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.jws1.Discoverer;
40 import jalview.ws.jws2.Jws2Discoverer;
48 public class AlignFrame extends GAlignFrame implements DropTargetListener,
53 public static final int DEFAULT_WIDTH = 700;
56 public static final int DEFAULT_HEIGHT = 500;
58 public AlignmentPanel alignPanel;
60 AlignViewport viewport;
62 Vector alignPanels = new Vector();
65 * Last format used to load or save alignments in this window
67 String currentFileFormat = null;
70 * Current filename for this alignment
72 String fileName = null;
75 * Creates a new AlignFrame object with specific width and height.
81 public AlignFrame(AlignmentI al, int width, int height)
83 this(al, null, width, height);
87 * Creates a new AlignFrame object with specific width, height and
93 * @param sequenceSetId
95 public AlignFrame(AlignmentI al, int width, int height,
98 this(al, null, width, height, sequenceSetId);
102 * Creates a new AlignFrame object with specific width, height and
108 * @param sequenceSetId
111 public AlignFrame(AlignmentI al, int width, int height,
112 String sequenceSetId, String viewId)
114 this(al, null, width, height, sequenceSetId, viewId);
118 * new alignment window with hidden columns
122 * @param hiddenColumns
123 * ColumnSelection or null
125 * Width of alignment frame
129 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
130 int width, int height)
132 this(al, hiddenColumns, width, height, null);
136 * Create alignment frame for al with hiddenColumns, a specific width and
137 * height, and specific sequenceId
140 * @param hiddenColumns
143 * @param sequenceSetId
146 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
147 int width, int height, String sequenceSetId)
149 this(al, hiddenColumns, width, height, sequenceSetId, null);
153 * Create alignment frame for al with hiddenColumns, a specific width and
154 * height, and specific sequenceId
157 * @param hiddenColumns
160 * @param sequenceSetId
165 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
166 int width, int height, String sequenceSetId, String viewId)
168 setSize(width, height);
169 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
171 alignPanel = new AlignmentPanel(this, viewport);
173 if (al.getDataset() == null)
178 addAlignmentPanel(alignPanel, true);
183 * Make a new AlignFrame from exisiting alignmentPanels
190 public AlignFrame(AlignmentPanel ap)
194 addAlignmentPanel(ap, false);
199 * initalise the alignframe from the underlying viewport data and the
204 if (viewport.conservation == null)
206 BLOSUM62Colour.setEnabled(false);
207 conservationMenuItem.setEnabled(false);
208 modifyConservation.setEnabled(false);
209 // PIDColour.setEnabled(false);
210 // abovePIDThreshold.setEnabled(false);
211 // modifyPID.setEnabled(false);
214 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
217 if (sortby.equals("Id"))
219 sortIDMenuItem_actionPerformed(null);
221 else if (sortby.equals("Pairwise Identity"))
223 sortPairwiseMenuItem_actionPerformed(null);
226 if (Desktop.desktop != null)
228 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
229 addServiceListeners();
230 setGUINucleotide(viewport.alignment.isNucleotide());
233 setMenusFromViewport(viewport);
234 buildSortByAnnotationScoresMenu();
235 if (viewport.wrapAlignment)
237 wrapMenuItem_actionPerformed(null);
240 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
242 this.overviewMenuItem_actionPerformed(null);
250 * Change the filename and format for the alignment, and enable the 'reload'
251 * button functionality.
258 public void setFileName(String file, String format)
261 currentFileFormat = format;
262 reload.setEnabled(true);
265 void addKeyListener()
267 addKeyListener(new KeyAdapter()
269 public void keyPressed(KeyEvent evt)
271 if (viewport.cursorMode
272 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
273 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
274 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
275 && Character.isDigit(evt.getKeyChar()))
276 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
278 switch (evt.getKeyCode())
281 case 27: // escape key
282 deselectAllSequenceMenuItem_actionPerformed(null);
286 case KeyEvent.VK_DOWN:
287 if (evt.isAltDown() || !viewport.cursorMode)
288 moveSelectedSequences(false);
289 if (viewport.cursorMode)
290 alignPanel.seqPanel.moveCursor(0, 1);
294 if (evt.isAltDown() || !viewport.cursorMode)
295 moveSelectedSequences(true);
296 if (viewport.cursorMode)
297 alignPanel.seqPanel.moveCursor(0, -1);
301 case KeyEvent.VK_LEFT:
302 if (evt.isAltDown() || !viewport.cursorMode)
303 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
305 alignPanel.seqPanel.moveCursor(-1, 0);
309 case KeyEvent.VK_RIGHT:
310 if (evt.isAltDown() || !viewport.cursorMode)
311 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
313 alignPanel.seqPanel.moveCursor(1, 0);
316 case KeyEvent.VK_SPACE:
317 if (viewport.cursorMode)
319 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
320 || evt.isShiftDown() || evt.isAltDown());
324 case KeyEvent.VK_DELETE:
325 case KeyEvent.VK_BACK_SPACE:
326 if (!viewport.cursorMode)
328 cut_actionPerformed(null);
332 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
333 || evt.isShiftDown() || evt.isAltDown());
339 if (viewport.cursorMode)
341 alignPanel.seqPanel.setCursorRow();
345 if (viewport.cursorMode && !evt.isControlDown())
347 alignPanel.seqPanel.setCursorColumn();
351 if (viewport.cursorMode)
353 alignPanel.seqPanel.setCursorPosition();
357 case KeyEvent.VK_ENTER:
358 case KeyEvent.VK_COMMA:
359 if (viewport.cursorMode)
361 alignPanel.seqPanel.setCursorRowAndColumn();
366 if (viewport.cursorMode)
368 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
372 if (viewport.cursorMode)
374 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
379 viewport.cursorMode = !viewport.cursorMode;
380 statusBar.setText("Keyboard editing mode is "
381 + (viewport.cursorMode ? "on" : "off"));
382 if (viewport.cursorMode)
384 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
385 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
387 alignPanel.seqPanel.seqCanvas.repaint();
393 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
394 java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
396 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
398 javax.help.HelpBroker hb = hs.createHelpBroker();
399 hb.setCurrentID("home");
400 hb.setDisplayed(true);
401 } catch (Exception ex)
403 ex.printStackTrace();
408 boolean toggleSeqs = !evt.isControlDown();
409 boolean toggleCols = !evt.isShiftDown();
410 toggleHiddenRegions(toggleSeqs, toggleCols);
413 case KeyEvent.VK_PAGE_UP:
414 if (viewport.wrapAlignment)
416 alignPanel.scrollUp(true);
420 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
421 - viewport.endSeq + viewport.startSeq);
424 case KeyEvent.VK_PAGE_DOWN:
425 if (viewport.wrapAlignment)
427 alignPanel.scrollUp(false);
431 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
432 + viewport.endSeq - viewport.startSeq);
438 public void keyReleased(KeyEvent evt)
440 switch (evt.getKeyCode())
442 case KeyEvent.VK_LEFT:
443 if (evt.isAltDown() || !viewport.cursorMode)
444 viewport.firePropertyChange("alignment", null, viewport
445 .getAlignment().getSequences());
448 case KeyEvent.VK_RIGHT:
449 if (evt.isAltDown() || !viewport.cursorMode)
450 viewport.firePropertyChange("alignment", null, viewport
451 .getAlignment().getSequences());
458 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
460 ap.alignFrame = this;
462 alignPanels.addElement(ap);
464 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
466 int aSize = alignPanels.size();
468 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
470 if (aSize == 1 && ap.av.viewName == null)
472 this.getContentPane().add(ap, BorderLayout.CENTER);
478 setInitialTabVisible();
481 expandViews.setEnabled(true);
482 gatherViews.setEnabled(true);
483 tabbedPane.addTab(ap.av.viewName, ap);
485 ap.setVisible(false);
492 ap.av.alignment.padGaps();
494 ap.av.updateConservation(ap);
495 ap.av.updateConsensus(ap);
499 public void setInitialTabVisible()
501 expandViews.setEnabled(true);
502 gatherViews.setEnabled(true);
503 tabbedPane.setVisible(true);
504 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
505 tabbedPane.addTab(first.av.viewName, first);
506 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
509 public AlignViewport getViewport()
514 /* Set up intrinsic listeners for dynamically generated GUI bits. */
515 private void addServiceListeners()
517 final java.beans.PropertyChangeListener thisListener, thatListener;
518 // Do this once to get current state
519 BuildWebServiceMenu();
521 .addPropertyChangeListener(thisListener = new java.beans.PropertyChangeListener()
523 public void propertyChange(PropertyChangeEvent evt)
525 // System.out.println("Discoverer property change.");
526 if (evt.getPropertyName().equals("services"))
528 SwingUtilities.invokeLater(new Runnable()
534 System.err.println("Change support JWS1: build services again.");
535 BuildWebServiceMenu();
542 jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
543 .addPropertyChangeListener(
544 thatListener = new java.beans.PropertyChangeListener()
546 public void propertyChange(PropertyChangeEvent evt)
548 System.err.println("Change support JWS2: build services again.");
549 BuildWebServiceMenu();
552 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
554 public void internalFrameClosed(
555 javax.swing.event.InternalFrameEvent evt)
557 // System.out.println("deregistering discoverer listener");
558 Desktop.discoverer.removePropertyChangeListener(thisListener);
559 jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
560 .removePropertyChangeListener(thatListener);
561 closeMenuItem_actionPerformed(true);
566 public void setGUINucleotide(boolean nucleotide)
568 showTranslation.setVisible(nucleotide);
569 conservationMenuItem.setEnabled(!nucleotide);
570 modifyConservation.setEnabled(!nucleotide);
571 showGroupConservation.setEnabled(!nucleotide);
572 // Remember AlignFrame always starts as protein
575 calculateMenu.remove(calculateMenu.getItemCount() - 2);
580 * set up menus for the currently viewport. This may be called after any
581 * operation that affects the data in the current view (selection changed,
582 * etc) to update the menus to reflect the new state.
584 public void setMenusForViewport()
586 setMenusFromViewport(viewport);
590 * Need to call this method when tabs are selected for multiple views, or when
591 * loading from Jalview2XML.java
596 void setMenusFromViewport(AlignViewport av)
598 padGapsMenuitem.setSelected(av.padGaps);
599 colourTextMenuItem.setSelected(av.showColourText);
600 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
601 conservationMenuItem.setSelected(av.getConservationSelected());
602 seqLimits.setSelected(av.getShowJVSuffix());
603 idRightAlign.setSelected(av.rightAlignIds);
604 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
605 renderGapsMenuItem.setSelected(av.renderGaps);
606 wrapMenuItem.setSelected(av.wrapAlignment);
607 scaleAbove.setVisible(av.wrapAlignment);
608 scaleLeft.setVisible(av.wrapAlignment);
609 scaleRight.setVisible(av.wrapAlignment);
610 annotationPanelMenuItem.setState(av.showAnnotation);
611 viewBoxesMenuItem.setSelected(av.showBoxes);
612 viewTextMenuItem.setSelected(av.showText);
613 showUnconservedMenuItem.setSelected(av.showUnconserved);
614 showGroupConsensus.setSelected(av.showGroupConsensus);
615 showGroupConservation.setSelected(av.showGroupConservation);
616 showConsensusHistogram.setSelected(av.showConsensusHistogram);
617 showSequenceLogo.setSelected(av.showSequenceLogo);
618 setColourSelected(ColourSchemeProperty.getColourName(av
619 .getGlobalColourScheme()));
621 showSeqFeatures.setSelected(av.showSequenceFeatures);
622 hiddenMarkers.setState(av.showHiddenMarkers);
623 applyToAllGroups.setState(av.colourAppliesToAllGroups);
624 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
625 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
627 setShowProductsEnabled();
632 Hashtable progressBars, progressBarHandlers;
637 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
639 public void setProgressBar(String message, long id)
641 if (progressBars == null)
643 progressBars = new Hashtable();
644 progressBarHandlers = new Hashtable();
647 JPanel progressPanel;
648 Long lId = new Long(id);
649 GridLayout layout = (GridLayout) statusPanel.getLayout();
650 if (progressBars.get(lId) != null)
652 progressPanel = (JPanel) progressBars.get(new Long(id));
653 statusPanel.remove(progressPanel);
654 progressBars.remove(lId);
655 progressPanel = null;
658 statusBar.setText(message);
660 if (progressBarHandlers.contains(lId))
662 progressBarHandlers.remove(lId);
664 layout.setRows(layout.getRows() - 1);
668 progressPanel = new JPanel(new BorderLayout(10, 5));
670 JProgressBar progressBar = new JProgressBar();
671 progressBar.setIndeterminate(true);
673 progressPanel.add(new JLabel(message), BorderLayout.WEST);
674 progressPanel.add(progressBar, BorderLayout.CENTER);
676 layout.setRows(layout.getRows() + 1);
677 statusPanel.add(progressPanel);
679 progressBars.put(lId, progressPanel);
682 setMenusForViewport();
686 public void registerHandler(final long id,
687 final IProgressIndicatorHandler handler)
689 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
692 "call setProgressBar before registering the progress bar's handler.");
694 progressBarHandlers.put(new Long(id), handler);
695 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
696 if (handler.canCancel())
698 JButton cancel = new JButton("Cancel");
699 final IProgressIndicator us = this;
700 cancel.addActionListener(new ActionListener()
703 public void actionPerformed(ActionEvent e)
705 handler.cancelActivity(id);
706 us.setProgressBar("Cancelled "
707 + ((JLabel) progressPanel.getComponent(0)).getText(), id);
710 progressPanel.add(cancel, BorderLayout.EAST);
716 * @return true if any progress bars are still active
718 public boolean operationInProgress()
720 if (progressBars != null && progressBars.size() > 0)
728 * Added so Castor Mapping file can obtain Jalview Version
730 public String getVersion()
732 return jalview.bin.Cache.getProperty("VERSION");
735 public FeatureRenderer getFeatureRenderer()
737 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
740 public void fetchSequence_actionPerformed(ActionEvent e)
742 new SequenceFetcher(this);
745 public void addFromFile_actionPerformed(ActionEvent e)
747 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
750 public void reload_actionPerformed(ActionEvent e)
752 if (fileName != null)
754 // TODO: work out how to recover feature settings for correct view(s) when
756 if (currentFileFormat.equals("Jalview"))
758 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
759 for (int i = 0; i < frames.length; i++)
761 if (frames[i] instanceof AlignFrame && frames[i] != this
762 && ((AlignFrame) frames[i]).fileName.equals(fileName))
766 frames[i].setSelected(true);
767 Desktop.instance.closeAssociatedWindows();
768 } catch (java.beans.PropertyVetoException ex)
774 Desktop.instance.closeAssociatedWindows();
776 FileLoader loader = new FileLoader();
777 String protocol = fileName.startsWith("http:") ? "URL" : "File";
778 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
782 Rectangle bounds = this.getBounds();
784 FileLoader loader = new FileLoader();
785 String protocol = fileName.startsWith("http:") ? "URL" : "File";
786 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
787 protocol, currentFileFormat);
789 newframe.setBounds(bounds);
790 if (featureSettings != null && featureSettings.isShowing())
792 final Rectangle fspos = featureSettings.frame.getBounds();
793 // TODO: need a 'show feature settings' function that takes bounds -
794 // need to refactor Desktop.addFrame
795 newframe.featureSettings_actionPerformed(null);
796 final FeatureSettings nfs = newframe.featureSettings;
797 SwingUtilities.invokeLater(new Runnable()
801 nfs.frame.setBounds(fspos);
804 this.featureSettings.close();
805 this.featureSettings = null;
807 this.closeMenuItem_actionPerformed(true);
812 public void addFromText_actionPerformed(ActionEvent e)
814 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
817 public void addFromURL_actionPerformed(ActionEvent e)
819 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
822 public void save_actionPerformed(ActionEvent e)
825 || (currentFileFormat == null || !jalview.io.FormatAdapter
826 .isValidIOFormat(currentFileFormat, true))
827 || fileName.startsWith("http"))
829 saveAs_actionPerformed(null);
833 saveAlignment(fileName, currentFileFormat);
843 public void saveAs_actionPerformed(ActionEvent e)
845 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
846 .getProperty("LAST_DIRECTORY"),
847 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
848 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
849 currentFileFormat, false);
851 chooser.setFileView(new JalviewFileView());
852 chooser.setDialogTitle("Save Alignment to file");
853 chooser.setToolTipText("Save");
855 int value = chooser.showSaveDialog(this);
857 if (value == JalviewFileChooser.APPROVE_OPTION)
859 currentFileFormat = chooser.getSelectedFormat();
860 if (currentFileFormat == null)
862 JOptionPane.showInternalMessageDialog(Desktop.desktop,
863 "You must select a file format before saving!",
864 "File format not specified", JOptionPane.WARNING_MESSAGE);
865 value = chooser.showSaveDialog(this);
869 fileName = chooser.getSelectedFile().getPath();
871 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
874 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
875 if (currentFileFormat.indexOf(" ") > -1)
877 currentFileFormat = currentFileFormat.substring(0,
878 currentFileFormat.indexOf(" "));
880 saveAlignment(fileName, currentFileFormat);
884 public boolean saveAlignment(String file, String format)
886 boolean success = true;
888 if (format.equalsIgnoreCase("Jalview"))
890 String shortName = title;
892 if (shortName.indexOf(java.io.File.separatorChar) > -1)
894 shortName = shortName.substring(shortName
895 .lastIndexOf(java.io.File.separatorChar) + 1);
898 success = new Jalview2XML().SaveAlignment(this, file, shortName);
900 statusBar.setText("Successfully saved to file: " + fileName + " in "
901 + format + " format.");
906 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
908 warningMessage("Cannot save file " + fileName + " using format "
909 + format, "Alignment output format not supported");
910 saveAs_actionPerformed(null);
911 // JBPNote need to have a raise_gui flag here
915 String[] omitHidden = null;
917 if (viewport.hasHiddenColumns)
919 int reply = JOptionPane
920 .showInternalConfirmDialog(
922 "The Alignment contains hidden columns."
923 + "\nDo you want to save only the visible alignment?",
924 "Save / Omit Hidden Columns",
925 JOptionPane.YES_NO_OPTION,
926 JOptionPane.QUESTION_MESSAGE);
928 if (reply == JOptionPane.YES_OPTION)
930 omitHidden = viewport.getViewAsString(false);
933 FormatAdapter f = new FormatAdapter();
934 String output = f.formatSequences(format,
935 (Alignment) viewport.alignment, // class cast exceptions will
936 // occur in the distant future
937 omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
947 java.io.PrintWriter out = new java.io.PrintWriter(
948 new java.io.FileWriter(file));
953 statusBar.setText("Successfully saved to file: " + fileName
954 + " in " + format + " format.");
955 } catch (Exception ex)
958 ex.printStackTrace();
965 JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
966 + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
972 private void warningMessage(String warning, String title)
974 if (new jalview.util.Platform().isHeadless())
976 System.err.println("Warning: " + title + "\nWarning: " + warning);
981 JOptionPane.showInternalMessageDialog(this, warning, title,
982 JOptionPane.WARNING_MESSAGE);
993 protected void outputText_actionPerformed(ActionEvent e)
995 String[] omitHidden = null;
997 if (viewport.hasHiddenColumns)
999 int reply = JOptionPane
1000 .showInternalConfirmDialog(
1002 "The Alignment contains hidden columns."
1003 + "\nDo you want to output only the visible alignment?",
1004 "Save / Omit Hidden Columns",
1005 JOptionPane.YES_NO_OPTION,
1006 JOptionPane.QUESTION_MESSAGE);
1008 if (reply == JOptionPane.YES_OPTION)
1010 omitHidden = viewport.getViewAsString(false);
1014 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1015 cap.setForInput(null);
1016 Desktop.addInternalFrame(cap, "Alignment output - "
1017 + e.getActionCommand(), 600, 500);
1019 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1020 viewport.alignment, omitHidden, viewport.colSel));
1029 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1031 new HTMLOutput(alignPanel, alignPanel.seqPanel.seqCanvas
1032 .getSequenceRenderer(), alignPanel.seqPanel.seqCanvas
1033 .getFeatureRenderer());
1036 public void createImageMap(File file, String image)
1038 alignPanel.makePNGImageMap(file, image);
1047 public void createPNG(File f)
1049 alignPanel.makePNG(f);
1058 public void createEPS(File f)
1060 alignPanel.makeEPS(f);
1063 public void pageSetup_actionPerformed(ActionEvent e)
1065 PrinterJob printJob = PrinterJob.getPrinterJob();
1066 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1075 public void printMenuItem_actionPerformed(ActionEvent e)
1077 // Putting in a thread avoids Swing painting problems
1078 PrintThread thread = new PrintThread(alignPanel);
1082 public void exportFeatures_actionPerformed(ActionEvent e)
1084 new AnnotationExporter().exportFeatures(alignPanel);
1087 public void exportAnnotations_actionPerformed(ActionEvent e)
1089 new AnnotationExporter().exportAnnotations(alignPanel,
1090 viewport.showAnnotation ? viewport.alignment
1091 .getAlignmentAnnotation() : null, viewport.alignment
1093 ((Alignment) viewport.alignment).alignmentProperties);
1096 public void associatedData_actionPerformed(ActionEvent e)
1098 // Pick the tree file
1099 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
1100 .getProperty("LAST_DIRECTORY"));
1101 chooser.setFileView(new JalviewFileView());
1102 chooser.setDialogTitle("Load Jalview Annotations or Features File");
1103 chooser.setToolTipText("Load Jalview Annotations / Features file");
1105 int value = chooser.showOpenDialog(null);
1107 if (value == JalviewFileChooser.APPROVE_OPTION)
1109 String choice = chooser.getSelectedFile().getPath();
1110 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1111 loadJalviewDataFile(choice);
1117 * Close the current view or all views in the alignment frame. If the frame
1118 * only contains one view then the alignment will be removed from memory.
1120 * @param closeAllTabs
1122 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1124 if (alignPanels != null && alignPanels.size() < 2)
1126 closeAllTabs = true;
1131 if (alignPanels != null)
1135 if (this.isClosed())
1137 // really close all the windows - otherwise wait till
1138 // setClosed(true) is called
1139 for (int i = 0; i < alignPanels.size(); i++)
1141 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1148 closeView(alignPanel);
1154 this.setClosed(true);
1156 } catch (Exception ex)
1158 ex.printStackTrace();
1163 * close alignPanel2 and shuffle tabs appropriately.
1165 * @param alignPanel2
1167 public void closeView(AlignmentPanel alignPanel2)
1169 int index = tabbedPane.getSelectedIndex();
1170 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1171 alignPanels.removeElement(alignPanel2);
1173 // if (viewport == alignPanel2.av)
1177 alignPanel2.closePanel();
1180 tabbedPane.removeTabAt(closedindex);
1181 tabbedPane.validate();
1183 if (index > closedindex || index == tabbedPane.getTabCount())
1185 // modify currently selected tab index if necessary.
1189 this.tabSelectionChanged(index);
1195 void updateEditMenuBar()
1198 if (viewport.historyList.size() > 0)
1200 undoMenuItem.setEnabled(true);
1201 CommandI command = (CommandI) viewport.historyList.peek();
1202 undoMenuItem.setText("Undo " + command.getDescription());
1206 undoMenuItem.setEnabled(false);
1207 undoMenuItem.setText("Undo");
1210 if (viewport.redoList.size() > 0)
1212 redoMenuItem.setEnabled(true);
1214 CommandI command = (CommandI) viewport.redoList.peek();
1215 redoMenuItem.setText("Redo " + command.getDescription());
1219 redoMenuItem.setEnabled(false);
1220 redoMenuItem.setText("Redo");
1224 public void addHistoryItem(CommandI command)
1226 if (command.getSize() > 0)
1228 viewport.historyList.push(command);
1229 viewport.redoList.clear();
1230 updateEditMenuBar();
1231 viewport.hasHiddenColumns = (viewport.colSel != null
1232 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1233 .getHiddenColumns().size() > 0);
1239 * @return alignment objects for all views
1241 AlignmentI[] getViewAlignments()
1243 if (alignPanels != null)
1245 Enumeration e = alignPanels.elements();
1246 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1247 for (int i = 0; e.hasMoreElements(); i++)
1249 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1253 if (viewport != null)
1255 return new AlignmentI[]
1256 { viewport.alignment };
1267 protected void undoMenuItem_actionPerformed(ActionEvent e)
1269 if (viewport.historyList.empty())
1271 CommandI command = (CommandI) viewport.historyList.pop();
1272 viewport.redoList.push(command);
1273 command.undoCommand(getViewAlignments());
1275 AlignViewport originalSource = getOriginatingSource(command);
1276 updateEditMenuBar();
1278 if (originalSource != null)
1280 originalSource.hasHiddenColumns = (viewport.colSel != null
1281 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1282 .getHiddenColumns().size() > 0);
1283 originalSource.firePropertyChange("alignment", null,
1284 originalSource.alignment.getSequences());
1294 protected void redoMenuItem_actionPerformed(ActionEvent e)
1296 if (viewport.redoList.size() < 1)
1301 CommandI command = (CommandI) viewport.redoList.pop();
1302 viewport.historyList.push(command);
1303 command.doCommand(getViewAlignments());
1305 AlignViewport originalSource = getOriginatingSource(command);
1306 updateEditMenuBar();
1308 if (originalSource != null)
1310 originalSource.hasHiddenColumns = (viewport.colSel != null
1311 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1312 .getHiddenColumns().size() > 0);
1313 originalSource.firePropertyChange("alignment", null,
1314 originalSource.alignment.getSequences());
1318 AlignViewport getOriginatingSource(CommandI command)
1320 AlignViewport originalSource = null;
1321 // For sequence removal and addition, we need to fire
1322 // the property change event FROM the viewport where the
1323 // original alignment was altered
1324 AlignmentI al = null;
1325 if (command instanceof EditCommand)
1327 EditCommand editCommand = (EditCommand) command;
1328 al = editCommand.getAlignment();
1329 Vector comps = (Vector) PaintRefresher.components.get(viewport
1330 .getSequenceSetId());
1332 for (int i = 0; i < comps.size(); i++)
1334 if (comps.elementAt(i) instanceof AlignmentPanel)
1336 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
1338 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1345 if (originalSource == null)
1347 // The original view is closed, we must validate
1348 // the current view against the closed view first
1351 PaintRefresher.validateSequences(al, viewport.alignment);
1354 originalSource = viewport;
1357 return originalSource;
1366 public void moveSelectedSequences(boolean up)
1368 SequenceGroup sg = viewport.getSelectionGroup();
1377 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1379 SequenceI seq = viewport.alignment.getSequenceAt(i);
1381 if (!sg.getSequences(null).contains(seq))
1386 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1388 if (sg.getSequences(null).contains(temp))
1393 viewport.alignment.getSequences().setElementAt(temp, i);
1394 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1399 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1401 SequenceI seq = viewport.alignment.getSequenceAt(i);
1403 if (!sg.getSequences(null).contains(seq))
1408 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1410 if (sg.getSequences(null).contains(temp))
1415 viewport.alignment.getSequences().setElementAt(temp, i);
1416 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1420 alignPanel.paintAlignment(true);
1423 synchronized void slideSequences(boolean right, int size)
1425 Vector sg = new Vector();
1426 if (viewport.cursorMode)
1428 sg.addElement(viewport.alignment
1429 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1431 else if (viewport.getSelectionGroup() != null
1432 && viewport.getSelectionGroup().getSize() != viewport.alignment
1435 sg = viewport.getSelectionGroup().getSequences(
1436 viewport.hiddenRepSequences);
1444 Vector invertGroup = new Vector();
1446 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1448 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
1449 invertGroup.add(viewport.alignment.getSequenceAt(i));
1452 SequenceI[] seqs1 = new SequenceI[sg.size()];
1453 for (int i = 0; i < sg.size(); i++)
1454 seqs1[i] = (SequenceI) sg.elementAt(i);
1456 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1457 for (int i = 0; i < invertGroup.size(); i++)
1458 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1460 SlideSequencesCommand ssc;
1462 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1463 size, viewport.getGapCharacter());
1465 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1466 size, viewport.getGapCharacter());
1468 int groupAdjustment = 0;
1469 if (ssc.getGapsInsertedBegin() && right)
1471 if (viewport.cursorMode)
1472 alignPanel.seqPanel.moveCursor(size, 0);
1474 groupAdjustment = size;
1476 else if (!ssc.getGapsInsertedBegin() && !right)
1478 if (viewport.cursorMode)
1479 alignPanel.seqPanel.moveCursor(-size, 0);
1481 groupAdjustment = -size;
1484 if (groupAdjustment != 0)
1486 viewport.getSelectionGroup().setStartRes(
1487 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1488 viewport.getSelectionGroup().setEndRes(
1489 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1492 boolean appendHistoryItem = false;
1493 if (viewport.historyList != null && viewport.historyList.size() > 0
1494 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1496 appendHistoryItem = ssc
1497 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1501 if (!appendHistoryItem)
1502 addHistoryItem(ssc);
1513 protected void copy_actionPerformed(ActionEvent e)
1516 if (viewport.getSelectionGroup() == null)
1520 // TODO: preserve the ordering of displayed alignment annotation in any
1521 // internal paste (particularly sequence associated annotation)
1522 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1523 String[] omitHidden = null;
1525 if (viewport.hasHiddenColumns)
1527 omitHidden = viewport.getViewAsString(true);
1530 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1533 StringSelection ss = new StringSelection(output);
1537 jalview.gui.Desktop.internalCopy = true;
1538 // Its really worth setting the clipboard contents
1539 // to empty before setting the large StringSelection!!
1540 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
1541 new StringSelection(""), null);
1543 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1545 } catch (OutOfMemoryError er)
1547 new OOMWarning("copying region", er);
1551 Vector hiddenColumns = null;
1552 if (viewport.hasHiddenColumns)
1554 hiddenColumns = new Vector();
1555 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1556 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1559 int[] region = (int[]) viewport.getColumnSelection()
1560 .getHiddenColumns().elementAt(i);
1562 hiddenColumns.addElement(new int[]
1563 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1567 Desktop.jalviewClipboard = new Object[]
1568 { seqs, viewport.alignment.getDataset(), hiddenColumns };
1569 statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
1578 protected void pasteNew_actionPerformed(ActionEvent e)
1589 protected void pasteThis_actionPerformed(ActionEvent e)
1595 * Paste contents of Jalview clipboard
1597 * @param newAlignment
1598 * true to paste to a new alignment, otherwise add to this.
1600 void paste(boolean newAlignment)
1602 boolean externalPaste = true;
1605 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1606 Transferable contents = c.getContents(this);
1608 if (contents == null)
1616 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1617 if (str.length() < 1)
1622 format = new IdentifyFile().Identify(str, "Paste");
1624 } catch (OutOfMemoryError er)
1626 new OOMWarning("Out of memory pasting sequences!!", er);
1630 SequenceI[] sequences;
1631 boolean annotationAdded = false;
1632 AlignmentI alignment = null;
1634 if (Desktop.jalviewClipboard != null)
1636 // The clipboard was filled from within Jalview, we must use the
1638 // And dataset from the copied alignment
1639 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1640 // be doubly sure that we create *new* sequence objects.
1641 sequences = new SequenceI[newseq.length];
1642 for (int i = 0; i < newseq.length; i++)
1644 sequences[i] = new Sequence(newseq[i]);
1646 alignment = new Alignment(sequences);
1647 externalPaste = false;
1651 // parse the clipboard as an alignment.
1652 alignment = new FormatAdapter().readFile(str, "Paste", format);
1653 sequences = alignment.getSequencesArray();
1661 if (Desktop.jalviewClipboard != null)
1663 // dataset is inherited
1664 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1668 // new dataset is constructed
1669 alignment.setDataset(null);
1671 alwidth = alignment.getWidth() + 1;
1675 AlignmentI pastedal = alignment; // preserve pasted alignment object
1676 // Add pasted sequences and dataset into existing alignment.
1677 alignment = viewport.getAlignment();
1678 alwidth = alignment.getWidth() + 1;
1679 // decide if we need to import sequences from an existing dataset
1680 boolean importDs = Desktop.jalviewClipboard != null
1681 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1682 // importDs==true instructs us to copy over new dataset sequences from
1683 // an existing alignment
1684 Vector newDs = (importDs) ? new Vector() : null; // used to create
1685 // minimum dataset set
1687 for (int i = 0; i < sequences.length; i++)
1691 newDs.addElement(null);
1693 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1695 if (importDs && ds != null)
1697 if (!newDs.contains(ds))
1699 newDs.setElementAt(ds, i);
1700 ds = new Sequence(ds);
1701 // update with new dataset sequence
1702 sequences[i].setDatasetSequence(ds);
1706 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1711 // copy and derive new dataset sequence
1712 sequences[i] = sequences[i].deriveSequence();
1713 alignment.getDataset().addSequence(
1714 sequences[i].getDatasetSequence());
1715 // TODO: avoid creation of duplicate dataset sequences with a
1716 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1718 alignment.addSequence(sequences[i]); // merges dataset
1722 newDs.clear(); // tidy up
1724 if (pastedal.getAlignmentAnnotation() != null)
1726 // Add any annotation attached to alignment.
1727 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1728 for (int i = 0; i < alann.length; i++)
1730 annotationAdded = true;
1731 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1733 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1734 newann.padAnnotation(alwidth);
1735 alignment.addAnnotation(newann);
1745 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1746 sequences, 0, alignment.getWidth(), alignment));
1748 // Add any annotations attached to sequences
1749 for (int i = 0; i < sequences.length; i++)
1751 if (sequences[i].getAnnotation() != null)
1753 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1755 annotationAdded = true;
1756 sequences[i].getAnnotation()[a].adjustForAlignment();
1757 sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1758 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1763 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1770 // propagate alignment changed.
1771 viewport.setEndSeq(alignment.getHeight());
1772 if (annotationAdded)
1774 // Duplicate sequence annotation in all views.
1775 AlignmentI[] alview = this.getViewAlignments();
1776 for (int i = 0; i < sequences.length; i++)
1778 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1781 for (int avnum = 0; avnum < alview.length; avnum++)
1783 if (alview[avnum] != alignment)
1785 // duplicate in a view other than the one with input focus
1786 int avwidth = alview[avnum].getWidth() + 1;
1787 // this relies on sann being preserved after we
1788 // modify the sequence's annotation array for each duplication
1789 for (int a = 0; a < sann.length; a++)
1791 AlignmentAnnotation newann = new AlignmentAnnotation(
1793 sequences[i].addAlignmentAnnotation(newann);
1794 newann.padAnnotation(avwidth);
1795 alview[avnum].addAnnotation(newann); // annotation was
1796 // duplicated earlier
1797 alview[avnum].setAnnotationIndex(newann, a);
1802 buildSortByAnnotationScoresMenu();
1804 viewport.firePropertyChange("alignment", null, alignment
1810 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
1812 String newtitle = new String("Copied sequences");
1814 if (Desktop.jalviewClipboard != null
1815 && Desktop.jalviewClipboard[2] != null)
1817 Vector hc = (Vector) Desktop.jalviewClipboard[2];
1818 for (int i = 0; i < hc.size(); i++)
1820 int[] region = (int[]) hc.elementAt(i);
1821 af.viewport.hideColumns(region[0], region[1]);
1825 // >>>This is a fix for the moment, until a better solution is
1827 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
1829 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1831 // TODO: maintain provenance of an alignment, rather than just make the
1832 // title a concatenation of operations.
1835 if (title.startsWith("Copied sequences"))
1841 newtitle = newtitle.concat("- from " + title);
1846 newtitle = new String("Pasted sequences");
1849 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1854 } catch (Exception ex)
1856 ex.printStackTrace();
1857 System.out.println("Exception whilst pasting: " + ex);
1858 // could be anything being pasted in here
1869 protected void cut_actionPerformed(ActionEvent e)
1871 copy_actionPerformed(null);
1872 delete_actionPerformed(null);
1881 protected void delete_actionPerformed(ActionEvent evt)
1884 SequenceGroup sg = viewport.getSelectionGroup();
1890 Vector seqs = new Vector();
1892 for (int i = 0; i < sg.getSize(); i++)
1894 seq = sg.getSequenceAt(i);
1895 seqs.addElement(seq);
1898 // If the cut affects all sequences, remove highlighted columns
1899 if (sg.getSize() == viewport.alignment.getHeight())
1901 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1902 sg.getEndRes() + 1);
1905 SequenceI[] cut = new SequenceI[seqs.size()];
1906 for (int i = 0; i < seqs.size(); i++)
1908 cut[i] = (SequenceI) seqs.elementAt(i);
1912 * //ADD HISTORY ITEM
1914 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1915 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1916 viewport.alignment));
1918 viewport.setSelectionGroup(null);
1919 viewport.sendSelection();
1920 viewport.alignment.deleteGroup(sg);
1922 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1924 if (viewport.getAlignment().getHeight() < 1)
1928 this.setClosed(true);
1929 } catch (Exception ex)
1941 protected void deleteGroups_actionPerformed(ActionEvent e)
1943 viewport.alignment.deleteAllGroups();
1944 viewport.sequenceColours = null;
1945 viewport.setSelectionGroup(null);
1946 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1947 alignPanel.updateAnnotation();
1948 alignPanel.paintAlignment(true);
1957 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1959 SequenceGroup sg = new SequenceGroup();
1961 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1963 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1966 sg.setEndRes(viewport.alignment.getWidth() - 1);
1967 viewport.setSelectionGroup(sg);
1968 viewport.sendSelection();
1969 alignPanel.paintAlignment(true);
1970 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1979 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1981 if (viewport.cursorMode)
1983 alignPanel.seqPanel.keyboardNo1 = null;
1984 alignPanel.seqPanel.keyboardNo2 = null;
1986 viewport.setSelectionGroup(null);
1987 viewport.getColumnSelection().clear();
1988 viewport.setSelectionGroup(null);
1989 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1990 alignPanel.idPanel.idCanvas.searchResults = null;
1991 alignPanel.paintAlignment(true);
1992 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2001 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2003 SequenceGroup sg = viewport.getSelectionGroup();
2007 selectAllSequenceMenuItem_actionPerformed(null);
2012 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2014 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2017 alignPanel.paintAlignment(true);
2018 viewport.sendSelection();
2019 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2022 public void invertColSel_actionPerformed(ActionEvent e)
2024 viewport.invertColumnSelection();
2025 alignPanel.paintAlignment(true);
2034 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2036 trimAlignment(true);
2045 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2047 trimAlignment(false);
2050 void trimAlignment(boolean trimLeft)
2052 ColumnSelection colSel = viewport.getColumnSelection();
2055 if (colSel.size() > 0)
2059 column = colSel.getMin();
2063 column = colSel.getMax();
2067 if (viewport.getSelectionGroup() != null)
2069 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2070 viewport.hiddenRepSequences);
2074 seqs = viewport.alignment.getSequencesArray();
2077 TrimRegionCommand trimRegion;
2080 trimRegion = new TrimRegionCommand("Remove Left",
2081 TrimRegionCommand.TRIM_LEFT, seqs, column,
2082 viewport.alignment, viewport.colSel,
2083 viewport.selectionGroup);
2084 viewport.setStartRes(0);
2088 trimRegion = new TrimRegionCommand("Remove Right",
2089 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2090 viewport.alignment, viewport.colSel,
2091 viewport.selectionGroup);
2094 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2096 addHistoryItem(trimRegion);
2098 Vector groups = viewport.alignment.getGroups();
2100 for (int i = 0; i < groups.size(); i++)
2102 SequenceGroup sg = (SequenceGroup) groups.get(i);
2104 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2105 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2107 viewport.alignment.deleteGroup(sg);
2111 viewport.firePropertyChange("alignment", null, viewport
2112 .getAlignment().getSequences());
2122 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2124 int start = 0, end = viewport.alignment.getWidth() - 1;
2127 if (viewport.getSelectionGroup() != null)
2129 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2130 viewport.hiddenRepSequences);
2131 start = viewport.getSelectionGroup().getStartRes();
2132 end = viewport.getSelectionGroup().getEndRes();
2136 seqs = viewport.alignment.getSequencesArray();
2139 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2140 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
2142 addHistoryItem(removeGapCols);
2144 statusBar.setText("Removed " + removeGapCols.getSize()
2145 + " empty columns.");
2147 // This is to maintain viewport position on first residue
2148 // of first sequence
2149 SequenceI seq = viewport.alignment.getSequenceAt(0);
2150 int startRes = seq.findPosition(viewport.startRes);
2151 // ShiftList shifts;
2152 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2153 // edit.alColumnChanges=shifts.getInverse();
2154 // if (viewport.hasHiddenColumns)
2155 // viewport.getColumnSelection().compensateForEdits(shifts);
2156 viewport.setStartRes(seq.findIndex(startRes) - 1);
2157 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2168 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2170 int start = 0, end = viewport.alignment.getWidth() - 1;
2173 if (viewport.getSelectionGroup() != null)
2175 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2176 viewport.hiddenRepSequences);
2177 start = viewport.getSelectionGroup().getStartRes();
2178 end = viewport.getSelectionGroup().getEndRes();
2182 seqs = viewport.alignment.getSequencesArray();
2185 // This is to maintain viewport position on first residue
2186 // of first sequence
2187 SequenceI seq = viewport.alignment.getSequenceAt(0);
2188 int startRes = seq.findPosition(viewport.startRes);
2190 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2191 viewport.alignment));
2193 viewport.setStartRes(seq.findIndex(startRes) - 1);
2195 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2206 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2208 viewport.padGaps = padGapsMenuitem.isSelected();
2209 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2215 // if (justifySeqs>0)
2217 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2229 public void findMenuItem_actionPerformed(ActionEvent e)
2234 public void newView_actionPerformed(ActionEvent e)
2236 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2239 newap.av.gatherViewsHere = false;
2241 if (viewport.viewName == null)
2243 viewport.viewName = "Original";
2246 newap.av.historyList = viewport.historyList;
2247 newap.av.redoList = viewport.redoList;
2249 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2250 String newViewName = "View " + index;
2252 Vector comps = (Vector) PaintRefresher.components.get(viewport
2253 .getSequenceSetId());
2254 Vector existingNames = new Vector();
2255 for (int i = 0; i < comps.size(); i++)
2257 if (comps.elementAt(i) instanceof AlignmentPanel)
2259 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2260 if (!existingNames.contains(ap.av.viewName))
2262 existingNames.addElement(ap.av.viewName);
2267 while (existingNames.contains(newViewName))
2269 newViewName = "View " + (++index);
2272 newap.av.viewName = newViewName;
2274 addAlignmentPanel(newap, true);
2276 if (alignPanels.size() == 2)
2278 viewport.gatherViewsHere = true;
2280 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2283 public void expandViews_actionPerformed(ActionEvent e)
2285 Desktop.instance.explodeViews(this);
2288 public void gatherViews_actionPerformed(ActionEvent e)
2290 Desktop.instance.gatherViews(this);
2299 public void font_actionPerformed(ActionEvent e)
2301 new FontChooser(alignPanel);
2310 protected void seqLimit_actionPerformed(ActionEvent e)
2312 viewport.setShowJVSuffix(seqLimits.isSelected());
2314 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2315 .calculateIdWidth());
2316 alignPanel.paintAlignment(true);
2319 public void idRightAlign_actionPerformed(ActionEvent e)
2321 viewport.rightAlignIds = idRightAlign.isSelected();
2322 alignPanel.paintAlignment(true);
2325 public void centreColumnLabels_actionPerformed(ActionEvent e)
2327 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2328 alignPanel.paintAlignment(true);
2334 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2336 protected void followHighlight_actionPerformed()
2338 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2340 alignPanel.scrollToPosition(
2341 alignPanel.seqPanel.seqCanvas.searchResults, false);
2351 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2353 viewport.setColourText(colourTextMenuItem.isSelected());
2354 alignPanel.paintAlignment(true);
2363 public void wrapMenuItem_actionPerformed(ActionEvent e)
2365 scaleAbove.setVisible(wrapMenuItem.isSelected());
2366 scaleLeft.setVisible(wrapMenuItem.isSelected());
2367 scaleRight.setVisible(wrapMenuItem.isSelected());
2368 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2369 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2372 public void showAllSeqs_actionPerformed(ActionEvent e)
2374 viewport.showAllHiddenSeqs();
2377 public void showAllColumns_actionPerformed(ActionEvent e)
2379 viewport.showAllHiddenColumns();
2383 public void hideSelSequences_actionPerformed(ActionEvent e)
2385 viewport.hideAllSelectedSeqs();
2386 alignPanel.paintAlignment(true);
2390 * called by key handler and the hide all/show all menu items
2395 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2398 boolean hide = false;
2399 SequenceGroup sg = viewport.getSelectionGroup();
2400 if (!toggleSeqs && !toggleCols)
2402 // Hide everything by the current selection - this is a hack - we do the
2403 // invert and then hide
2404 // first check that there will be visible columns after the invert.
2405 if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
2406 .getSelected().size() > 0)
2407 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2410 // now invert the sequence set, if required - empty selection implies
2411 // that no hiding is required.
2414 invertSequenceMenuItem_actionPerformed(null);
2415 sg = viewport.getSelectionGroup();
2419 viewport.expandColSelection(sg, true);
2420 // finally invert the column selection and get the new sequence
2422 invertColSel_actionPerformed(null);
2429 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
2431 hideSelSequences_actionPerformed(null);
2434 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
2436 showAllSeqs_actionPerformed(null);
2442 if (viewport.colSel.getSelected().size() > 0)
2444 hideSelColumns_actionPerformed(null);
2447 viewport.selectionGroup = sg;
2452 showAllColumns_actionPerformed(null);
2461 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2462 * event.ActionEvent)
2464 public void hideAllButSelection_actionPerformed(ActionEvent e)
2466 toggleHiddenRegions(false, false);
2473 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2476 public void hideAllSelection_actionPerformed(ActionEvent e)
2478 SequenceGroup sg = viewport.getSelectionGroup();
2479 viewport.expandColSelection(sg, false);
2480 viewport.hideAllSelectedSeqs();
2481 viewport.hideSelectedColumns();
2482 alignPanel.paintAlignment(true);
2489 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2492 public void showAllhidden_actionPerformed(ActionEvent e)
2494 viewport.showAllHiddenColumns();
2495 viewport.showAllHiddenSeqs();
2496 alignPanel.paintAlignment(true);
2499 public void hideSelColumns_actionPerformed(ActionEvent e)
2501 viewport.hideSelectedColumns();
2502 alignPanel.paintAlignment(true);
2505 public void hiddenMarkers_actionPerformed(ActionEvent e)
2507 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2517 protected void scaleAbove_actionPerformed(ActionEvent e)
2519 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2520 alignPanel.paintAlignment(true);
2529 protected void scaleLeft_actionPerformed(ActionEvent e)
2531 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2532 alignPanel.paintAlignment(true);
2541 protected void scaleRight_actionPerformed(ActionEvent e)
2543 viewport.setScaleRightWrapped(scaleRight.isSelected());
2544 alignPanel.paintAlignment(true);
2553 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2555 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2556 alignPanel.paintAlignment(true);
2565 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2567 viewport.setShowText(viewTextMenuItem.isSelected());
2568 alignPanel.paintAlignment(true);
2577 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2579 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2580 alignPanel.paintAlignment(true);
2583 public FeatureSettings featureSettings;
2585 public void featureSettings_actionPerformed(ActionEvent e)
2587 if (featureSettings != null)
2589 featureSettings.close();
2590 featureSettings = null;
2592 if (!showSeqFeatures.isSelected())
2594 // make sure features are actually displayed
2595 showSeqFeatures.setSelected(true);
2596 showSeqFeatures_actionPerformed(null);
2598 featureSettings = new FeatureSettings(this);
2602 * Set or clear 'Show Sequence Features'
2607 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2609 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2610 alignPanel.paintAlignment(true);
2611 if (alignPanel.getOverviewPanel() != null)
2613 alignPanel.getOverviewPanel().updateOverviewImage();
2618 * Set or clear 'Show Sequence Features'
2623 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2625 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2627 if (viewport.getShowSequenceFeaturesHeight())
2629 // ensure we're actually displaying features
2630 viewport.setShowSequenceFeatures(true);
2631 showSeqFeatures.setSelected(true);
2633 alignPanel.paintAlignment(true);
2634 if (alignPanel.getOverviewPanel() != null)
2636 alignPanel.getOverviewPanel().updateOverviewImage();
2646 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2648 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2649 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2652 public void alignmentProperties()
2654 JEditorPane editPane = new JEditorPane("text/html", "");
2655 editPane.setEditable(false);
2656 StringBuffer contents = new StringBuffer("<html>");
2659 int min = Integer.MAX_VALUE, max = 0;
2660 for (int i = 0; i < viewport.alignment.getHeight(); i++)
2662 int size = viewport.alignment.getSequenceAt(i).getEnd()
2663 - viewport.alignment.getSequenceAt(i).getStart();
2670 avg = avg / (float) viewport.alignment.getHeight();
2672 contents.append("<br>Sequences: " + viewport.alignment.getHeight());
2673 contents.append("<br>Minimum Sequence Length: " + min);
2674 contents.append("<br>Maximum Sequence Length: " + max);
2675 contents.append("<br>Average Length: " + (int) avg);
2677 if (((Alignment) viewport.alignment).getProperties() != null)
2679 Hashtable props = ((Alignment) viewport.alignment).getProperties();
2680 Enumeration en = props.keys();
2681 contents.append("<br><br><table border=\"1\">");
2682 while (en.hasMoreElements())
2684 String key = en.nextElement().toString();
2685 StringBuffer val = new StringBuffer();
2686 String vals = props.get(key).toString();
2690 npos = vals.indexOf("\n", pos);
2693 val.append(vals.substring(pos));
2697 val.append(vals.substring(pos, npos));
2701 } while (npos != -1);
2703 .append("<tr><td>" + key + "</td><td>" + val + "</td></tr>");
2705 contents.append("</table>");
2707 editPane.setText(contents.toString() + "</html>");
2708 JInternalFrame frame = new JInternalFrame();
2709 frame.getContentPane().add(new JScrollPane(editPane));
2711 Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
2712 + getTitle(), 500, 400);
2721 public void overviewMenuItem_actionPerformed(ActionEvent e)
2723 if (alignPanel.overviewPanel != null)
2728 JInternalFrame frame = new JInternalFrame();
2729 OverviewPanel overview = new OverviewPanel(alignPanel);
2730 frame.setContentPane(overview);
2731 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(), frame
2732 .getWidth(), frame.getHeight());
2734 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2736 .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2738 public void internalFrameClosed(
2739 javax.swing.event.InternalFrameEvent evt)
2741 alignPanel.setOverviewPanel(null);
2745 alignPanel.setOverviewPanel(overview);
2748 public void textColour_actionPerformed(ActionEvent e)
2750 new TextColourChooser().chooseColour(alignPanel, null);
2759 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2770 public void clustalColour_actionPerformed(ActionEvent e)
2772 changeColour(new ClustalxColourScheme(
2773 viewport.alignment.getSequences(), viewport.alignment
2783 public void zappoColour_actionPerformed(ActionEvent e)
2785 changeColour(new ZappoColourScheme());
2794 public void taylorColour_actionPerformed(ActionEvent e)
2796 changeColour(new TaylorColourScheme());
2805 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2807 changeColour(new HydrophobicColourScheme());
2816 public void helixColour_actionPerformed(ActionEvent e)
2818 changeColour(new HelixColourScheme());
2827 public void strandColour_actionPerformed(ActionEvent e)
2829 changeColour(new StrandColourScheme());
2838 public void turnColour_actionPerformed(ActionEvent e)
2840 changeColour(new TurnColourScheme());
2849 public void buriedColour_actionPerformed(ActionEvent e)
2851 changeColour(new BuriedColourScheme());
2860 public void nucleotideColour_actionPerformed(ActionEvent e)
2862 changeColour(new NucleotideColourScheme());
2865 public void annotationColour_actionPerformed(ActionEvent e)
2867 new AnnotationColourChooser(viewport, alignPanel);
2876 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2878 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2887 public void changeColour(ColourSchemeI cs)
2893 if (viewport.getAbovePIDThreshold())
2895 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2898 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2900 viewport.setGlobalColourScheme(cs);
2904 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2907 if (viewport.getConservationSelected())
2910 Alignment al = (Alignment) viewport.alignment;
2911 Conservation c = new Conservation("All",
2912 ResidueProperties.propHash, 3, al.getSequences(), 0, al
2916 c.verdict(false, viewport.ConsPercGaps);
2918 cs.setConservation(c);
2920 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
2925 cs.setConservation(null);
2928 cs.setConsensus(viewport.hconsensus);
2931 viewport.setGlobalColourScheme(cs);
2933 if (viewport.getColourAppliesToAllGroups())
2935 Vector groups = viewport.alignment.getGroups();
2937 for (int i = 0; i < groups.size(); i++)
2939 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2947 if (cs instanceof ClustalxColourScheme)
2949 sg.cs = new ClustalxColourScheme(sg
2950 .getSequences(viewport.hiddenRepSequences), sg.getWidth());
2952 else if (cs instanceof UserColourScheme)
2954 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
2960 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2961 } catch (Exception ex)
2966 if (viewport.getAbovePIDThreshold()
2967 || cs instanceof PIDColourScheme
2968 || cs instanceof Blosum62ColourScheme)
2970 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2972 sg.cs.setConsensus(AAFrequency.calculate(sg
2973 .getSequences(viewport.hiddenRepSequences), sg
2974 .getStartRes(), sg.getEndRes() + 1));
2978 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2981 if (viewport.getConservationSelected())
2983 Conservation c = new Conservation("Group",
2984 ResidueProperties.propHash, 3, sg
2985 .getSequences(viewport.hiddenRepSequences), sg
2986 .getStartRes(), sg.getEndRes() + 1);
2988 c.verdict(false, viewport.ConsPercGaps);
2989 sg.cs.setConservation(c);
2993 sg.cs.setConservation(null);
2998 if (alignPanel.getOverviewPanel() != null)
3000 alignPanel.getOverviewPanel().updateOverviewImage();
3003 alignPanel.paintAlignment(true);
3012 protected void modifyPID_actionPerformed(ActionEvent e)
3014 if (viewport.getAbovePIDThreshold()
3015 && viewport.globalColourScheme != null)
3017 SliderPanel.setPIDSliderSource(alignPanel, viewport
3018 .getGlobalColourScheme(), "Background");
3019 SliderPanel.showPIDSlider();
3029 protected void modifyConservation_actionPerformed(ActionEvent e)
3031 if (viewport.getConservationSelected()
3032 && viewport.globalColourScheme != null)
3034 SliderPanel.setConservationSlider(alignPanel,
3035 viewport.globalColourScheme, "Background");
3036 SliderPanel.showConservationSlider();
3046 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3048 viewport.setConservationSelected(conservationMenuItem.isSelected());
3050 viewport.setAbovePIDThreshold(false);
3051 abovePIDThreshold.setSelected(false);
3053 changeColour(viewport.getGlobalColourScheme());
3055 modifyConservation_actionPerformed(null);
3064 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3066 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3068 conservationMenuItem.setSelected(false);
3069 viewport.setConservationSelected(false);
3071 changeColour(viewport.getGlobalColourScheme());
3073 modifyPID_actionPerformed(null);
3082 public void userDefinedColour_actionPerformed(ActionEvent e)
3084 if (e.getActionCommand().equals("User Defined..."))
3086 new UserDefinedColours(alignPanel, null);
3090 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3091 .getUserColourSchemes().get(e.getActionCommand());
3097 public void updateUserColourMenu()
3100 Component[] menuItems = colourMenu.getMenuComponents();
3101 int i, iSize = menuItems.length;
3102 for (i = 0; i < iSize; i++)
3104 if (menuItems[i].getName() != null
3105 && menuItems[i].getName().equals("USER_DEFINED"))
3107 colourMenu.remove(menuItems[i]);
3111 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3113 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3114 .getUserColourSchemes().keys();
3116 while (userColours.hasMoreElements())
3118 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3119 userColours.nextElement().toString());
3120 radioItem.setName("USER_DEFINED");
3121 radioItem.addMouseListener(new MouseAdapter()
3123 public void mousePressed(MouseEvent evt)
3125 if (evt.isControlDown()
3126 || SwingUtilities.isRightMouseButton(evt))
3129 .removeActionListener(radioItem.getActionListeners()[0]);
3131 int option = JOptionPane.showInternalConfirmDialog(
3132 jalview.gui.Desktop.desktop,
3133 "Remove from default list?",
3134 "Remove user defined colour",
3135 JOptionPane.YES_NO_OPTION);
3136 if (option == JOptionPane.YES_OPTION)
3138 jalview.gui.UserDefinedColours
3139 .removeColourFromDefaults(radioItem.getText());
3140 colourMenu.remove(radioItem);
3144 radioItem.addActionListener(new ActionListener()
3146 public void actionPerformed(ActionEvent evt)
3148 userDefinedColour_actionPerformed(evt);
3155 radioItem.addActionListener(new ActionListener()
3157 public void actionPerformed(ActionEvent evt)
3159 userDefinedColour_actionPerformed(evt);
3163 colourMenu.insert(radioItem, 15);
3164 colours.add(radioItem);
3175 public void PIDColour_actionPerformed(ActionEvent e)
3177 changeColour(new PIDColourScheme());
3186 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3188 changeColour(new Blosum62ColourScheme());
3197 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3199 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3200 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3201 .getAlignment().getSequenceAt(0), null);
3202 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3203 viewport.alignment));
3204 alignPanel.paintAlignment(true);
3213 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3215 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3216 AlignmentSorter.sortByID(viewport.getAlignment());
3217 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
3218 alignPanel.paintAlignment(true);
3227 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3229 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3230 AlignmentSorter.sortByLength(viewport.getAlignment());
3231 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3232 viewport.alignment));
3233 alignPanel.paintAlignment(true);
3242 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3244 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3245 AlignmentSorter.sortByGroup(viewport.getAlignment());
3246 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3247 viewport.alignment));
3249 alignPanel.paintAlignment(true);
3258 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3260 new RedundancyPanel(alignPanel, this);
3269 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3271 if ((viewport.getSelectionGroup() == null)
3272 || (viewport.getSelectionGroup().getSize() < 2))
3274 JOptionPane.showInternalMessageDialog(this,
3275 "You must select at least 2 sequences.", "Invalid Selection",
3276 JOptionPane.WARNING_MESSAGE);
3280 JInternalFrame frame = new JInternalFrame();
3281 frame.setContentPane(new PairwiseAlignPanel(viewport));
3282 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
3292 public void PCAMenuItem_actionPerformed(ActionEvent e)
3294 if (((viewport.getSelectionGroup() != null)
3295 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3296 .getSelectionGroup().getSize() > 0))
3297 || (viewport.getAlignment().getHeight() < 4))
3299 JOptionPane.showInternalMessageDialog(this,
3300 "Principal component analysis must take\n"
3301 + "at least 4 input sequences.",
3302 "Sequence selection insufficient",
3303 JOptionPane.WARNING_MESSAGE);
3308 new PCAPanel(alignPanel);
3311 public void autoCalculate_actionPerformed(ActionEvent e)
3313 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3314 if (viewport.autoCalculateConsensus)
3316 viewport.firePropertyChange("alignment", null, viewport
3317 .getAlignment().getSequences());
3327 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3329 NewTreePanel("AV", "PID", "Average distance tree using PID");
3338 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3340 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3349 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3351 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3360 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3362 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3375 void NewTreePanel(String type, String pwType, String title)
3379 if (viewport.getSelectionGroup() != null)
3381 if (viewport.getSelectionGroup().getSize() < 3)
3386 "You need to have more than two sequences selected to build a tree!",
3387 "Not enough sequences", JOptionPane.WARNING_MESSAGE);
3392 SequenceGroup sg = viewport.getSelectionGroup();
3394 /* Decide if the selection is a column region */
3395 while (s < sg.getSize())
3397 if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
3403 "The selected region to create a tree may\nonly contain residues or gaps.\n"
3404 + "Try using the Pad function in the edit menu,\n"
3405 + "or one of the multiple sequence alignment web services.",
3406 "Sequences in selection are not aligned",
3407 JOptionPane.WARNING_MESSAGE);
3413 title = title + " on region";
3414 tp = new TreePanel(alignPanel, type, pwType);
3418 // are the visible sequences aligned?
3419 if (!viewport.alignment.isAligned(false))
3424 "The sequences must be aligned before creating a tree.\n"
3425 + "Try using the Pad function in the edit menu,\n"
3426 + "or one of the multiple sequence alignment web services.",
3427 "Sequences not aligned",
3428 JOptionPane.WARNING_MESSAGE);
3433 if (viewport.alignment.getHeight() < 2)
3438 tp = new TreePanel(alignPanel, type, pwType);
3443 if (viewport.viewName != null)
3445 title += viewport.viewName + " of ";
3448 title += this.title;
3450 Desktop.addInternalFrame(tp, title, 600, 500);
3461 public void addSortByOrderMenuItem(String title,
3462 final AlignmentOrder order)
3464 final JMenuItem item = new JMenuItem("by " + title);
3466 item.addActionListener(new java.awt.event.ActionListener()
3468 public void actionPerformed(ActionEvent e)
3470 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3472 // TODO: JBPNote - have to map order entries to curent SequenceI
3474 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3476 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3477 viewport.alignment));
3479 alignPanel.paintAlignment(true);
3485 * Add a new sort by annotation score menu item
3488 * the menu to add the option to
3490 * the label used to retrieve scores for each sequence on the
3493 public void addSortByAnnotScoreMenuItem(JMenu sort,
3494 final String scoreLabel)
3496 final JMenuItem item = new JMenuItem(scoreLabel);
3498 item.addActionListener(new java.awt.event.ActionListener()
3500 public void actionPerformed(ActionEvent e)
3502 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3503 AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport
3504 .getAlignment());// ,viewport.getSelectionGroup());
3505 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3506 viewport.alignment));
3507 alignPanel.paintAlignment(true);
3513 * last hash for alignment's annotation array - used to minimise cost of
3516 protected int _annotationScoreVectorHash;
3519 * search the alignment and rebuild the sort by annotation score submenu the
3520 * last alignment annotation vector hash is stored to minimize cost of
3521 * rebuilding in subsequence calls.
3524 public void buildSortByAnnotationScoresMenu()
3526 if (viewport.alignment.getAlignmentAnnotation() == null)
3531 if (viewport.alignment.getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3533 sortByAnnotScore.removeAll();
3534 // almost certainly a quicker way to do this - but we keep it simple
3535 Hashtable scoreSorts = new Hashtable();
3536 AlignmentAnnotation aann[];
3537 Enumeration sq = viewport.alignment.getSequences().elements();
3538 while (sq.hasMoreElements())
3540 aann = ((SequenceI) sq.nextElement()).getAnnotation();
3541 for (int i = 0; aann != null && i < aann.length; i++)
3543 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3545 scoreSorts.put(aann[i].label, aann[i].label);
3549 Enumeration labels = scoreSorts.keys();
3550 while (labels.hasMoreElements())
3552 addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels
3555 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3558 _annotationScoreVectorHash = viewport.alignment
3559 .getAlignmentAnnotation().hashCode();
3564 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3565 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3566 * call. Listeners are added to remove the menu item when the treePanel is
3567 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3571 * Displayed tree window.
3573 * SortBy menu item title.
3575 public void buildTreeMenu()
3577 sortByTreeMenu.removeAll();
3579 Vector comps = (Vector) PaintRefresher.components.get(viewport
3580 .getSequenceSetId());
3581 Vector treePanels = new Vector();
3582 int i, iSize = comps.size();
3583 for (i = 0; i < iSize; i++)
3585 if (comps.elementAt(i) instanceof TreePanel)
3587 treePanels.add(comps.elementAt(i));
3591 iSize = treePanels.size();
3595 sortByTreeMenu.setVisible(false);
3599 sortByTreeMenu.setVisible(true);
3601 for (i = 0; i < treePanels.size(); i++)
3603 TreePanel tp = (TreePanel) treePanels.elementAt(i);
3604 final JMenuItem item = new JMenuItem(tp.getTitle());
3605 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3606 item.addActionListener(new java.awt.event.ActionListener()
3608 public void actionPerformed(ActionEvent e)
3610 SequenceI[] oldOrder = viewport.getAlignment()
3611 .getSequencesArray();
3612 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
3614 addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
3615 viewport.alignment));
3617 alignPanel.paintAlignment(true);
3621 sortByTreeMenu.add(item);
3626 * Work out whether the whole set of sequences or just the selected set will
3627 * be submitted for multiple alignment.
3630 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3632 // Now, check we have enough sequences
3633 AlignmentView msa = null;
3635 if ((viewport.getSelectionGroup() != null)
3636 && (viewport.getSelectionGroup().getSize() > 1))
3638 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3639 // some common interface!
3641 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3642 * SequenceI[sz = seqs.getSize(false)];
3644 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3645 * seqs.getSequenceAt(i); }
3647 msa = viewport.getAlignmentView(true);
3652 * Vector seqs = viewport.getAlignment().getSequences();
3654 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3656 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3657 * seqs.elementAt(i); } }
3659 msa = viewport.getAlignmentView(false);
3665 * Decides what is submitted to a secondary structure prediction service: the
3666 * first sequence in the alignment, or in the current selection, or, if the
3667 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3668 * region or the whole alignment. (where the first sequence in the set is the
3669 * one that the prediction will be for).
3671 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3673 AlignmentView seqs = null;
3675 if ((viewport.getSelectionGroup() != null)
3676 && (viewport.getSelectionGroup().getSize() > 0))
3678 seqs = viewport.getAlignmentView(true);
3682 seqs = viewport.getAlignmentView(false);
3684 // limit sequences - JBPNote in future - could spawn multiple prediction
3686 // TODO: viewport.alignment.isAligned is a global state - the local
3687 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3688 if (!viewport.alignment.isAligned(false))
3690 seqs.setSequences(new SeqCigar[]
3691 { seqs.getSequences()[0] });
3692 // TODO: if seqs.getSequences().length>1 then should really have warned
3705 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3707 // Pick the tree file
3708 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
3709 .getProperty("LAST_DIRECTORY"));
3710 chooser.setFileView(new JalviewFileView());
3711 chooser.setDialogTitle("Select a newick-like tree file");
3712 chooser.setToolTipText("Load a tree file");
3714 int value = chooser.showOpenDialog(null);
3716 if (value == JalviewFileChooser.APPROVE_OPTION)
3718 String choice = chooser.getSelectedFile().getPath();
3719 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3720 jalview.io.NewickFile fin = null;
3723 fin = new jalview.io.NewickFile(choice, "File");
3724 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3725 } catch (Exception ex)
3727 JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3728 "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
3729 ex.printStackTrace();
3731 if (fin != null && fin.hasWarningMessage())
3733 JOptionPane.showMessageDialog(Desktop.desktop, fin
3734 .getWarningMessage(), "Possible problem with tree file",
3735 JOptionPane.WARNING_MESSAGE);
3740 public TreePanel ShowNewickTree(NewickFile nf, String title)
3742 return ShowNewickTree(nf, title, 600, 500, 4, 5);
3745 public TreePanel ShowNewickTree(NewickFile nf, String title,
3746 AlignmentView input)
3748 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
3751 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
3752 int h, int x, int y)
3754 return ShowNewickTree(nf, title, null, w, h, x, y);
3758 * Add a treeviewer for the tree extracted from a newick file object to the
3759 * current alignment view
3766 * Associated alignment input data (or null)
3775 * @return TreePanel handle
3777 public TreePanel ShowNewickTree(NewickFile nf, String title,
3778 AlignmentView input, int w, int h, int x, int y)
3780 TreePanel tp = null;
3786 if (nf.getTree() != null)
3788 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
3794 tp.setLocation(x, y);
3797 Desktop.addInternalFrame(tp, title, w, h);
3799 } catch (Exception ex)
3801 ex.printStackTrace();
3807 private boolean buildingMenu = false;
3810 * Generates menu items and listener event actions for web service clients
3813 public void BuildWebServiceMenu()
3815 while (buildingMenu)
3819 System.err.println("Waiting for building menu to finish.");
3821 } catch (Exception e)
3826 buildingMenu = true;
3830 .println("Building ws menu again " + Thread.currentThread());
3831 // TODO: add support for context dependent disabling of services based on
3832 // alignment and current selection
3833 // TODO: add additional serviceHandle parameter to specify abstract
3835 // class independently of AbstractName
3836 // TODO: add in rediscovery GUI function to restart discoverer
3837 // TODO: group services by location as well as function and/or introduce
3838 // object broker mechanism.
3839 Vector wsmenu = new Vector();
3840 final IProgressIndicator af = this;
3841 if ((Discoverer.services != null) && (Discoverer.services.size() > 0))
3843 // TODO: refactor to allow list of AbstractName/Handler bindings to be
3844 // stored or retrieved from elsewhere
3845 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
3846 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
3847 Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
3848 // TODO: move GUI generation code onto service implementation - so a
3849 // client instance attaches itself to the GUI with method call like
3850 // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
3854 // Add any Multiple Sequence Alignment Services
3855 final JMenu msawsmenu = new JMenu("Alignment");
3856 for (int i = 0, j = msaws.size(); i < j; i++)
3858 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
3860 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
3861 .getServiceClient(sh);
3862 impl.attachWSMenuEntry(msawsmenu, this);
3865 wsmenu.add(msawsmenu);
3867 if (secstrpr != null)
3869 // Add any secondary structure prediction services
3870 final JMenu secstrmenu = new JMenu(
3871 "Secondary Structure Prediction");
3872 for (int i = 0, j = secstrpr.size(); i < j; i++)
3874 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
3876 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
3877 .getServiceClient(sh);
3878 impl.attachWSMenuEntry(secstrmenu, this);
3880 wsmenu.add(secstrmenu);
3882 if (seqsrch != null)
3884 // Add any sequence search services
3885 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
3886 for (int i = 0, j = seqsrch.size(); i < j; i++)
3888 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
3890 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
3891 .getServiceClient(sh);
3892 impl.attachWSMenuEntry(seqsrchmenu, this);
3894 wsmenu.add(seqsrchmenu);
3898 // TODO: move into separate menu builder class.
3900 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
3901 if (jws2servs != null)
3903 if (jws2servs.hasServices())
3905 JMenu jws2men = new JMenu("Jalview 2 Services");
3906 jws2servs.attachWSMenuEntry(jws2men, this);
3907 wsmenu.add(jws2men);
3911 if (!jws2servs.isRunning())
3913 new Thread(jws2servs).start();
3918 resetWebServiceMenu();
3919 // finally, add the whole shebang onto the webservices menu
3920 if (wsmenu.size() > 0)
3922 for (int i = 0, j = wsmenu.size(); i < j; i++)
3924 webService.add((JMenu) wsmenu.get(i));
3929 this.webService.add(this.webServiceNoServices);
3931 } catch (Exception e)
3935 buildingMenu = false;
3939 * empty the web service menu and add any ad-hoc functions not dynamically
3943 private void resetWebServiceMenu()
3945 webService.removeAll();
3946 build_fetchdbmenu(webService);
3947 build_urlServiceMenu(webService);
3951 * construct any groupURL type service menu entries.
3955 private void build_urlServiceMenu(JMenu webService)
3957 jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
3962 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
3963 * chooser = new JalviewFileChooser(jalview.bin.Cache.
3964 * getProperty("LAST_DIRECTORY"));
3966 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
3967 * to Vamsas file"); chooser.setToolTipText("Export");
3969 * int value = chooser.showSaveDialog(this);
3971 * if (value == JalviewFileChooser.APPROVE_OPTION) {
3972 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
3973 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
3974 * chooser.getSelectedFile().getAbsolutePath(), this); } }
3977 * prototype of an automatically enabled/disabled analysis function
3980 protected void setShowProductsEnabled()
3982 SequenceI[] selection = viewport.getSequenceSelection();
3983 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
3984 viewport.getAlignment().getDataset()))
3986 showProducts.setEnabled(true);
3991 showProducts.setEnabled(false);
3996 * search selection for sequence xRef products and build the show products
4001 * @return true if showProducts menu should be enabled.
4003 public boolean canShowProducts(SequenceI[] selection,
4004 boolean isRegionSelection, Alignment dataset)
4006 boolean showp = false;
4009 showProducts.removeAll();
4010 final boolean dna = viewport.getAlignment().isNucleotide();
4011 final Alignment ds = dataset;
4012 String[] ptypes = (selection == null || selection.length == 0) ? null
4013 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4015 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4016 // selection, dataset, true);
4017 final SequenceI[] sel = selection;
4018 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4021 final boolean isRegSel = isRegionSelection;
4022 final AlignFrame af = this;
4023 final String source = ptypes[t];
4024 JMenuItem xtype = new JMenuItem(ptypes[t]);
4025 xtype.addActionListener(new ActionListener()
4028 public void actionPerformed(ActionEvent e)
4030 // TODO: new thread for this call with vis-delay
4031 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4032 isRegSel, dna, source);
4036 showProducts.add(xtype);
4038 showProducts.setVisible(showp);
4039 showProducts.setEnabled(showp);
4040 } catch (Exception e)
4042 jalview.bin.Cache.log
4044 "canTranslate threw an exception - please report to help@jalview.org",
4051 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4052 boolean isRegSel, boolean dna, String source)
4054 final boolean fisRegSel = isRegSel;
4055 final boolean fdna = dna;
4056 final String fsrc = source;
4057 final AlignFrame ths = this;
4058 final SequenceI[] fsel = sel;
4059 Runnable foo = new Runnable()
4064 final long sttime = System.currentTimeMillis();
4065 ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4068 Alignment ds = ths.getViewport().alignment.getDataset(); // update
4072 Alignment prods = CrossRef
4073 .findXrefSequences(fsel, fdna, fsrc, ds);
4076 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4077 for (int s = 0; s < sprods.length; s++)
4079 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4080 if (ds.getSequences() == null
4081 || !ds.getSequences().contains(
4082 sprods[s].getDatasetSequence()))
4083 ds.addSequence(sprods[s].getDatasetSequence());
4084 sprods[s].updatePDBIds();
4086 Alignment al = new Alignment(sprods);
4087 AlignedCodonFrame[] cf = prods.getCodonFrames();
4089 for (int s = 0; cf != null && s < cf.length; s++)
4091 al.addCodonFrame(cf[s]);
4094 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4096 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4097 + " for " + ((fisRegSel) ? "selected region of " : "")
4099 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4104 System.err.println("No Sequences generated for xRef type "
4107 } catch (Exception e)
4109 jalview.bin.Cache.log.error(
4110 "Exception when finding crossreferences", e);
4111 } catch (OutOfMemoryError e)
4113 new OOMWarning("whilst fetching crossreferences", e);
4116 jalview.bin.Cache.log.error("Error when finding crossreferences",
4119 ths.setProgressBar("Finished searching for sequences from " + fsrc,
4124 Thread frunner = new Thread(foo);
4128 public boolean canShowTranslationProducts(SequenceI[] selection,
4129 AlignmentI alignment)
4134 return (jalview.analysis.Dna.canTranslate(selection, viewport
4135 .getViewAsVisibleContigs(true)));
4136 } catch (Exception e)
4138 jalview.bin.Cache.log
4140 "canTranslate threw an exception - please report to help@jalview.org",
4146 public void showProducts_actionPerformed(ActionEvent e)
4148 // /////////////////////////////
4149 // Collect Data to be translated/transferred
4151 SequenceI[] selection = viewport.getSequenceSelection();
4152 AlignmentI al = null;
4155 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4156 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4157 viewport.getAlignment().getDataset());
4158 } catch (Exception ex)
4161 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4168 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4169 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4173 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4174 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4175 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4179 public void showTranslation_actionPerformed(ActionEvent e)
4181 // /////////////////////////////
4182 // Collect Data to be translated/transferred
4184 SequenceI[] selection = viewport.getSequenceSelection();
4185 String[] seqstring = viewport.getViewAsString(true);
4186 AlignmentI al = null;
4189 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4190 viewport.getViewAsVisibleContigs(true), viewport
4191 .getGapCharacter(), viewport.alignment
4192 .getAlignmentAnnotation(), viewport.alignment
4193 .getWidth(), viewport.getAlignment().getDataset());
4194 } catch (Exception ex)
4197 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4204 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4205 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4209 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4210 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4211 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4216 * Try to load a features file onto the alignment.
4219 * contents or path to retrieve file
4221 * access mode of file (see jalview.io.AlignFile)
4222 * @return true if features file was parsed corectly.
4224 public boolean parseFeaturesFile(String file, String type)
4226 boolean featuresFile = false;
4229 featuresFile = new FeaturesFile(file, type).parse(viewport.alignment
4230 .getDataset(), alignPanel.seqPanel.seqCanvas
4231 .getFeatureRenderer().featureColours, false);
4232 } catch (Exception ex)
4234 ex.printStackTrace();
4239 viewport.showSequenceFeatures = true;
4240 showSeqFeatures.setSelected(true);
4241 if (alignPanel.seqPanel.seqCanvas.fr != null)
4243 // update the min/max ranges where necessary
4244 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4246 if (featureSettings != null)
4248 featureSettings.setTableData();
4250 alignPanel.paintAlignment(true);
4253 return featuresFile;
4256 public void dragEnter(DropTargetDragEvent evt)
4260 public void dragExit(DropTargetEvent evt)
4264 public void dragOver(DropTargetDragEvent evt)
4268 public void dropActionChanged(DropTargetDragEvent evt)
4272 public void drop(DropTargetDropEvent evt)
4274 Transferable t = evt.getTransferable();
4275 java.util.List files = null;
4279 DataFlavor uriListFlavor = new DataFlavor(
4280 "text/uri-list;class=java.lang.String");
4281 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4283 // Works on Windows and MacOSX
4284 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4285 files = (java.util.List) t
4286 .getTransferData(DataFlavor.javaFileListFlavor);
4288 else if (t.isDataFlavorSupported(uriListFlavor))
4290 // This is used by Unix drag system
4291 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4292 String data = (String) t.getTransferData(uriListFlavor);
4293 files = new java.util.ArrayList(1);
4294 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4295 data, "\r\n"); st.hasMoreTokens();)
4297 String s = st.nextToken();
4298 if (s.startsWith("#"))
4300 // the line is a comment (as per the RFC 2483)
4304 java.net.URI uri = new java.net.URI(s);
4305 // check to see if we can handle this kind of URI
4306 if (uri.getScheme().toLowerCase().startsWith("http"))
4308 files.add(uri.toString());
4312 // otherwise preserve old behaviour: catch all for file objects
4313 java.io.File file = new java.io.File(uri);
4314 files.add(file.toString());
4318 } catch (Exception e)
4320 e.printStackTrace();
4327 for (int i = 0; i < files.size(); i++)
4329 loadJalviewDataFile(files.get(i).toString());
4331 } catch (Exception ex)
4333 ex.printStackTrace();
4339 * Attempt to load a "dropped" file or URL string: First by testing whether
4340 * it's and Annotation file, then a JNet file, and finally a features file. If
4341 * all are false then the user may have dropped an alignment file onto this
4345 * either a filename or a URL string.
4347 public void loadJalviewDataFile(String file)
4351 String protocol = jalview.io.FormatAdapter.FILE;
4352 String f = file.toLowerCase();
4353 if (f.indexOf("http:") == 0 || f.indexOf("https:") == 0
4354 || f.indexOf("file:") == 0)
4356 protocol = jalview.io.FormatAdapter.URL;
4359 boolean isAnnotation = new AnnotationFile().readAnnotationFile(
4360 viewport.alignment, file, protocol);
4364 // try to see if its a JNet 'concise' style annotation file *before* we
4365 // try to parse it as a features file
4366 String format = new IdentifyFile().Identify(file, protocol);
4367 if (format.equalsIgnoreCase("JnetFile"))
4369 jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
4371 new JnetAnnotationMaker().add_annotation(predictions, viewport
4372 .getAlignment(), 0, false);
4373 isAnnotation = true;
4377 // try to parse it as a features file
4378 boolean isGroupsFile = parseFeaturesFile(file, protocol);
4379 // if it wasn't a features file then we just treat it as a general
4380 // alignment file to load into the current view.
4383 new FileLoader().LoadFile(viewport, file, protocol, format);
4387 alignPanel.paintAlignment(true);
4394 alignPanel.adjustAnnotationHeight();
4395 viewport.updateSequenceIdColours();
4396 buildSortByAnnotationScoresMenu();
4397 alignPanel.paintAlignment(true);
4399 } catch (Exception ex)
4401 ex.printStackTrace();
4405 public void tabSelectionChanged(int index)
4409 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
4410 viewport = alignPanel.av;
4411 setMenusFromViewport(viewport);
4415 public void tabbedPane_mousePressed(MouseEvent e)
4417 if (SwingUtilities.isRightMouseButton(e))
4419 String reply = JOptionPane.showInternalInputDialog(this,
4420 "Enter View Name", "Edit View Name",
4421 JOptionPane.QUESTION_MESSAGE);
4425 viewport.viewName = reply;
4426 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4431 public AlignViewport getCurrentView()
4437 * Open the dialog for regex description parsing.
4439 protected void extractScores_actionPerformed(ActionEvent e)
4441 ParseProperties pp = new jalview.analysis.ParseProperties(
4442 viewport.alignment);
4443 // TODO: verify regex and introduce GUI dialog for version 2.5
4444 // if (pp.getScoresFromDescription("col", "score column ",
4445 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4447 if (pp.getScoresFromDescription("description column",
4448 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4450 buildSortByAnnotationScoresMenu();
4458 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4461 protected void showDbRefs_actionPerformed(ActionEvent e)
4463 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
4469 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4472 protected void showNpFeats_actionPerformed(ActionEvent e)
4474 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
4478 * find the viewport amongst the tabs in this alignment frame and close that
4483 public boolean closeView(AlignViewport av)
4487 this.closeMenuItem_actionPerformed(false);
4490 Component[] comp = tabbedPane.getComponents();
4491 for (int i = 0; comp != null && i < comp.length; i++)
4493 if (comp[i] instanceof AlignmentPanel)
4495 if (((AlignmentPanel) comp[i]).av == av)
4498 closeView((AlignmentPanel) comp[i]);
4506 protected void build_fetchdbmenu(JMenu webService)
4508 // Temporary hack - DBRef Fetcher always top level ws entry.
4509 // TODO We probably want to store a sequence database checklist in
4510 // preferences and have checkboxes.. rather than individual sources selected
4512 JMenu rfetch = new JMenu("Fetch DB References");
4514 .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
4515 webService.add(rfetch);
4517 JMenuItem fetchr = new JMenuItem("Standard Databases");
4519 .setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
4520 fetchr.addActionListener(new ActionListener()
4523 public void actionPerformed(ActionEvent e)
4525 new Thread(new Runnable()
4530 new jalview.ws.DBRefFetcher(alignPanel.av
4531 .getSequenceSelection(), alignPanel.alignFrame)
4532 .fetchDBRefs(false);
4540 JMenu dfetch = new JMenu();
4542 jalview.ws.SequenceFetcher sf = SequenceFetcher
4543 .getSequenceFetcherSingleton(this);
4544 String[] otherdb = sf.getOrderedSupportedSources();
4545 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4546 // jalview.util.QuickSort.sort(otherdb, otherdb);
4547 int comp = 0, mcomp = 15;
4548 String mname = null;
4549 if (otherdb != null && otherdb.length > 0)
4551 for (int i = 0; i < otherdb.length; i++)
4553 String dbname = sf.getSourceProxy(otherdb[i]).getDbName();
4556 mname = "from '" + dbname + "'";
4558 fetchr = new JMenuItem(otherdb[i]);
4559 final String[] dassource = new String[]
4561 fetchr.addActionListener(new ActionListener()
4564 public void actionPerformed(ActionEvent e)
4566 new Thread(new Runnable()
4571 new jalview.ws.DBRefFetcher(alignPanel.av
4572 .getSequenceSelection(), alignPanel.alignFrame,
4573 dassource).fetchDBRefs(false);
4579 fetchr.setToolTipText("Retrieve from " + dbname);
4581 if (comp++ == mcomp || i == (otherdb.length - 1))
4583 dfetch.setText(mname + " to '" + dbname + "'");
4585 dfetch = new JMenu();
4594 * Left justify the whole alignment.
4596 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
4598 AlignmentI al = viewport.getAlignment();
4600 viewport.firePropertyChange("alignment", null, al);
4604 * Right justify the whole alignment.
4606 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
4608 AlignmentI al = viewport.getAlignment();
4610 viewport.firePropertyChange("alignment", null, al);
4613 public void setShowSeqFeatures(boolean b)
4615 showSeqFeatures.setSelected(true);
4616 viewport.setShowSequenceFeatures(true);
4623 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
4624 * awt.event.ActionEvent)
4626 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
4628 viewport.setShowUnconserved(showUnconservedMenuItem.getState());
4629 alignPanel.paintAlignment(true);
4636 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
4639 protected void showGroupConsensus_actionPerformed(ActionEvent e)
4641 viewport.setShowGroupConsensus(showGroupConsensus.getState());
4642 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4650 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
4651 * .event.ActionEvent)
4653 protected void showGroupConservation_actionPerformed(ActionEvent e)
4655 viewport.setShowGroupConservation(showGroupConservation.getState());
4656 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4663 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
4664 * .event.ActionEvent)
4666 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
4668 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
4669 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4676 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
4677 * .event.ActionEvent)
4679 protected void showSequenceLogo_actionPerformed(ActionEvent e)
4681 viewport.setShowSequenceLogo(showSequenceLogo.getState());
4682 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4685 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
4687 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4694 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
4695 * .event.ActionEvent)
4697 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
4699 if (viewport.getSelectionGroup() != null)
4701 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
4702 viewport.getSequenceSelection(), viewport.getAlignmentView(
4703 true).getSequenceStrings(viewport.getGapCharacter()),
4704 viewport.alignment.getGroups());
4705 viewport.alignment.deleteAllGroups();
4706 viewport.sequenceColours = null;
4707 viewport.setSelectionGroup(null);
4708 // set view properties for each group
4709 for (int g = 0; g < gps.length; g++)
4711 gps[g].setShowunconserved(viewport.getShowUnconserved());
4712 gps[g].setIncludeAllConsSymbols(viewport
4713 .isIncludeAllConsensusSymbols());
4714 viewport.alignment.addGroup(gps[g]);
4715 Color col = new Color((int) (Math.random() * 255), (int) (Math
4716 .random() * 255), (int) (Math.random() * 255));
4717 col = col.brighter();
4718 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
4719 .hasMoreElements(); viewport.setSequenceColour(
4720 (SequenceI) sq.nextElement(), col))
4723 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
4724 alignPanel.updateAnnotation();
4725 alignPanel.paintAlignment(true);
4730 class PrintThread extends Thread
4734 public PrintThread(AlignmentPanel ap)
4739 static PageFormat pf;
4743 PrinterJob printJob = PrinterJob.getPrinterJob();
4747 printJob.setPrintable(ap, pf);
4751 printJob.setPrintable(ap);
4754 if (printJob.printDialog())
4759 } catch (Exception PrintException)
4761 PrintException.printStackTrace();