARNING_MESSAGE);
3392 title = title + " on region";
3393 tp = new TreePanel(alignPanel, type, pwType);
3397 // are the visible sequences aligned?
3398 if (!viewport.alignment.isAligned(false))
3403 "The sequences must be aligned before creating a tree.\n"
3404 + "Try using the Pad function in the edit menu,\n"
3405 + "or one of the multiple sequence alignment web services.",
3406 "Sequences not aligned",
3407 JOptionPane.WARNING_MESSAGE);
3412 if (viewport.alignment.getHeight() < 2)
3417 tp = new TreePanel(alignPanel, type, pwType);
3422 if (viewport.viewName != null)
3424 title += viewport.viewName + " of ";
3427 title += this.title;
3429 Desktop.addInternalFrame(tp, title, 600, 500);
3440 public void addSortByOrderMenuItem(String title,
3441 final AlignmentOrder order)
3443 final JMenuItem item = new JMenuItem("by " + title);
3445 item.addActionListener(new java.awt.event.ActionListener()
3447 public void actionPerformed(ActionEvent e)
3449 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3451 // TODO: JBPNote - have to map order entries to curent SequenceI
3453 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3455 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3456 viewport.alignment));
3458 alignPanel.paintAlignment(true);
3464 * Add a new sort by annotation score menu item
3467 * the menu to add the option to
3469 * the label used to retrieve scores for each sequence on the
3472 public void addSortByAnnotScoreMenuItem(JMenu sort,
3473 final String scoreLabel)
3475 final JMenuItem item = new JMenuItem(scoreLabel);
3477 item.addActionListener(new java.awt.event.ActionListener()
3479 public void actionPerformed(ActionEvent e)
3481 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3482 AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport
3483 .getAlignment());// ,viewport.getSelectionGroup());
3484 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3485 viewport.alignment));
3486 alignPanel.paintAlignment(true);
3492 * last hash for alignment's annotation array - used to minimise cost of
3495 protected int _annotationScoreVectorHash;
3498 * search the alignment and rebuild the sort by annotation score submenu the
3499 * last alignment annotation vector hash is stored to minimize cost of
3500 * rebuilding in subsequence calls.
3503 public void buildSortByAnnotationScoresMenu()
3505 if (viewport.alignment.getAlignmentAnnotation() == null)
3510 if (viewport.alignment.getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3512 sortByAnnotScore.removeAll();
3513 // almost certainly a quicker way to do this - but we keep it simple
3514 Hashtable scoreSorts = new Hashtable();
3515 AlignmentAnnotation aann[];
3516 Enumeration sq = viewport.alignment.getSequences().elements();
3517 while (sq.hasMoreElements())
3519 aann = ((SequenceI) sq.nextElement()).getAnnotation();
3520 for (int i = 0; aann != null && i < aann.length; i++)
3522 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3524 scoreSorts.put(aann[i].label, aann[i].label);
3528 Enumeration labels = scoreSorts.keys();
3529 while (labels.hasMoreElements())
3531 addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels
3534 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3537 _annotationScoreVectorHash = viewport.alignment
3538 .getAlignmentAnnotation().hashCode();
3543 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3544 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3545 * call. Listeners are added to remove the menu item when the treePanel is
3546 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3550 * Displayed tree window.
3552 * SortBy menu item title.
3554 public void buildTreeMenu()
3556 sortByTreeMenu.removeAll();
3558 Vector comps = (Vector) PaintRefresher.components.get(viewport
3559 .getSequenceSetId());
3560 Vector treePanels = new Vector();
3561 int i, iSize = comps.size();
3562 for (i = 0; i < iSize; i++)
3564 if (comps.elementAt(i) instanceof TreePanel)
3566 treePanels.add(comps.elementAt(i));
3570 iSize = treePanels.size();
3574 sortByTreeMenu.setVisible(false);
3578 sortByTreeMenu.setVisible(true);
3580 for (i = 0; i < treePanels.size(); i++)
3582 TreePanel tp = (TreePanel) treePanels.elementAt(i);
3583 final JMenuItem item = new JMenuItem(tp.getTitle());
3584 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3585 item.addActionListener(new java.awt.event.ActionListener()
3587 public void actionPerformed(ActionEvent e)
3589 SequenceI[] oldOrder = viewport.getAlignment()
3590 .getSequencesArray();
3591 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
3593 addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
3594 viewport.alignment));
3596 alignPanel.paintAlignment(true);
3600 sortByTreeMenu.add(item);
3605 * Work out whether the whole set of sequences or just the selected set will
3606 * be submitted for multiple alignment.
3609 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3611 // Now, check we have enough sequences
3612 AlignmentView msa = null;
3614 if ((viewport.getSelectionGroup() != null)
3615 && (viewport.getSelectionGroup().getSize() > 1))
3617 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3618 // some common interface!
3620 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3621 * SequenceI[sz = seqs.getSize(false)];
3623 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3624 * seqs.getSequenceAt(i); }
3626 msa = viewport.getAlignmentView(true);
3631 * Vector seqs = viewport.getAlignment().getSequences();
3633 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3635 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3636 * seqs.elementAt(i); } }
3638 msa = viewport.getAlignmentView(false);
3644 * Decides what is submitted to a secondary structure prediction service: the
3645 * first sequence in the alignment, or in the current selection, or, if the
3646 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3647 * region or the whole alignment. (where the first sequence in the set is the
3648 * one that the prediction will be for).
3650 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3652 AlignmentView seqs = null;
3654 if ((viewport.getSelectionGroup() != null)
3655 && (viewport.getSelectionGroup().getSize() > 0))
3657 seqs = viewport.getAlignmentView(true);
3661 seqs = viewport.getAlignmentView(false);
3663 // limit sequences - JBPNote in future - could spawn multiple prediction
3665 // TODO: viewport.alignment.isAligned is a global state - the local
3666 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3667 if (!viewport.alignment.isAligned(false))
3669 seqs.setSequences(new SeqCigar[]
3670 { seqs.getSequences()[0] });
3671 // TODO: if seqs.getSequences().length>1 then should really have warned
3684 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3686 // Pick the tree file
3687 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
3688 .getProperty("LAST_DIRECTORY"));
3689 chooser.setFileView(new JalviewFileView());
3690 chooser.setDialogTitle("Select a newick-like tree file");
3691 chooser.setToolTipText("Load a tree file");
3693 int value = chooser.showOpenDialog(null);
3695 if (value == JalviewFileChooser.APPROVE_OPTION)
3697 String choice = chooser.getSelectedFile().getPath();
3698 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3699 jalview.io.NewickFile fin = null;
3702 fin = new jalview.io.NewickFile(choice, "File");
3703 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3704 } catch (Exception ex)
3706 JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3707 "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
3708 ex.printStackTrace();
3710 if (fin != null && fin.hasWarningMessage())
3712 JOptionPane.showMessageDialog(Desktop.desktop, fin
3713 .getWarningMessage(), "Possible problem with tree file",
3714 JOptionPane.WARNING_MESSAGE);
3719 public TreePanel ShowNewickTree(NewickFile nf, String title)
3721 return ShowNewickTree(nf, title, 600, 500, 4, 5);
3724 public TreePanel ShowNewickTree(NewickFile nf, String title,
3725 AlignmentView input)
3727 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
3730 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
3731 int h, int x, int y)
3733 return ShowNewickTree(nf, title, null, w, h, x, y);
3737 * Add a treeviewer for the tree extracted from a newick file object to the
3738 * current alignment view
3745 * Associated alignment input data (or null)
3754 * @return TreePanel handle
3756 public TreePanel ShowNewickTree(NewickFile nf, String title,
3757 AlignmentView input, int w, int h, int x, int y)
3759 TreePanel tp = null;
3765 if (nf.getTree() != null)
3767 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
3773 tp.setLocation(x, y);
3776 Desktop.addInternalFrame(tp, title, w, h);
3778 } catch (Exception ex)
3780 ex.printStackTrace();
3787 * Generates menu items and listener event actions for web service clients
3790 public void BuildWebServiceMenu()
3792 // TODO: add support for context dependent disabling of services based on
3793 // alignment and current selection
3794 // TODO: add additional serviceHandle parameter to specify abstract handler
3795 // class independently of AbstractName
3796 // TODO: add in rediscovery GUI function to restart discoverer
3797 // TODO: group services by location as well as function and/or introduce
3798 // object broker mechanism.
3799 if ((Discoverer.services != null) && (Discoverer.services.size() > 0))
3801 // TODO: refactor to allow list of AbstractName/Handler bindings to be
3802 // stored or retrieved from elsewhere
3803 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
3804 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
3805 Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
3806 // TODO: move GUI generation code onto service implementation - so a
3807 // client instance attaches itself to the GUI with method call like
3808 // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
3810 Vector wsmenu = new Vector();
3811 final IProgressIndicator af = this;
3814 // Add any Multiple Sequence Alignment Services
3815 final JMenu msawsmenu = new JMenu("Alignment");
3816 for (int i = 0, j = msaws.size(); i < j; i++)
3818 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
3820 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.Discoverer
3821 .getServiceClient(sh);
3822 impl.attachWSMenuEntry(msawsmenu, this);
3825 wsmenu.add(msawsmenu);
3827 if (secstrpr != null)
3829 // Add any secondary structure prediction services
3830 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
3831 for (int i = 0, j = secstrpr.size(); i < j; i++)
3833 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
3835 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.Discoverer
3836 .getServiceClient(sh);
3837 impl.attachWSMenuEntry(secstrmenu, this);
3839 wsmenu.add(secstrmenu);
3841 if (seqsrch != null)
3843 // Add any sequence search services
3844 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
3845 for (int i = 0, j = seqsrch.size(); i < j; i++)
3847 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
3849 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.Discoverer
3850 .getServiceClient(sh);
3851 impl.attachWSMenuEntry(seqsrchmenu, this);
3853 wsmenu.add(seqsrchmenu);
3855 // TODO: move into separate menu builder class.
3857 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
3858 if (jws2servs!=null && jws2servs.hasServices())
3860 JMenu jws2men = new JMenu("Jalview 2 Services");
3861 jws2servs.attachWSMenuEntry(jws2men, this);
3862 wsmenu.add(jws2men);
3865 // finally, add the whole shebang onto the webservices menu
3866 resetWebServiceMenu();
3867 for (int i = 0, j = wsmenu.size(); i < j; i++)
3869 webService.add((JMenu) wsmenu.get(i));
3874 resetWebServiceMenu();
3875 this.webService.add(this.webServiceNoServices);
3880 * empty the web service menu and add any ad-hoc functions not dynamically
3884 private void resetWebServiceMenu()
3886 webService.removeAll();
3887 build_fetchdbmenu(webService);
3888 build_urlServiceMenu(webService);
3892 * construct any groupURL type service menu entries.
3896 private void build_urlServiceMenu(JMenu webService)
3898 jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
3903 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
3904 * chooser = new JalviewFileChooser(jalview.bin.Cache.
3905 * getProperty("LAST_DIRECTORY"));
3907 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
3908 * to Vamsas file"); chooser.setToolTipText("Export");
3910 * int value = chooser.showSaveDialog(this);
3912 * if (value == JalviewFileChooser.APPROVE_OPTION) {
3913 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
3914 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
3915 * chooser.getSelectedFile().getAbsolutePath(), this); } }
3918 * prototype of an automatically enabled/disabled analysis function
3921 protected void setShowProductsEnabled()
3923 SequenceI[] selection = viewport.getSequenceSelection();
3924 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
3925 viewport.getAlignment().getDataset()))
3927 showProducts.setEnabled(true);
3932 showProducts.setEnabled(false);
3937 * search selection for sequence xRef products and build the show products
3942 * @return true if showProducts menu should be enabled.
3944 public boolean canShowProducts(SequenceI[] selection,
3945 boolean isRegionSelection, Alignment dataset)
3947 boolean showp = false;
3950 showProducts.removeAll();
3951 final boolean dna = viewport.getAlignment().isNucleotide();
3952 final Alignment ds = dataset;
3953 String[] ptypes = (selection == null || selection.length == 0) ? null
3954 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
3956 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
3957 // selection, dataset, true);
3958 final SequenceI[] sel = selection;
3959 for (int t = 0; ptypes != null && t < ptypes.length; t++)
3962 final boolean isRegSel = isRegionSelection;
3963 final AlignFrame af = this;
3964 final String source = ptypes[t];
3965 JMenuItem xtype = new JMenuItem(ptypes[t]);
3966 xtype.addActionListener(new ActionListener()
3969 public void actionPerformed(ActionEvent e)
3971 // TODO: new thread for this call with vis-delay
3972 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
3973 isRegSel, dna, source);
3977 showProducts.add(xtype);
3979 showProducts.setVisible(showp);
3980 showProducts.setEnabled(showp);
3981 } catch (Exception e)
3983 jalview.bin.Cache.log
3985 "canTranslate threw an exception - please report to help@jalview.org",
3992 protected void showProductsFor(SequenceI[] sel, Alignment ds,
3993 boolean isRegSel, boolean dna, String source)
3995 final boolean fisRegSel = isRegSel;
3996 final boolean fdna = dna;
3997 final String fsrc = source;
3998 final AlignFrame ths = this;
3999 final SequenceI[] fsel = sel;
4000 Runnable foo = new Runnable()
4005 final long sttime = System.currentTimeMillis();
4006 ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4009 Alignment ds = ths.getViewport().alignment.getDataset(); // update
4013 Alignment prods = CrossRef
4014 .findXrefSequences(fsel, fdna, fsrc, ds);
4017 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4018 for (int s = 0; s < sprods.length; s++)
4020 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4021 if (ds.getSequences() == null
4022 || !ds.getSequences().contains(
4023 sprods[s].getDatasetSequence()))
4024 ds.addSequence(sprods[s].getDatasetSequence());
4025 sprods[s].updatePDBIds();
4027 Alignment al = new Alignment(sprods);
4028 AlignedCodonFrame[] cf = prods.getCodonFrames();
4030 for (int s = 0; cf != null && s < cf.length; s++)
4032 al.addCodonFrame(cf[s]);
4035 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4037 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4038 + " for " + ((fisRegSel) ? "selected region of " : "")
4040 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4045 System.err.println("No Sequences generated for xRef type "
4048 } catch (Exception e)
4050 jalview.bin.Cache.log.error(
4051 "Exception when finding crossreferences", e);
4052 } catch (OutOfMemoryError e)
4054 new OOMWarning("whilst fetching crossreferences", e);
4057 jalview.bin.Cache.log.error("Error when finding crossreferences",
4060 ths.setProgressBar("Finished searching for sequences from " + fsrc,
4065 Thread frunner = new Thread(foo);
4069 public boolean canShowTranslationProducts(SequenceI[] selection,
4070 AlignmentI alignment)
4075 return (jalview.analysis.Dna.canTranslate(selection, viewport
4076 .getViewAsVisibleContigs(true)));
4077 } catch (Exception e)
4079 jalview.bin.Cache.log
4081 "canTranslate threw an exception - please report to help@jalview.org",
4087 public void showProducts_actionPerformed(ActionEvent e)
4089 // /////////////////////////////
4090 // Collect Data to be translated/transferred
4092 SequenceI[] selection = viewport.getSequenceSelection();
4093 AlignmentI al = null;
4096 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4097 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4098 viewport.getAlignment().getDataset());
4099 } catch (Exception ex)
4102 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4109 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4110 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4114 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4115 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4116 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4120 public void showTranslation_actionPerformed(ActionEvent e)
4122 // /////////////////////////////
4123 // Collect Data to be translated/transferred
4125 SequenceI[] selection = viewport.getSequenceSelection();
4126 String[] seqstring = viewport.getViewAsString(true);
4127 AlignmentI al = null;
4130 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4131 viewport.getViewAsVisibleContigs(true), viewport
4132 .getGapCharacter(), viewport.alignment
4133 .getAlignmentAnnotation(), viewport.alignment
4134 .getWidth(), viewport.getAlignment().getDataset());
4135 } catch (Exception ex)
4138 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4145 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4146 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4150 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4151 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4152 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4157 * Try to load a features file onto the alignment.
4160 * contents or path to retrieve file
4162 * access mode of file (see jalview.io.AlignFile)
4163 * @return true if features file was parsed corectly.
4165 public boolean parseFeaturesFile(String file, String type)
4167 boolean featuresFile = false;
4170 featuresFile = new FeaturesFile(file, type).parse(viewport.alignment
4171 .getDataset(), alignPanel.seqPanel.seqCanvas
4172 .getFeatureRenderer().featureColours, false);
4173 } catch (Exception ex)
4175 ex.printStackTrace();
4180 viewport.showSequenceFeatures = true;
4181 showSeqFeatures.setSelected(true);
4182 if (alignPanel.seqPanel.seqCanvas.fr != null)
4184 // update the min/max ranges where necessary
4185 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4187 if (featureSettings != null)
4189 featureSettings.setTableData();
4191 alignPanel.paintAlignment(true);
4194 return featuresFile;
4197 public void dragEnter(DropTargetDragEvent evt)
4201 public void dragExit(DropTargetEvent evt)
4205 public void dragOver(DropTargetDragEvent evt)
4209 public void dropActionChanged(DropTargetDragEvent evt)
4213 public void drop(DropTargetDropEvent evt)
4215 Transferable t = evt.getTransferable();
4216 java.util.List files = null;
4220 DataFlavor uriListFlavor = new DataFlavor(
4221 "text/uri-list;class=java.lang.String");
4222 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4224 // Works on Windows and MacOSX
4225 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4226 files = (java.util.List) t
4227 .getTransferData(DataFlavor.javaFileListFlavor);
4229 else if (t.isDataFlavorSupported(uriListFlavor))
4231 // This is used by Unix drag system
4232 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4233 String data = (String) t.getTransferData(uriListFlavor);
4234 files = new java.util.ArrayList(1);
4235 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4236 data, "\r\n"); st.hasMoreTokens();)
4238 String s = st.nextToken();
4239 if (s.startsWith("#"))
4241 // the line is a comment (as per the RFC 2483)
4245 java.net.URI uri = new java.net.URI(s);
4246 // check to see if we can handle this kind of URI
4247 if (uri.getScheme().toLowerCase().startsWith("http"))
4249 files.add(uri.toString());
4253 // otherwise preserve old behaviour: catch all for file objects
4254 java.io.File file = new java.io.File(uri);
4255 files.add(file.toString());
4259 } catch (Exception e)
4261 e.printStackTrace();
4268 for (int i = 0; i < files.size(); i++)
4270 loadJalviewDataFile(files.get(i).toString());
4272 } catch (Exception ex)
4274 ex.printStackTrace();
4280 * Attempt to load a "dropped" file or URL string: First by testing whether
4281 * it's and Annotation file, then a JNet file, and finally a features file. If
4282 * all are false then the user may have dropped an alignment file onto this
4286 * either a filename or a URL string.
4288 public void loadJalviewDataFile(String file)
4292 String protocol = jalview.io.FormatAdapter.FILE;
4293 String f = file.toLowerCase();
4294 if (f.indexOf("http:") == 0 || f.indexOf("https:") == 0
4295 || f.indexOf("file:") == 0)
4297 protocol = jalview.io.FormatAdapter.URL;
4300 boolean isAnnotation = new AnnotationFile().readAnnotationFile(
4301 viewport.alignment, file, protocol);
4305 // try to see if its a JNet 'concise' style annotation file *before* we
4306 // try to parse it as a features file
4307 String format = new IdentifyFile().Identify(file, protocol);
4308 if (format.equalsIgnoreCase("JnetFile"))
4310 jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
4312 new JnetAnnotationMaker().add_annotation(predictions, viewport
4313 .getAlignment(), 0, false);
4314 isAnnotation = true;
4318 // try to parse it as a features file
4319 boolean isGroupsFile = parseFeaturesFile(file, protocol);
4320 // if it wasn't a features file then we just treat it as a general
4321 // alignment file to load into the current view.
4324 new FileLoader().LoadFile(viewport, file, protocol, format);
4328 alignPanel.paintAlignment(true);
4335 alignPanel.adjustAnnotationHeight();
4336 viewport.updateSequenceIdColours();
4337 buildSortByAnnotationScoresMenu();
4338 alignPanel.paintAlignment(true);
4340 } catch (Exception ex)
4342 ex.printStackTrace();
4346 public void tabSelectionChanged(int index)
4350 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
4351 viewport = alignPanel.av;
4352 setMenusFromViewport(viewport);
4356 public void tabbedPane_mousePressed(MouseEvent e)
4358 if (SwingUtilities.isRightMouseButton(e))
4360 String reply = JOptionPane.showInternalInputDialog(this,
4361 "Enter View Name", "Edit View Name",
4362 JOptionPane.QUESTION_MESSAGE);
4366 viewport.viewName = reply;
4367 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4372 public AlignViewport getCurrentView()
4378 * Open the dialog for regex description parsing.
4380 protected void extractScores_actionPerformed(ActionEvent e)
4382 ParseProperties pp = new jalview.analysis.ParseProperties(
4383 viewport.alignment);
4384 // TODO: verify regex and introduce GUI dialog for version 2.5
4385 // if (pp.getScoresFromDescription("col", "score column ",
4386 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4388 if (pp.getScoresFromDescription("description column",
4389 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4391 buildSortByAnnotationScoresMenu();
4399 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4402 protected void showDbRefs_actionPerformed(ActionEvent e)
4404 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
4410 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4413 protected void showNpFeats_actionPerformed(ActionEvent e)
4415 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
4419 * find the viewport amongst the tabs in this alignment frame and close that
4424 public boolean closeView(AlignViewport av)
4428 this.closeMenuItem_actionPerformed(false);
4431 Component[] comp = tabbedPane.getComponents();
4432 for (int i = 0; comp != null && i < comp.length; i++)
4434 if (comp[i] instanceof AlignmentPanel)
4436 if (((AlignmentPanel) comp[i]).av == av)
4439 closeView((AlignmentPanel) comp[i]);
4447 protected void build_fetchdbmenu(JMenu webService)
4449 // Temporary hack - DBRef Fetcher always top level ws entry.
4450 // TODO We probably want to store a sequence database checklist in
4451 // preferences and have checkboxes.. rather than individual sources selected
4453 JMenu rfetch = new JMenu("Fetch DB References");
4455 .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
4456 webService.add(rfetch);
4458 JMenuItem fetchr = new JMenuItem("Standard Databases");
4460 .setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
4461 fetchr.addActionListener(new ActionListener()
4464 public void actionPerformed(ActionEvent e)
4466 new Thread(new Runnable()
4471 new jalview.ws.DBRefFetcher(alignPanel.av
4472 .getSequenceSelection(), alignPanel.alignFrame)
4473 .fetchDBRefs(false);
4481 JMenu dfetch = new JMenu();
4483 jalview.ws.SequenceFetcher sf = SequenceFetcher
4484 .getSequenceFetcherSingleton(this);
4485 String[] otherdb = sf.getOrderedSupportedSources();
4486 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4487 // jalview.util.QuickSort.sort(otherdb, otherdb);
4488 int comp = 0, mcomp = 15;
4489 String mname = null;
4490 if (otherdb != null && otherdb.length > 0)
4492 for (int i = 0; i < otherdb.length; i++)
4494 String dbname = sf.getSourceProxy(otherdb[i]).getDbName();
4497 mname = "from '" + dbname + "'";
4499 fetchr = new JMenuItem(otherdb[i]);
4500 final String[] dassource = new String[]
4502 fetchr.addActionListener(new ActionListener()
4505 public void actionPerformed(ActionEvent e)
4507 new Thread(new Runnable()
4512 new jalview.ws.DBRefFetcher(alignPanel.av
4513 .getSequenceSelection(), alignPanel.alignFrame,
4514 dassource).fetchDBRefs(false);
4520 fetchr.setToolTipText("Retrieve from " + dbname);
4522 if (comp++ == mcomp || i == (otherdb.length - 1))
4524 dfetch.setText(mname + " to '" + dbname + "'");
4526 dfetch = new JMenu();
4535 * Left justify the whole alignment.
4537 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
4539 AlignmentI al = viewport.getAlignment();
4541 viewport.firePropertyChange("alignment", null, al);
4545 * Right justify the whole alignment.
4547 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
4549 AlignmentI al = viewport.getAlignment();
4551 viewport.firePropertyChange("alignment", null, al);
4554 public void setShowSeqFeatures(boolean b)
4556 showSeqFeatures.setSelected(true);
4557 viewport.setShowSequenceFeatures(true);
4564 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
4565 * awt.event.ActionEvent)
4567 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
4569 viewport.setShowUnconserved(showUnconservedMenuItem.getState());
4570 alignPanel.paintAlignment(true);
4577 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
4580 protected void showGroupConsensus_actionPerformed(ActionEvent e)
4582 viewport.setShowGroupConsensus(showGroupConsensus.getState());
4583 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4591 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
4592 * .event.ActionEvent)
4594 protected void showGroupConservation_actionPerformed(ActionEvent e)
4596 viewport.setShowGroupConservation(showGroupConservation.getState());
4597 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4604 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
4605 * .event.ActionEvent)
4607 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
4609 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
4610 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4617 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
4618 * .event.ActionEvent)
4620 protected void showSequenceLogo_actionPerformed(ActionEvent e)
4622 viewport.setShowSequenceLogo(showSequenceLogo.getState());
4623 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4626 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
4628 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4635 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
4636 * .event.ActionEvent)
4638 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
4640 if (viewport.getSelectionGroup() != null)
4642 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
4643 viewport.getSequenceSelection(), viewport.getAlignmentView(
4644 true).getSequenceStrings(viewport.getGapCharacter()),
4645 viewport.alignment.getGroups());
4646 viewport.alignment.deleteAllGroups();
4647 viewport.sequenceColours = null;
4648 viewport.setSelectionGroup(null);
4649 // set view properties for each group
4650 for (int g = 0; g < gps.length; g++)
4652 gps[g].setShowunconserved(viewport.getShowUnconserved());
4653 gps[g].setIncludeAllConsSymbols(viewport
4654 .isIncludeAllConsensusSymbols());
4655 viewport.alignment.addGroup(gps[g]);
4656 Color col = new Color((int) (Math.random() * 255), (int) (Math
4657 .random() * 255), (int) (Math.random() * 255));
4658 col = col.brighter();
4659 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
4660 .hasMoreElements(); viewport.setSequenceColour(
4661 (SequenceI) sq.nextElement(), col))
4664 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
4665 alignPanel.updateAnnotation();
4666 alignPanel.paintAlignment(true);
4671 class PrintThread extends Thread
4675 public PrintThread(AlignmentPanel ap)
4680 static PageFormat pf;
4684 PrinterJob printJob = PrinterJob.getPrinterJob();
4688 printJob.setPrintable(ap, pf);
4692 printJob.setPrintable(ap);
4695 if (printJob.printDialog())
4700 } catch (Exception PrintException)
4702 PrintException.printStackTrace();