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()
535 .println("Change support JWS1: build services again.");
536 BuildWebServiceMenu();
543 jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
544 .addPropertyChangeListener(
545 thatListener = new java.beans.PropertyChangeListener()
547 public void propertyChange(PropertyChangeEvent evt)
550 .println("Change support JWS2: build services again.");
551 BuildWebServiceMenu();
554 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
556 public void internalFrameClosed(
557 javax.swing.event.InternalFrameEvent evt)
559 // System.out.println("deregistering discoverer listener");
560 Desktop.discoverer.removePropertyChangeListener(thisListener);
561 jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
562 .removePropertyChangeListener(thatListener);
563 closeMenuItem_actionPerformed(true);
568 public void setGUINucleotide(boolean nucleotide)
570 showTranslation.setVisible(nucleotide);
571 conservationMenuItem.setEnabled(!nucleotide);
572 modifyConservation.setEnabled(!nucleotide);
573 showGroupConservation.setEnabled(!nucleotide);
574 // Remember AlignFrame always starts as protein
577 calculateMenu.remove(calculateMenu.getItemCount() - 2);
582 * set up menus for the currently viewport. This may be called after any
583 * operation that affects the data in the current view (selection changed,
584 * etc) to update the menus to reflect the new state.
586 public void setMenusForViewport()
588 setMenusFromViewport(viewport);
592 * Need to call this method when tabs are selected for multiple views, or when
593 * loading from Jalview2XML.java
598 void setMenusFromViewport(AlignViewport av)
600 padGapsMenuitem.setSelected(av.padGaps);
601 colourTextMenuItem.setSelected(av.showColourText);
602 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
603 conservationMenuItem.setSelected(av.getConservationSelected());
604 seqLimits.setSelected(av.getShowJVSuffix());
605 idRightAlign.setSelected(av.rightAlignIds);
606 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
607 renderGapsMenuItem.setSelected(av.renderGaps);
608 wrapMenuItem.setSelected(av.wrapAlignment);
609 scaleAbove.setVisible(av.wrapAlignment);
610 scaleLeft.setVisible(av.wrapAlignment);
611 scaleRight.setVisible(av.wrapAlignment);
612 annotationPanelMenuItem.setState(av.showAnnotation);
613 viewBoxesMenuItem.setSelected(av.showBoxes);
614 viewTextMenuItem.setSelected(av.showText);
615 showNonconservedMenuItem.setSelected(av.showUnconserved);
616 showGroupConsensus.setSelected(av.showGroupConsensus);
617 showGroupConservation.setSelected(av.showGroupConservation);
618 showConsensusHistogram.setSelected(av.showConsensusHistogram);
619 showSequenceLogo.setSelected(av.showSequenceLogo);
620 setColourSelected(ColourSchemeProperty.getColourName(av
621 .getGlobalColourScheme()));
623 showSeqFeatures.setSelected(av.showSequenceFeatures);
624 hiddenMarkers.setState(av.showHiddenMarkers);
625 applyToAllGroups.setState(av.colourAppliesToAllGroups);
626 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
627 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
629 setShowProductsEnabled();
634 Hashtable progressBars, progressBarHandlers;
639 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
641 public void setProgressBar(String message, long id)
643 if (progressBars == null)
645 progressBars = new Hashtable();
646 progressBarHandlers = new Hashtable();
649 JPanel progressPanel;
650 Long lId = new Long(id);
651 GridLayout layout = (GridLayout) statusPanel.getLayout();
652 if (progressBars.get(lId) != null)
654 progressPanel = (JPanel) progressBars.get(new Long(id));
655 statusPanel.remove(progressPanel);
656 progressBars.remove(lId);
657 progressPanel = null;
660 statusBar.setText(message);
662 if (progressBarHandlers.contains(lId))
664 progressBarHandlers.remove(lId);
666 layout.setRows(layout.getRows() - 1);
670 progressPanel = new JPanel(new BorderLayout(10, 5));
672 JProgressBar progressBar = new JProgressBar();
673 progressBar.setIndeterminate(true);
675 progressPanel.add(new JLabel(message), BorderLayout.WEST);
676 progressPanel.add(progressBar, BorderLayout.CENTER);
678 layout.setRows(layout.getRows() + 1);
679 statusPanel.add(progressPanel);
681 progressBars.put(lId, progressPanel);
684 setMenusForViewport();
688 public void registerHandler(final long id,
689 final IProgressIndicatorHandler handler)
691 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
694 "call setProgressBar before registering the progress bar's handler.");
696 progressBarHandlers.put(new Long(id), handler);
697 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
698 if (handler.canCancel())
700 JButton cancel = new JButton("Cancel");
701 final IProgressIndicator us = this;
702 cancel.addActionListener(new ActionListener()
705 public void actionPerformed(ActionEvent e)
707 handler.cancelActivity(id);
708 us.setProgressBar("Cancelled "
709 + ((JLabel) progressPanel.getComponent(0)).getText(), id);
712 progressPanel.add(cancel, BorderLayout.EAST);
718 * @return true if any progress bars are still active
720 public boolean operationInProgress()
722 if (progressBars != null && progressBars.size() > 0)
730 * Added so Castor Mapping file can obtain Jalview Version
732 public String getVersion()
734 return jalview.bin.Cache.getProperty("VERSION");
737 public FeatureRenderer getFeatureRenderer()
739 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
742 public void fetchSequence_actionPerformed(ActionEvent e)
744 new SequenceFetcher(this);
747 public void addFromFile_actionPerformed(ActionEvent e)
749 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
752 public void reload_actionPerformed(ActionEvent e)
754 if (fileName != null)
756 // TODO: work out how to recover feature settings for correct view(s) when
758 if (currentFileFormat.equals("Jalview"))
760 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
761 for (int i = 0; i < frames.length; i++)
763 if (frames[i] instanceof AlignFrame && frames[i] != this
764 && ((AlignFrame) frames[i]).fileName.equals(fileName))
768 frames[i].setSelected(true);
769 Desktop.instance.closeAssociatedWindows();
770 } catch (java.beans.PropertyVetoException ex)
776 Desktop.instance.closeAssociatedWindows();
778 FileLoader loader = new FileLoader();
779 String protocol = fileName.startsWith("http:") ? "URL" : "File";
780 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
784 Rectangle bounds = this.getBounds();
786 FileLoader loader = new FileLoader();
787 String protocol = fileName.startsWith("http:") ? "URL" : "File";
788 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
789 protocol, currentFileFormat);
791 newframe.setBounds(bounds);
792 if (featureSettings != null && featureSettings.isShowing())
794 final Rectangle fspos = featureSettings.frame.getBounds();
795 // TODO: need a 'show feature settings' function that takes bounds -
796 // need to refactor Desktop.addFrame
797 newframe.featureSettings_actionPerformed(null);
798 final FeatureSettings nfs = newframe.featureSettings;
799 SwingUtilities.invokeLater(new Runnable()
803 nfs.frame.setBounds(fspos);
806 this.featureSettings.close();
807 this.featureSettings = null;
809 this.closeMenuItem_actionPerformed(true);
814 public void addFromText_actionPerformed(ActionEvent e)
816 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
819 public void addFromURL_actionPerformed(ActionEvent e)
821 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
824 public void save_actionPerformed(ActionEvent e)
827 || (currentFileFormat == null || !jalview.io.FormatAdapter
828 .isValidIOFormat(currentFileFormat, true))
829 || fileName.startsWith("http"))
831 saveAs_actionPerformed(null);
835 saveAlignment(fileName, currentFileFormat);
845 public void saveAs_actionPerformed(ActionEvent e)
847 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
848 .getProperty("LAST_DIRECTORY"),
849 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
850 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
851 currentFileFormat, false);
853 chooser.setFileView(new JalviewFileView());
854 chooser.setDialogTitle("Save Alignment to file");
855 chooser.setToolTipText("Save");
857 int value = chooser.showSaveDialog(this);
859 if (value == JalviewFileChooser.APPROVE_OPTION)
861 currentFileFormat = chooser.getSelectedFormat();
862 if (currentFileFormat == null)
864 JOptionPane.showInternalMessageDialog(Desktop.desktop,
865 "You must select a file format before saving!",
866 "File format not specified", JOptionPane.WARNING_MESSAGE);
867 value = chooser.showSaveDialog(this);
871 fileName = chooser.getSelectedFile().getPath();
873 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
876 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
877 if (currentFileFormat.indexOf(" ") > -1)
879 currentFileFormat = currentFileFormat.substring(0,
880 currentFileFormat.indexOf(" "));
882 saveAlignment(fileName, currentFileFormat);
886 public boolean saveAlignment(String file, String format)
888 boolean success = true;
890 if (format.equalsIgnoreCase("Jalview"))
892 String shortName = title;
894 if (shortName.indexOf(java.io.File.separatorChar) > -1)
896 shortName = shortName.substring(shortName
897 .lastIndexOf(java.io.File.separatorChar) + 1);
900 success = new Jalview2XML().SaveAlignment(this, file, shortName);
902 statusBar.setText("Successfully saved to file: " + fileName + " in "
903 + format + " format.");
908 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
910 warningMessage("Cannot save file " + fileName + " using format "
911 + format, "Alignment output format not supported");
912 saveAs_actionPerformed(null);
913 // JBPNote need to have a raise_gui flag here
917 String[] omitHidden = null;
919 if (viewport.hasHiddenColumns)
921 int reply = JOptionPane
922 .showInternalConfirmDialog(
924 "The Alignment contains hidden columns."
925 + "\nDo you want to save only the visible alignment?",
926 "Save / Omit Hidden Columns",
927 JOptionPane.YES_NO_OPTION,
928 JOptionPane.QUESTION_MESSAGE);
930 if (reply == JOptionPane.YES_OPTION)
932 omitHidden = viewport.getViewAsString(false);
935 FormatAdapter f = new FormatAdapter();
936 String output = f.formatSequences(format,
937 (Alignment) viewport.alignment, // class cast exceptions will
938 // occur in the distant future
939 omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
949 java.io.PrintWriter out = new java.io.PrintWriter(
950 new java.io.FileWriter(file));
955 statusBar.setText("Successfully saved to file: " + fileName
956 + " in " + format + " format.");
957 } catch (Exception ex)
960 ex.printStackTrace();
967 JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
968 + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
974 private void warningMessage(String warning, String title)
976 if (new jalview.util.Platform().isHeadless())
978 System.err.println("Warning: " + title + "\nWarning: " + warning);
983 JOptionPane.showInternalMessageDialog(this, warning, title,
984 JOptionPane.WARNING_MESSAGE);
995 protected void outputText_actionPerformed(ActionEvent e)
997 String[] omitHidden = null;
999 if (viewport.hasHiddenColumns)
1001 int reply = JOptionPane
1002 .showInternalConfirmDialog(
1004 "The Alignment contains hidden columns."
1005 + "\nDo you want to output only the visible alignment?",
1006 "Save / Omit Hidden Columns",
1007 JOptionPane.YES_NO_OPTION,
1008 JOptionPane.QUESTION_MESSAGE);
1010 if (reply == JOptionPane.YES_OPTION)
1012 omitHidden = viewport.getViewAsString(false);
1016 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1017 cap.setForInput(null);
1018 Desktop.addInternalFrame(cap, "Alignment output - "
1019 + e.getActionCommand(), 600, 500);
1021 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1022 viewport.alignment, omitHidden, viewport.colSel));
1031 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1033 new HTMLOutput(alignPanel, alignPanel.seqPanel.seqCanvas
1034 .getSequenceRenderer(), alignPanel.seqPanel.seqCanvas
1035 .getFeatureRenderer());
1038 public void createImageMap(File file, String image)
1040 alignPanel.makePNGImageMap(file, image);
1049 public void createPNG(File f)
1051 alignPanel.makePNG(f);
1060 public void createEPS(File f)
1062 alignPanel.makeEPS(f);
1065 public void pageSetup_actionPerformed(ActionEvent e)
1067 PrinterJob printJob = PrinterJob.getPrinterJob();
1068 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1077 public void printMenuItem_actionPerformed(ActionEvent e)
1079 // Putting in a thread avoids Swing painting problems
1080 PrintThread thread = new PrintThread(alignPanel);
1084 public void exportFeatures_actionPerformed(ActionEvent e)
1086 new AnnotationExporter().exportFeatures(alignPanel);
1089 public void exportAnnotations_actionPerformed(ActionEvent e)
1091 new AnnotationExporter().exportAnnotations(alignPanel,
1092 viewport.showAnnotation ? viewport.alignment
1093 .getAlignmentAnnotation() : null, viewport.alignment
1095 ((Alignment) viewport.alignment).alignmentProperties);
1098 public void associatedData_actionPerformed(ActionEvent e)
1100 // Pick the tree file
1101 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
1102 .getProperty("LAST_DIRECTORY"));
1103 chooser.setFileView(new JalviewFileView());
1104 chooser.setDialogTitle("Load Jalview Annotations or Features File");
1105 chooser.setToolTipText("Load Jalview Annotations / Features file");
1107 int value = chooser.showOpenDialog(null);
1109 if (value == JalviewFileChooser.APPROVE_OPTION)
1111 String choice = chooser.getSelectedFile().getPath();
1112 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1113 loadJalviewDataFile(choice);
1119 * Close the current view or all views in the alignment frame. If the frame
1120 * only contains one view then the alignment will be removed from memory.
1122 * @param closeAllTabs
1124 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1126 if (alignPanels != null && alignPanels.size() < 2)
1128 closeAllTabs = true;
1133 if (alignPanels != null)
1137 if (this.isClosed())
1139 // really close all the windows - otherwise wait till
1140 // setClosed(true) is called
1141 for (int i = 0; i < alignPanels.size(); i++)
1143 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1150 closeView(alignPanel);
1156 this.setClosed(true);
1158 } catch (Exception ex)
1160 ex.printStackTrace();
1165 * close alignPanel2 and shuffle tabs appropriately.
1167 * @param alignPanel2
1169 public void closeView(AlignmentPanel alignPanel2)
1171 int index = tabbedPane.getSelectedIndex();
1172 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1173 alignPanels.removeElement(alignPanel2);
1175 // if (viewport == alignPanel2.av)
1179 alignPanel2.closePanel();
1182 tabbedPane.removeTabAt(closedindex);
1183 tabbedPane.validate();
1185 if (index > closedindex || index == tabbedPane.getTabCount())
1187 // modify currently selected tab index if necessary.
1191 this.tabSelectionChanged(index);
1197 void updateEditMenuBar()
1200 if (viewport.historyList.size() > 0)
1202 undoMenuItem.setEnabled(true);
1203 CommandI command = (CommandI) viewport.historyList.peek();
1204 undoMenuItem.setText("Undo " + command.getDescription());
1208 undoMenuItem.setEnabled(false);
1209 undoMenuItem.setText("Undo");
1212 if (viewport.redoList.size() > 0)
1214 redoMenuItem.setEnabled(true);
1216 CommandI command = (CommandI) viewport.redoList.peek();
1217 redoMenuItem.setText("Redo " + command.getDescription());
1221 redoMenuItem.setEnabled(false);
1222 redoMenuItem.setText("Redo");
1226 public void addHistoryItem(CommandI command)
1228 if (command.getSize() > 0)
1230 viewport.historyList.push(command);
1231 viewport.redoList.clear();
1232 updateEditMenuBar();
1233 viewport.hasHiddenColumns = (viewport.colSel != null
1234 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1235 .getHiddenColumns().size() > 0);
1241 * @return alignment objects for all views
1243 AlignmentI[] getViewAlignments()
1245 if (alignPanels != null)
1247 Enumeration e = alignPanels.elements();
1248 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1249 for (int i = 0; e.hasMoreElements(); i++)
1251 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1255 if (viewport != null)
1257 return new AlignmentI[]
1258 { viewport.alignment };
1269 protected void undoMenuItem_actionPerformed(ActionEvent e)
1271 if (viewport.historyList.empty())
1273 CommandI command = (CommandI) viewport.historyList.pop();
1274 viewport.redoList.push(command);
1275 command.undoCommand(getViewAlignments());
1277 AlignViewport originalSource = getOriginatingSource(command);
1278 updateEditMenuBar();
1280 if (originalSource != null)
1282 originalSource.hasHiddenColumns = (viewport.colSel != null
1283 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1284 .getHiddenColumns().size() > 0);
1285 originalSource.firePropertyChange("alignment", null,
1286 originalSource.alignment.getSequences());
1296 protected void redoMenuItem_actionPerformed(ActionEvent e)
1298 if (viewport.redoList.size() < 1)
1303 CommandI command = (CommandI) viewport.redoList.pop();
1304 viewport.historyList.push(command);
1305 command.doCommand(getViewAlignments());
1307 AlignViewport originalSource = getOriginatingSource(command);
1308 updateEditMenuBar();
1310 if (originalSource != null)
1312 originalSource.hasHiddenColumns = (viewport.colSel != null
1313 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1314 .getHiddenColumns().size() > 0);
1315 originalSource.firePropertyChange("alignment", null,
1316 originalSource.alignment.getSequences());
1320 AlignViewport getOriginatingSource(CommandI command)
1322 AlignViewport originalSource = null;
1323 // For sequence removal and addition, we need to fire
1324 // the property change event FROM the viewport where the
1325 // original alignment was altered
1326 AlignmentI al = null;
1327 if (command instanceof EditCommand)
1329 EditCommand editCommand = (EditCommand) command;
1330 al = editCommand.getAlignment();
1331 Vector comps = (Vector) PaintRefresher.components.get(viewport
1332 .getSequenceSetId());
1334 for (int i = 0; i < comps.size(); i++)
1336 if (comps.elementAt(i) instanceof AlignmentPanel)
1338 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
1340 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1347 if (originalSource == null)
1349 // The original view is closed, we must validate
1350 // the current view against the closed view first
1353 PaintRefresher.validateSequences(al, viewport.alignment);
1356 originalSource = viewport;
1359 return originalSource;
1368 public void moveSelectedSequences(boolean up)
1370 SequenceGroup sg = viewport.getSelectionGroup();
1379 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1381 SequenceI seq = viewport.alignment.getSequenceAt(i);
1383 if (!sg.getSequences(null).contains(seq))
1388 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1390 if (sg.getSequences(null).contains(temp))
1395 viewport.alignment.getSequences().setElementAt(temp, i);
1396 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1401 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1403 SequenceI seq = viewport.alignment.getSequenceAt(i);
1405 if (!sg.getSequences(null).contains(seq))
1410 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1412 if (sg.getSequences(null).contains(temp))
1417 viewport.alignment.getSequences().setElementAt(temp, i);
1418 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1422 alignPanel.paintAlignment(true);
1425 synchronized void slideSequences(boolean right, int size)
1427 Vector sg = new Vector();
1428 if (viewport.cursorMode)
1430 sg.addElement(viewport.alignment
1431 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1433 else if (viewport.getSelectionGroup() != null
1434 && viewport.getSelectionGroup().getSize() != viewport.alignment
1437 sg = viewport.getSelectionGroup().getSequences(
1438 viewport.hiddenRepSequences);
1446 Vector invertGroup = new Vector();
1448 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1450 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
1451 invertGroup.add(viewport.alignment.getSequenceAt(i));
1454 SequenceI[] seqs1 = new SequenceI[sg.size()];
1455 for (int i = 0; i < sg.size(); i++)
1456 seqs1[i] = (SequenceI) sg.elementAt(i);
1458 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1459 for (int i = 0; i < invertGroup.size(); i++)
1460 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1462 SlideSequencesCommand ssc;
1464 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1465 size, viewport.getGapCharacter());
1467 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1468 size, viewport.getGapCharacter());
1470 int groupAdjustment = 0;
1471 if (ssc.getGapsInsertedBegin() && right)
1473 if (viewport.cursorMode)
1474 alignPanel.seqPanel.moveCursor(size, 0);
1476 groupAdjustment = size;
1478 else if (!ssc.getGapsInsertedBegin() && !right)
1480 if (viewport.cursorMode)
1481 alignPanel.seqPanel.moveCursor(-size, 0);
1483 groupAdjustment = -size;
1486 if (groupAdjustment != 0)
1488 viewport.getSelectionGroup().setStartRes(
1489 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1490 viewport.getSelectionGroup().setEndRes(
1491 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1494 boolean appendHistoryItem = false;
1495 if (viewport.historyList != null && viewport.historyList.size() > 0
1496 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1498 appendHistoryItem = ssc
1499 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1503 if (!appendHistoryItem)
1504 addHistoryItem(ssc);
1515 protected void copy_actionPerformed(ActionEvent e)
1518 if (viewport.getSelectionGroup() == null)
1522 // TODO: preserve the ordering of displayed alignment annotation in any
1523 // internal paste (particularly sequence associated annotation)
1524 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1525 String[] omitHidden = null;
1527 if (viewport.hasHiddenColumns)
1529 omitHidden = viewport.getViewAsString(true);
1532 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1535 StringSelection ss = new StringSelection(output);
1539 jalview.gui.Desktop.internalCopy = true;
1540 // Its really worth setting the clipboard contents
1541 // to empty before setting the large StringSelection!!
1542 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
1543 new StringSelection(""), null);
1545 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1547 } catch (OutOfMemoryError er)
1549 new OOMWarning("copying region", er);
1553 Vector hiddenColumns = null;
1554 if (viewport.hasHiddenColumns)
1556 hiddenColumns = new Vector();
1557 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1558 .getSelectionGroup().getEndRes();
1559 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1562 int[] region = (int[]) viewport.getColumnSelection()
1563 .getHiddenColumns().elementAt(i);
1564 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1566 hiddenColumns.addElement(new int[]
1567 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1572 Desktop.jalviewClipboard = new Object[]
1573 { seqs, viewport.alignment.getDataset(), hiddenColumns };
1574 statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
1583 protected void pasteNew_actionPerformed(ActionEvent e)
1594 protected void pasteThis_actionPerformed(ActionEvent e)
1600 * Paste contents of Jalview clipboard
1602 * @param newAlignment
1603 * true to paste to a new alignment, otherwise add to this.
1605 void paste(boolean newAlignment)
1607 boolean externalPaste = true;
1610 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1611 Transferable contents = c.getContents(this);
1613 if (contents == null)
1621 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1622 if (str.length() < 1)
1627 format = new IdentifyFile().Identify(str, "Paste");
1629 } catch (OutOfMemoryError er)
1631 new OOMWarning("Out of memory pasting sequences!!", er);
1635 SequenceI[] sequences;
1636 boolean annotationAdded = false;
1637 AlignmentI alignment = null;
1639 if (Desktop.jalviewClipboard != null)
1641 // The clipboard was filled from within Jalview, we must use the
1643 // And dataset from the copied alignment
1644 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1645 // be doubly sure that we create *new* sequence objects.
1646 sequences = new SequenceI[newseq.length];
1647 for (int i = 0; i < newseq.length; i++)
1649 sequences[i] = new Sequence(newseq[i]);
1651 alignment = new Alignment(sequences);
1652 externalPaste = false;
1656 // parse the clipboard as an alignment.
1657 alignment = new FormatAdapter().readFile(str, "Paste", format);
1658 sequences = alignment.getSequencesArray();
1666 if (Desktop.jalviewClipboard != null)
1668 // dataset is inherited
1669 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1673 // new dataset is constructed
1674 alignment.setDataset(null);
1676 alwidth = alignment.getWidth() + 1;
1680 AlignmentI pastedal = alignment; // preserve pasted alignment object
1681 // Add pasted sequences and dataset into existing alignment.
1682 alignment = viewport.getAlignment();
1683 alwidth = alignment.getWidth() + 1;
1684 // decide if we need to import sequences from an existing dataset
1685 boolean importDs = Desktop.jalviewClipboard != null
1686 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1687 // importDs==true instructs us to copy over new dataset sequences from
1688 // an existing alignment
1689 Vector newDs = (importDs) ? new Vector() : null; // used to create
1690 // minimum dataset set
1692 for (int i = 0; i < sequences.length; i++)
1696 newDs.addElement(null);
1698 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1700 if (importDs && ds != null)
1702 if (!newDs.contains(ds))
1704 newDs.setElementAt(ds, i);
1705 ds = new Sequence(ds);
1706 // update with new dataset sequence
1707 sequences[i].setDatasetSequence(ds);
1711 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1716 // copy and derive new dataset sequence
1717 sequences[i] = sequences[i].deriveSequence();
1718 alignment.getDataset().addSequence(
1719 sequences[i].getDatasetSequence());
1720 // TODO: avoid creation of duplicate dataset sequences with a
1721 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1723 alignment.addSequence(sequences[i]); // merges dataset
1727 newDs.clear(); // tidy up
1729 if (pastedal.getAlignmentAnnotation() != null)
1731 // Add any annotation attached to alignment.
1732 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1733 for (int i = 0; i < alann.length; i++)
1735 annotationAdded = true;
1736 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1738 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1739 newann.padAnnotation(alwidth);
1740 alignment.addAnnotation(newann);
1750 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1751 sequences, 0, alignment.getWidth(), alignment));
1753 // Add any annotations attached to sequences
1754 for (int i = 0; i < sequences.length; i++)
1756 if (sequences[i].getAnnotation() != null)
1758 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1760 annotationAdded = true;
1761 sequences[i].getAnnotation()[a].adjustForAlignment();
1762 sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1763 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1768 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1775 // propagate alignment changed.
1776 viewport.setEndSeq(alignment.getHeight());
1777 if (annotationAdded)
1779 // Duplicate sequence annotation in all views.
1780 AlignmentI[] alview = this.getViewAlignments();
1781 for (int i = 0; i < sequences.length; i++)
1783 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1786 for (int avnum = 0; avnum < alview.length; avnum++)
1788 if (alview[avnum] != alignment)
1790 // duplicate in a view other than the one with input focus
1791 int avwidth = alview[avnum].getWidth() + 1;
1792 // this relies on sann being preserved after we
1793 // modify the sequence's annotation array for each duplication
1794 for (int a = 0; a < sann.length; a++)
1796 AlignmentAnnotation newann = new AlignmentAnnotation(
1798 sequences[i].addAlignmentAnnotation(newann);
1799 newann.padAnnotation(avwidth);
1800 alview[avnum].addAnnotation(newann); // annotation was
1801 // duplicated earlier
1802 alview[avnum].setAnnotationIndex(newann, a);
1807 buildSortByAnnotationScoresMenu();
1809 viewport.firePropertyChange("alignment", null, alignment
1815 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
1817 String newtitle = new String("Copied sequences");
1819 if (Desktop.jalviewClipboard != null
1820 && Desktop.jalviewClipboard[2] != null)
1822 Vector hc = (Vector) Desktop.jalviewClipboard[2];
1823 for (int i = 0; i < hc.size(); i++)
1825 int[] region = (int[]) hc.elementAt(i);
1826 af.viewport.hideColumns(region[0], region[1]);
1830 // >>>This is a fix for the moment, until a better solution is
1832 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
1834 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1836 // TODO: maintain provenance of an alignment, rather than just make the
1837 // title a concatenation of operations.
1840 if (title.startsWith("Copied sequences"))
1846 newtitle = newtitle.concat("- from " + title);
1851 newtitle = new String("Pasted sequences");
1854 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1859 } catch (Exception ex)
1861 ex.printStackTrace();
1862 System.out.println("Exception whilst pasting: " + ex);
1863 // could be anything being pasted in here
1874 protected void cut_actionPerformed(ActionEvent e)
1876 copy_actionPerformed(null);
1877 delete_actionPerformed(null);
1886 protected void delete_actionPerformed(ActionEvent evt)
1889 SequenceGroup sg = viewport.getSelectionGroup();
1895 Vector seqs = new Vector();
1897 for (int i = 0; i < sg.getSize(); i++)
1899 seq = sg.getSequenceAt(i);
1900 seqs.addElement(seq);
1903 // If the cut affects all sequences, remove highlighted columns
1904 if (sg.getSize() == viewport.alignment.getHeight())
1906 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1907 sg.getEndRes() + 1);
1910 SequenceI[] cut = new SequenceI[seqs.size()];
1911 for (int i = 0; i < seqs.size(); i++)
1913 cut[i] = (SequenceI) seqs.elementAt(i);
1917 * //ADD HISTORY ITEM
1919 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1920 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1921 viewport.alignment));
1923 viewport.setSelectionGroup(null);
1924 viewport.sendSelection();
1925 viewport.alignment.deleteGroup(sg);
1927 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1929 if (viewport.getAlignment().getHeight() < 1)
1933 this.setClosed(true);
1934 } catch (Exception ex)
1946 protected void deleteGroups_actionPerformed(ActionEvent e)
1948 viewport.alignment.deleteAllGroups();
1949 viewport.sequenceColours = null;
1950 viewport.setSelectionGroup(null);
1951 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1952 alignPanel.updateAnnotation();
1953 alignPanel.paintAlignment(true);
1962 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1964 SequenceGroup sg = new SequenceGroup();
1966 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1968 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1971 sg.setEndRes(viewport.alignment.getWidth() - 1);
1972 viewport.setSelectionGroup(sg);
1973 viewport.sendSelection();
1974 alignPanel.paintAlignment(true);
1975 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1984 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1986 if (viewport.cursorMode)
1988 alignPanel.seqPanel.keyboardNo1 = null;
1989 alignPanel.seqPanel.keyboardNo2 = null;
1991 viewport.setSelectionGroup(null);
1992 viewport.getColumnSelection().clear();
1993 viewport.setSelectionGroup(null);
1994 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1995 alignPanel.idPanel.idCanvas.searchResults = null;
1996 alignPanel.paintAlignment(true);
1997 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2006 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2008 SequenceGroup sg = viewport.getSelectionGroup();
2012 selectAllSequenceMenuItem_actionPerformed(null);
2017 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2019 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2022 alignPanel.paintAlignment(true);
2023 viewport.sendSelection();
2024 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2027 public void invertColSel_actionPerformed(ActionEvent e)
2029 viewport.invertColumnSelection();
2030 alignPanel.paintAlignment(true);
2039 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2041 trimAlignment(true);
2050 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2052 trimAlignment(false);
2055 void trimAlignment(boolean trimLeft)
2057 ColumnSelection colSel = viewport.getColumnSelection();
2060 if (colSel.size() > 0)
2064 column = colSel.getMin();
2068 column = colSel.getMax();
2072 if (viewport.getSelectionGroup() != null)
2074 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2075 viewport.hiddenRepSequences);
2079 seqs = viewport.alignment.getSequencesArray();
2082 TrimRegionCommand trimRegion;
2085 trimRegion = new TrimRegionCommand("Remove Left",
2086 TrimRegionCommand.TRIM_LEFT, seqs, column,
2087 viewport.alignment, viewport.colSel,
2088 viewport.selectionGroup);
2089 viewport.setStartRes(0);
2093 trimRegion = new TrimRegionCommand("Remove Right",
2094 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2095 viewport.alignment, viewport.colSel,
2096 viewport.selectionGroup);
2099 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2101 addHistoryItem(trimRegion);
2103 Vector groups = viewport.alignment.getGroups();
2105 for (int i = 0; i < groups.size(); i++)
2107 SequenceGroup sg = (SequenceGroup) groups.get(i);
2109 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2110 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2112 viewport.alignment.deleteGroup(sg);
2116 viewport.firePropertyChange("alignment", null, viewport
2117 .getAlignment().getSequences());
2127 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2129 int start = 0, end = viewport.alignment.getWidth() - 1;
2132 if (viewport.getSelectionGroup() != null)
2134 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2135 viewport.hiddenRepSequences);
2136 start = viewport.getSelectionGroup().getStartRes();
2137 end = viewport.getSelectionGroup().getEndRes();
2141 seqs = viewport.alignment.getSequencesArray();
2144 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2145 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
2147 addHistoryItem(removeGapCols);
2149 statusBar.setText("Removed " + removeGapCols.getSize()
2150 + " empty columns.");
2152 // This is to maintain viewport position on first residue
2153 // of first sequence
2154 SequenceI seq = viewport.alignment.getSequenceAt(0);
2155 int startRes = seq.findPosition(viewport.startRes);
2156 // ShiftList shifts;
2157 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2158 // edit.alColumnChanges=shifts.getInverse();
2159 // if (viewport.hasHiddenColumns)
2160 // viewport.getColumnSelection().compensateForEdits(shifts);
2161 viewport.setStartRes(seq.findIndex(startRes) - 1);
2162 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2173 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2175 int start = 0, end = viewport.alignment.getWidth() - 1;
2178 if (viewport.getSelectionGroup() != null)
2180 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2181 viewport.hiddenRepSequences);
2182 start = viewport.getSelectionGroup().getStartRes();
2183 end = viewport.getSelectionGroup().getEndRes();
2187 seqs = viewport.alignment.getSequencesArray();
2190 // This is to maintain viewport position on first residue
2191 // of first sequence
2192 SequenceI seq = viewport.alignment.getSequenceAt(0);
2193 int startRes = seq.findPosition(viewport.startRes);
2195 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2196 viewport.alignment));
2198 viewport.setStartRes(seq.findIndex(startRes) - 1);
2200 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2211 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2213 viewport.padGaps = padGapsMenuitem.isSelected();
2214 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2220 // if (justifySeqs>0)
2222 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2234 public void findMenuItem_actionPerformed(ActionEvent e)
2239 public void newView_actionPerformed(ActionEvent e)
2241 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2244 newap.av.gatherViewsHere = false;
2246 if (viewport.viewName == null)
2248 viewport.viewName = "Original";
2251 newap.av.historyList = viewport.historyList;
2252 newap.av.redoList = viewport.redoList;
2254 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2255 String newViewName = "View " + index;
2257 Vector comps = (Vector) PaintRefresher.components.get(viewport
2258 .getSequenceSetId());
2259 Vector existingNames = new Vector();
2260 for (int i = 0; i < comps.size(); i++)
2262 if (comps.elementAt(i) instanceof AlignmentPanel)
2264 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2265 if (!existingNames.contains(ap.av.viewName))
2267 existingNames.addElement(ap.av.viewName);
2272 while (existingNames.contains(newViewName))
2274 newViewName = "View " + (++index);
2277 newap.av.viewName = newViewName;
2279 addAlignmentPanel(newap, true);
2281 if (alignPanels.size() == 2)
2283 viewport.gatherViewsHere = true;
2285 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2288 public void expandViews_actionPerformed(ActionEvent e)
2290 Desktop.instance.explodeViews(this);
2293 public void gatherViews_actionPerformed(ActionEvent e)
2295 Desktop.instance.gatherViews(this);
2304 public void font_actionPerformed(ActionEvent e)
2306 new FontChooser(alignPanel);
2315 protected void seqLimit_actionPerformed(ActionEvent e)
2317 viewport.setShowJVSuffix(seqLimits.isSelected());
2319 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2320 .calculateIdWidth());
2321 alignPanel.paintAlignment(true);
2324 public void idRightAlign_actionPerformed(ActionEvent e)
2326 viewport.rightAlignIds = idRightAlign.isSelected();
2327 alignPanel.paintAlignment(true);
2330 public void centreColumnLabels_actionPerformed(ActionEvent e)
2332 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2333 alignPanel.paintAlignment(true);
2339 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2341 protected void followHighlight_actionPerformed()
2343 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2345 alignPanel.scrollToPosition(
2346 alignPanel.seqPanel.seqCanvas.searchResults, false);
2356 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2358 viewport.setColourText(colourTextMenuItem.isSelected());
2359 alignPanel.paintAlignment(true);
2368 public void wrapMenuItem_actionPerformed(ActionEvent e)
2370 scaleAbove.setVisible(wrapMenuItem.isSelected());
2371 scaleLeft.setVisible(wrapMenuItem.isSelected());
2372 scaleRight.setVisible(wrapMenuItem.isSelected());
2373 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2374 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2377 public void showAllSeqs_actionPerformed(ActionEvent e)
2379 viewport.showAllHiddenSeqs();
2382 public void showAllColumns_actionPerformed(ActionEvent e)
2384 viewport.showAllHiddenColumns();
2388 public void hideSelSequences_actionPerformed(ActionEvent e)
2390 viewport.hideAllSelectedSeqs();
2391 alignPanel.paintAlignment(true);
2395 * called by key handler and the hide all/show all menu items
2400 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2403 boolean hide = false;
2404 SequenceGroup sg = viewport.getSelectionGroup();
2405 if (!toggleSeqs && !toggleCols)
2407 // Hide everything by the current selection - this is a hack - we do the
2408 // invert and then hide
2409 // first check that there will be visible columns after the invert.
2410 if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
2411 .getSelected().size() > 0)
2412 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2415 // now invert the sequence set, if required - empty selection implies
2416 // that no hiding is required.
2419 invertSequenceMenuItem_actionPerformed(null);
2420 sg = viewport.getSelectionGroup();
2424 viewport.expandColSelection(sg, true);
2425 // finally invert the column selection and get the new sequence
2427 invertColSel_actionPerformed(null);
2434 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
2436 hideSelSequences_actionPerformed(null);
2439 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
2441 showAllSeqs_actionPerformed(null);
2447 if (viewport.colSel.getSelected().size() > 0)
2449 hideSelColumns_actionPerformed(null);
2452 viewport.selectionGroup = sg;
2457 showAllColumns_actionPerformed(null);
2466 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2467 * event.ActionEvent)
2469 public void hideAllButSelection_actionPerformed(ActionEvent e)
2471 toggleHiddenRegions(false, false);
2478 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2481 public void hideAllSelection_actionPerformed(ActionEvent e)
2483 SequenceGroup sg = viewport.getSelectionGroup();
2484 viewport.expandColSelection(sg, false);
2485 viewport.hideAllSelectedSeqs();
2486 viewport.hideSelectedColumns();
2487 alignPanel.paintAlignment(true);
2494 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2497 public void showAllhidden_actionPerformed(ActionEvent e)
2499 viewport.showAllHiddenColumns();
2500 viewport.showAllHiddenSeqs();
2501 alignPanel.paintAlignment(true);
2504 public void hideSelColumns_actionPerformed(ActionEvent e)
2506 viewport.hideSelectedColumns();
2507 alignPanel.paintAlignment(true);
2510 public void hiddenMarkers_actionPerformed(ActionEvent e)
2512 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2522 protected void scaleAbove_actionPerformed(ActionEvent e)
2524 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2525 alignPanel.paintAlignment(true);
2534 protected void scaleLeft_actionPerformed(ActionEvent e)
2536 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2537 alignPanel.paintAlignment(true);
2546 protected void scaleRight_actionPerformed(ActionEvent e)
2548 viewport.setScaleRightWrapped(scaleRight.isSelected());
2549 alignPanel.paintAlignment(true);
2558 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2560 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2561 alignPanel.paintAlignment(true);
2570 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2572 viewport.setShowText(viewTextMenuItem.isSelected());
2573 alignPanel.paintAlignment(true);
2582 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2584 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2585 alignPanel.paintAlignment(true);
2588 public FeatureSettings featureSettings;
2590 public void featureSettings_actionPerformed(ActionEvent e)
2592 if (featureSettings != null)
2594 featureSettings.close();
2595 featureSettings = null;
2597 if (!showSeqFeatures.isSelected())
2599 // make sure features are actually displayed
2600 showSeqFeatures.setSelected(true);
2601 showSeqFeatures_actionPerformed(null);
2603 featureSettings = new FeatureSettings(this);
2607 * Set or clear 'Show Sequence Features'
2612 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2614 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2615 alignPanel.paintAlignment(true);
2616 if (alignPanel.getOverviewPanel() != null)
2618 alignPanel.getOverviewPanel().updateOverviewImage();
2623 * Set or clear 'Show Sequence Features'
2628 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2630 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2632 if (viewport.getShowSequenceFeaturesHeight())
2634 // ensure we're actually displaying features
2635 viewport.setShowSequenceFeatures(true);
2636 showSeqFeatures.setSelected(true);
2638 alignPanel.paintAlignment(true);
2639 if (alignPanel.getOverviewPanel() != null)
2641 alignPanel.getOverviewPanel().updateOverviewImage();
2651 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2653 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2654 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2657 public void alignmentProperties()
2659 JEditorPane editPane = new JEditorPane("text/html", "");
2660 editPane.setEditable(false);
2661 StringBuffer contents = new StringBuffer("<html>");
2664 int min = Integer.MAX_VALUE, max = 0;
2665 for (int i = 0; i < viewport.alignment.getHeight(); i++)
2667 int size = viewport.alignment.getSequenceAt(i).getEnd()
2668 - viewport.alignment.getSequenceAt(i).getStart();
2675 avg = avg / (float) viewport.alignment.getHeight();
2677 contents.append("<br>Sequences: " + viewport.alignment.getHeight());
2678 contents.append("<br>Minimum Sequence Length: " + min);
2679 contents.append("<br>Maximum Sequence Length: " + max);
2680 contents.append("<br>Average Length: " + (int) avg);
2682 if (((Alignment) viewport.alignment).getProperties() != null)
2684 Hashtable props = ((Alignment) viewport.alignment).getProperties();
2685 Enumeration en = props.keys();
2686 contents.append("<br><br><table border=\"1\">");
2687 while (en.hasMoreElements())
2689 String key = en.nextElement().toString();
2690 StringBuffer val = new StringBuffer();
2691 String vals = props.get(key).toString();
2695 npos = vals.indexOf("\n", pos);
2698 val.append(vals.substring(pos));
2702 val.append(vals.substring(pos, npos));
2706 } while (npos != -1);
2708 .append("<tr><td>" + key + "</td><td>" + val + "</td></tr>");
2710 contents.append("</table>");
2712 editPane.setText(contents.toString() + "</html>");
2713 JInternalFrame frame = new JInternalFrame();
2714 frame.getContentPane().add(new JScrollPane(editPane));
2716 Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
2717 + getTitle(), 500, 400);
2726 public void overviewMenuItem_actionPerformed(ActionEvent e)
2728 if (alignPanel.overviewPanel != null)
2733 JInternalFrame frame = new JInternalFrame();
2734 OverviewPanel overview = new OverviewPanel(alignPanel);
2735 frame.setContentPane(overview);
2736 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(), frame
2737 .getWidth(), frame.getHeight());
2739 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2741 .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2743 public void internalFrameClosed(
2744 javax.swing.event.InternalFrameEvent evt)
2746 alignPanel.setOverviewPanel(null);
2750 alignPanel.setOverviewPanel(overview);
2753 public void textColour_actionPerformed(ActionEvent e)
2755 new TextColourChooser().chooseColour(alignPanel, null);
2764 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2775 public void clustalColour_actionPerformed(ActionEvent e)
2777 changeColour(new ClustalxColourScheme(
2778 viewport.alignment.getSequences(), viewport.alignment
2788 public void zappoColour_actionPerformed(ActionEvent e)
2790 changeColour(new ZappoColourScheme());
2799 public void taylorColour_actionPerformed(ActionEvent e)
2801 changeColour(new TaylorColourScheme());
2810 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2812 changeColour(new HydrophobicColourScheme());
2821 public void helixColour_actionPerformed(ActionEvent e)
2823 changeColour(new HelixColourScheme());
2832 public void strandColour_actionPerformed(ActionEvent e)
2834 changeColour(new StrandColourScheme());
2843 public void turnColour_actionPerformed(ActionEvent e)
2845 changeColour(new TurnColourScheme());
2854 public void buriedColour_actionPerformed(ActionEvent e)
2856 changeColour(new BuriedColourScheme());
2865 public void nucleotideColour_actionPerformed(ActionEvent e)
2867 changeColour(new NucleotideColourScheme());
2870 public void annotationColour_actionPerformed(ActionEvent e)
2872 new AnnotationColourChooser(viewport, alignPanel);
2881 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2883 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2892 public void changeColour(ColourSchemeI cs)
2898 if (viewport.getAbovePIDThreshold())
2900 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2903 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2905 viewport.setGlobalColourScheme(cs);
2909 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2912 if (viewport.getConservationSelected())
2915 Alignment al = (Alignment) viewport.alignment;
2916 Conservation c = new Conservation("All",
2917 ResidueProperties.propHash, 3, al.getSequences(), 0, al
2921 c.verdict(false, viewport.ConsPercGaps);
2923 cs.setConservation(c);
2925 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
2930 cs.setConservation(null);
2933 cs.setConsensus(viewport.hconsensus);
2936 viewport.setGlobalColourScheme(cs);
2938 if (viewport.getColourAppliesToAllGroups())
2940 Vector groups = viewport.alignment.getGroups();
2942 for (int i = 0; i < groups.size(); i++)
2944 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2952 if (cs instanceof ClustalxColourScheme)
2954 sg.cs = new ClustalxColourScheme(sg
2955 .getSequences(viewport.hiddenRepSequences), sg.getWidth());
2957 else if (cs instanceof UserColourScheme)
2959 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
2965 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2966 } catch (Exception ex)
2971 if (viewport.getAbovePIDThreshold()
2972 || cs instanceof PIDColourScheme
2973 || cs instanceof Blosum62ColourScheme)
2975 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2977 sg.cs.setConsensus(AAFrequency.calculate(sg
2978 .getSequences(viewport.hiddenRepSequences), sg
2979 .getStartRes(), sg.getEndRes() + 1));
2983 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2986 if (viewport.getConservationSelected())
2988 Conservation c = new Conservation("Group",
2989 ResidueProperties.propHash, 3, sg
2990 .getSequences(viewport.hiddenRepSequences), sg
2991 .getStartRes(), sg.getEndRes() + 1);
2993 c.verdict(false, viewport.ConsPercGaps);
2994 sg.cs.setConservation(c);
2998 sg.cs.setConservation(null);
3003 if (alignPanel.getOverviewPanel() != null)
3005 alignPanel.getOverviewPanel().updateOverviewImage();
3008 alignPanel.paintAlignment(true);
3017 protected void modifyPID_actionPerformed(ActionEvent e)
3019 if (viewport.getAbovePIDThreshold()
3020 && viewport.globalColourScheme != null)
3022 SliderPanel.setPIDSliderSource(alignPanel, viewport
3023 .getGlobalColourScheme(), "Background");
3024 SliderPanel.showPIDSlider();
3034 protected void modifyConservation_actionPerformed(ActionEvent e)
3036 if (viewport.getConservationSelected()
3037 && viewport.globalColourScheme != null)
3039 SliderPanel.setConservationSlider(alignPanel,
3040 viewport.globalColourScheme, "Background");
3041 SliderPanel.showConservationSlider();
3051 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3053 viewport.setConservationSelected(conservationMenuItem.isSelected());
3055 viewport.setAbovePIDThreshold(false);
3056 abovePIDThreshold.setSelected(false);
3058 changeColour(viewport.getGlobalColourScheme());
3060 modifyConservation_actionPerformed(null);
3069 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3071 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3073 conservationMenuItem.setSelected(false);
3074 viewport.setConservationSelected(false);
3076 changeColour(viewport.getGlobalColourScheme());
3078 modifyPID_actionPerformed(null);
3087 public void userDefinedColour_actionPerformed(ActionEvent e)
3089 if (e.getActionCommand().equals("User Defined..."))
3091 new UserDefinedColours(alignPanel, null);
3095 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3096 .getUserColourSchemes().get(e.getActionCommand());
3102 public void updateUserColourMenu()
3105 Component[] menuItems = colourMenu.getMenuComponents();
3106 int i, iSize = menuItems.length;
3107 for (i = 0; i < iSize; i++)
3109 if (menuItems[i].getName() != null
3110 && menuItems[i].getName().equals("USER_DEFINED"))
3112 colourMenu.remove(menuItems[i]);
3116 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3118 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3119 .getUserColourSchemes().keys();
3121 while (userColours.hasMoreElements())
3123 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3124 userColours.nextElement().toString());
3125 radioItem.setName("USER_DEFINED");
3126 radioItem.addMouseListener(new MouseAdapter()
3128 public void mousePressed(MouseEvent evt)
3130 if (evt.isControlDown()
3131 || SwingUtilities.isRightMouseButton(evt))
3134 .removeActionListener(radioItem.getActionListeners()[0]);
3136 int option = JOptionPane.showInternalConfirmDialog(
3137 jalview.gui.Desktop.desktop,
3138 "Remove from default list?",
3139 "Remove user defined colour",
3140 JOptionPane.YES_NO_OPTION);
3141 if (option == JOptionPane.YES_OPTION)
3143 jalview.gui.UserDefinedColours
3144 .removeColourFromDefaults(radioItem.getText());
3145 colourMenu.remove(radioItem);
3149 radioItem.addActionListener(new ActionListener()
3151 public void actionPerformed(ActionEvent evt)
3153 userDefinedColour_actionPerformed(evt);
3160 radioItem.addActionListener(new ActionListener()
3162 public void actionPerformed(ActionEvent evt)
3164 userDefinedColour_actionPerformed(evt);
3168 colourMenu.insert(radioItem, 15);
3169 colours.add(radioItem);
3180 public void PIDColour_actionPerformed(ActionEvent e)
3182 changeColour(new PIDColourScheme());
3191 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3193 changeColour(new Blosum62ColourScheme());
3202 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3204 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3205 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3206 .getAlignment().getSequenceAt(0), null);
3207 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3208 viewport.alignment));
3209 alignPanel.paintAlignment(true);
3218 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3220 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3221 AlignmentSorter.sortByID(viewport.getAlignment());
3222 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
3223 alignPanel.paintAlignment(true);
3232 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3234 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3235 AlignmentSorter.sortByLength(viewport.getAlignment());
3236 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3237 viewport.alignment));
3238 alignPanel.paintAlignment(true);
3247 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3249 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3250 AlignmentSorter.sortByGroup(viewport.getAlignment());
3251 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3252 viewport.alignment));
3254 alignPanel.paintAlignment(true);
3263 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3265 new RedundancyPanel(alignPanel, this);
3274 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3276 if ((viewport.getSelectionGroup() == null)
3277 || (viewport.getSelectionGroup().getSize() < 2))
3279 JOptionPane.showInternalMessageDialog(this,
3280 "You must select at least 2 sequences.", "Invalid Selection",
3281 JOptionPane.WARNING_MESSAGE);
3285 JInternalFrame frame = new JInternalFrame();
3286 frame.setContentPane(new PairwiseAlignPanel(viewport));
3287 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
3297 public void PCAMenuItem_actionPerformed(ActionEvent e)
3299 if (((viewport.getSelectionGroup() != null)
3300 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3301 .getSelectionGroup().getSize() > 0))
3302 || (viewport.getAlignment().getHeight() < 4))
3304 JOptionPane.showInternalMessageDialog(this,
3305 "Principal component analysis must take\n"
3306 + "at least 4 input sequences.",
3307 "Sequence selection insufficient",
3308 JOptionPane.WARNING_MESSAGE);
3313 new PCAPanel(alignPanel);
3316 public void autoCalculate_actionPerformed(ActionEvent e)
3318 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3319 if (viewport.autoCalculateConsensus)
3321 viewport.firePropertyChange("alignment", null, viewport
3322 .getAlignment().getSequences());
3332 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3334 NewTreePanel("AV", "PID", "Average distance tree using PID");
3343 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3345 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3354 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3356 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3365 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3367 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3380 void NewTreePanel(String type, String pwType, String title)
3384 if (viewport.getSelectionGroup() != null)
3386 if (viewport.getSelectionGroup().getSize() < 3)
3391 "You need to have more than two sequences selected to build a tree!",
3392 "Not enough sequences", JOptionPane.WARNING_MESSAGE);
3397 SequenceGroup sg = viewport.getSelectionGroup();
3399 /* Decide if the selection is a column region */
3400 while (s < sg.getSize())
3402 if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
3408 "The selected region to create a tree may\nonly contain residues or gaps.\n"
3409 + "Try using the Pad function in the edit menu,\n"
3410 + "or one of the multiple sequence alignment web services.",
3411 "Sequences in selection are not aligned",
3412 JOptionPane.WARNING_MESSAGE);
3418 title = title + " on region";
3419 tp = new TreePanel(alignPanel, type, pwType);
3423 // are the visible sequences aligned?
3424 if (!viewport.alignment.isAligned(false))
3429 "The sequences must be aligned before creating a tree.\n"
3430 + "Try using the Pad function in the edit menu,\n"
3431 + "or one of the multiple sequence alignment web services.",
3432 "Sequences not aligned",
3433 JOptionPane.WARNING_MESSAGE);
3438 if (viewport.alignment.getHeight() < 2)
3443 tp = new TreePanel(alignPanel, type, pwType);
3448 if (viewport.viewName != null)
3450 title += viewport.viewName + " of ";
3453 title += this.title;
3455 Desktop.addInternalFrame(tp, title, 600, 500);
3466 public void addSortByOrderMenuItem(String title,
3467 final AlignmentOrder order)
3469 final JMenuItem item = new JMenuItem("by " + title);
3471 item.addActionListener(new java.awt.event.ActionListener()
3473 public void actionPerformed(ActionEvent e)
3475 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3477 // TODO: JBPNote - have to map order entries to curent SequenceI
3479 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3481 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3482 viewport.alignment));
3484 alignPanel.paintAlignment(true);
3490 * Add a new sort by annotation score menu item
3493 * the menu to add the option to
3495 * the label used to retrieve scores for each sequence on the
3498 public void addSortByAnnotScoreMenuItem(JMenu sort,
3499 final String scoreLabel)
3501 final JMenuItem item = new JMenuItem(scoreLabel);
3503 item.addActionListener(new java.awt.event.ActionListener()
3505 public void actionPerformed(ActionEvent e)
3507 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3508 AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport
3509 .getAlignment());// ,viewport.getSelectionGroup());
3510 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3511 viewport.alignment));
3512 alignPanel.paintAlignment(true);
3518 * last hash for alignment's annotation array - used to minimise cost of
3521 protected int _annotationScoreVectorHash;
3524 * search the alignment and rebuild the sort by annotation score submenu the
3525 * last alignment annotation vector hash is stored to minimize cost of
3526 * rebuilding in subsequence calls.
3529 public void buildSortByAnnotationScoresMenu()
3531 if (viewport.alignment.getAlignmentAnnotation() == null)
3536 if (viewport.alignment.getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3538 sortByAnnotScore.removeAll();
3539 // almost certainly a quicker way to do this - but we keep it simple
3540 Hashtable scoreSorts = new Hashtable();
3541 AlignmentAnnotation aann[];
3542 Enumeration sq = viewport.alignment.getSequences().elements();
3543 while (sq.hasMoreElements())
3545 aann = ((SequenceI) sq.nextElement()).getAnnotation();
3546 for (int i = 0; aann != null && i < aann.length; i++)
3548 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3550 scoreSorts.put(aann[i].label, aann[i].label);
3554 Enumeration labels = scoreSorts.keys();
3555 while (labels.hasMoreElements())
3557 addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels
3560 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3563 _annotationScoreVectorHash = viewport.alignment
3564 .getAlignmentAnnotation().hashCode();
3569 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3570 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3571 * call. Listeners are added to remove the menu item when the treePanel is
3572 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3576 * Displayed tree window.
3578 * SortBy menu item title.
3580 public void buildTreeMenu()
3582 sortByTreeMenu.removeAll();
3584 Vector comps = (Vector) PaintRefresher.components.get(viewport
3585 .getSequenceSetId());
3586 Vector treePanels = new Vector();
3587 int i, iSize = comps.size();
3588 for (i = 0; i < iSize; i++)
3590 if (comps.elementAt(i) instanceof TreePanel)
3592 treePanels.add(comps.elementAt(i));
3596 iSize = treePanels.size();
3600 sortByTreeMenu.setVisible(false);
3604 sortByTreeMenu.setVisible(true);
3606 for (i = 0; i < treePanels.size(); i++)
3608 TreePanel tp = (TreePanel) treePanels.elementAt(i);
3609 final JMenuItem item = new JMenuItem(tp.getTitle());
3610 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3611 item.addActionListener(new java.awt.event.ActionListener()
3613 public void actionPerformed(ActionEvent e)
3615 SequenceI[] oldOrder = viewport.getAlignment()
3616 .getSequencesArray();
3617 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
3619 addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
3620 viewport.alignment));
3622 alignPanel.paintAlignment(true);
3626 sortByTreeMenu.add(item);
3631 * Work out whether the whole set of sequences or just the selected set will
3632 * be submitted for multiple alignment.
3635 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3637 // Now, check we have enough sequences
3638 AlignmentView msa = null;
3640 if ((viewport.getSelectionGroup() != null)
3641 && (viewport.getSelectionGroup().getSize() > 1))
3643 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3644 // some common interface!
3646 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3647 * SequenceI[sz = seqs.getSize(false)];
3649 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3650 * seqs.getSequenceAt(i); }
3652 msa = viewport.getAlignmentView(true);
3657 * Vector seqs = viewport.getAlignment().getSequences();
3659 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3661 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3662 * seqs.elementAt(i); } }
3664 msa = viewport.getAlignmentView(false);
3670 * Decides what is submitted to a secondary structure prediction service: the
3671 * first sequence in the alignment, or in the current selection, or, if the
3672 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3673 * region or the whole alignment. (where the first sequence in the set is the
3674 * one that the prediction will be for).
3676 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3678 AlignmentView seqs = null;
3680 if ((viewport.getSelectionGroup() != null)
3681 && (viewport.getSelectionGroup().getSize() > 0))
3683 seqs = viewport.getAlignmentView(true);
3687 seqs = viewport.getAlignmentView(false);
3689 // limit sequences - JBPNote in future - could spawn multiple prediction
3691 // TODO: viewport.alignment.isAligned is a global state - the local
3692 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3693 if (!viewport.alignment.isAligned(false))
3695 seqs.setSequences(new SeqCigar[]
3696 { seqs.getSequences()[0] });
3697 // TODO: if seqs.getSequences().length>1 then should really have warned
3710 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3712 // Pick the tree file
3713 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
3714 .getProperty("LAST_DIRECTORY"));
3715 chooser.setFileView(new JalviewFileView());
3716 chooser.setDialogTitle("Select a newick-like tree file");
3717 chooser.setToolTipText("Load a tree file");
3719 int value = chooser.showOpenDialog(null);
3721 if (value == JalviewFileChooser.APPROVE_OPTION)
3723 String choice = chooser.getSelectedFile().getPath();
3724 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3725 jalview.io.NewickFile fin = null;
3728 fin = new jalview.io.NewickFile(choice, "File");
3729 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3730 } catch (Exception ex)
3732 JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3733 "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
3734 ex.printStackTrace();
3736 if (fin != null && fin.hasWarningMessage())
3738 JOptionPane.showMessageDialog(Desktop.desktop, fin
3739 .getWarningMessage(), "Possible problem with tree file",
3740 JOptionPane.WARNING_MESSAGE);
3745 public TreePanel ShowNewickTree(NewickFile nf, String title)
3747 return ShowNewickTree(nf, title, 600, 500, 4, 5);
3750 public TreePanel ShowNewickTree(NewickFile nf, String title,
3751 AlignmentView input)
3753 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
3756 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
3757 int h, int x, int y)
3759 return ShowNewickTree(nf, title, null, w, h, x, y);
3763 * Add a treeviewer for the tree extracted from a newick file object to the
3764 * current alignment view
3771 * Associated alignment input data (or null)
3780 * @return TreePanel handle
3782 public TreePanel ShowNewickTree(NewickFile nf, String title,
3783 AlignmentView input, int w, int h, int x, int y)
3785 TreePanel tp = null;
3791 if (nf.getTree() != null)
3793 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
3799 tp.setLocation(x, y);
3802 Desktop.addInternalFrame(tp, title, w, h);
3804 } catch (Exception ex)
3806 ex.printStackTrace();
3812 private boolean buildingMenu = false;
3815 * Generates menu items and listener event actions for web service clients
3818 public void BuildWebServiceMenu()
3820 while (buildingMenu)
3824 System.err.println("Waiting for building menu to finish.");
3826 } catch (Exception e)
3831 buildingMenu = true;
3835 .println("Building ws menu again " + Thread.currentThread());
3836 // TODO: add support for context dependent disabling of services based on
3837 // alignment and current selection
3838 // TODO: add additional serviceHandle parameter to specify abstract
3840 // class independently of AbstractName
3841 // TODO: add in rediscovery GUI function to restart discoverer
3842 // TODO: group services by location as well as function and/or introduce
3843 // object broker mechanism.
3844 Vector wsmenu = new Vector();
3845 final IProgressIndicator af = this;
3846 if ((Discoverer.services != null) && (Discoverer.services.size() > 0))
3848 // TODO: refactor to allow list of AbstractName/Handler bindings to be
3849 // stored or retrieved from elsewhere
3850 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
3851 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
3852 Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
3853 // TODO: move GUI generation code onto service implementation - so a
3854 // client instance attaches itself to the GUI with method call like
3855 // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
3859 // Add any Multiple Sequence Alignment Services
3860 final JMenu msawsmenu = new JMenu("Alignment");
3861 for (int i = 0, j = msaws.size(); i < j; i++)
3863 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
3865 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
3866 .getServiceClient(sh);
3867 impl.attachWSMenuEntry(msawsmenu, this);
3870 wsmenu.add(msawsmenu);
3872 if (secstrpr != null)
3874 // Add any secondary structure prediction services
3875 final JMenu secstrmenu = new JMenu(
3876 "Secondary Structure Prediction");
3877 for (int i = 0, j = secstrpr.size(); i < j; i++)
3879 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
3881 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
3882 .getServiceClient(sh);
3883 impl.attachWSMenuEntry(secstrmenu, this);
3885 wsmenu.add(secstrmenu);
3887 if (seqsrch != null)
3889 // Add any sequence search services
3890 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
3891 for (int i = 0, j = seqsrch.size(); i < j; i++)
3893 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
3895 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
3896 .getServiceClient(sh);
3897 impl.attachWSMenuEntry(seqsrchmenu, this);
3899 wsmenu.add(seqsrchmenu);
3903 // TODO: move into separate menu builder class.
3905 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
3906 if (jws2servs != null)
3908 if (jws2servs.hasServices())
3910 JMenu jws2men = new JMenu("Jalview 2 Services");
3911 jws2servs.attachWSMenuEntry(jws2men, this);
3912 wsmenu.add(jws2men);
3916 if (!jws2servs.isRunning())
3918 new Thread(jws2servs).start();
3923 resetWebServiceMenu();
3924 // finally, add the whole shebang onto the webservices menu
3925 if (wsmenu.size() > 0)
3927 for (int i = 0, j = wsmenu.size(); i < j; i++)
3929 webService.add((JMenu) wsmenu.get(i));
3934 this.webService.add(this.webServiceNoServices);
3936 } catch (Exception e)
3940 buildingMenu = false;
3944 * empty the web service menu and add any ad-hoc functions not dynamically
3948 private void resetWebServiceMenu()
3950 webService.removeAll();
3951 build_fetchdbmenu(webService);
3952 build_urlServiceMenu(webService);
3956 * construct any groupURL type service menu entries.
3960 private void build_urlServiceMenu(JMenu webService)
3962 jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
3967 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
3968 * chooser = new JalviewFileChooser(jalview.bin.Cache.
3969 * getProperty("LAST_DIRECTORY"));
3971 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
3972 * to Vamsas file"); chooser.setToolTipText("Export");
3974 * int value = chooser.showSaveDialog(this);
3976 * if (value == JalviewFileChooser.APPROVE_OPTION) {
3977 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
3978 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
3979 * chooser.getSelectedFile().getAbsolutePath(), this); } }
3982 * prototype of an automatically enabled/disabled analysis function
3985 protected void setShowProductsEnabled()
3987 SequenceI[] selection = viewport.getSequenceSelection();
3988 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
3989 viewport.getAlignment().getDataset()))
3991 showProducts.setEnabled(true);
3996 showProducts.setEnabled(false);
4001 * search selection for sequence xRef products and build the show products
4006 * @return true if showProducts menu should be enabled.
4008 public boolean canShowProducts(SequenceI[] selection,
4009 boolean isRegionSelection, Alignment dataset)
4011 boolean showp = false;
4014 showProducts.removeAll();
4015 final boolean dna = viewport.getAlignment().isNucleotide();
4016 final Alignment ds = dataset;
4017 String[] ptypes = (selection == null || selection.length == 0) ? null
4018 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4020 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4021 // selection, dataset, true);
4022 final SequenceI[] sel = selection;
4023 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4026 final boolean isRegSel = isRegionSelection;
4027 final AlignFrame af = this;
4028 final String source = ptypes[t];
4029 JMenuItem xtype = new JMenuItem(ptypes[t]);
4030 xtype.addActionListener(new ActionListener()
4033 public void actionPerformed(ActionEvent e)
4035 // TODO: new thread for this call with vis-delay
4036 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4037 isRegSel, dna, source);
4041 showProducts.add(xtype);
4043 showProducts.setVisible(showp);
4044 showProducts.setEnabled(showp);
4045 } catch (Exception e)
4047 jalview.bin.Cache.log
4049 "canTranslate threw an exception - please report to help@jalview.org",
4056 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4057 boolean isRegSel, boolean dna, String source)
4059 final boolean fisRegSel = isRegSel;
4060 final boolean fdna = dna;
4061 final String fsrc = source;
4062 final AlignFrame ths = this;
4063 final SequenceI[] fsel = sel;
4064 Runnable foo = new Runnable()
4069 final long sttime = System.currentTimeMillis();
4070 ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4073 Alignment ds = ths.getViewport().alignment.getDataset(); // update
4077 Alignment prods = CrossRef
4078 .findXrefSequences(fsel, fdna, fsrc, ds);
4081 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4082 for (int s = 0; s < sprods.length; s++)
4084 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4085 if (ds.getSequences() == null
4086 || !ds.getSequences().contains(
4087 sprods[s].getDatasetSequence()))
4088 ds.addSequence(sprods[s].getDatasetSequence());
4089 sprods[s].updatePDBIds();
4091 Alignment al = new Alignment(sprods);
4092 AlignedCodonFrame[] cf = prods.getCodonFrames();
4094 for (int s = 0; cf != null && s < cf.length; s++)
4096 al.addCodonFrame(cf[s]);
4099 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4101 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4102 + " for " + ((fisRegSel) ? "selected region of " : "")
4104 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4109 System.err.println("No Sequences generated for xRef type "
4112 } catch (Exception e)
4114 jalview.bin.Cache.log.error(
4115 "Exception when finding crossreferences", e);
4116 } catch (OutOfMemoryError e)
4118 new OOMWarning("whilst fetching crossreferences", e);
4121 jalview.bin.Cache.log.error("Error when finding crossreferences",
4124 ths.setProgressBar("Finished searching for sequences from " + fsrc,
4129 Thread frunner = new Thread(foo);
4133 public boolean canShowTranslationProducts(SequenceI[] selection,
4134 AlignmentI alignment)
4139 return (jalview.analysis.Dna.canTranslate(selection, viewport
4140 .getViewAsVisibleContigs(true)));
4141 } catch (Exception e)
4143 jalview.bin.Cache.log
4145 "canTranslate threw an exception - please report to help@jalview.org",
4151 public void showProducts_actionPerformed(ActionEvent e)
4153 // /////////////////////////////
4154 // Collect Data to be translated/transferred
4156 SequenceI[] selection = viewport.getSequenceSelection();
4157 AlignmentI al = null;
4160 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4161 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4162 viewport.getAlignment().getDataset());
4163 } catch (Exception ex)
4166 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4173 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4174 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4178 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4179 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4180 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4184 public void showTranslation_actionPerformed(ActionEvent e)
4186 // /////////////////////////////
4187 // Collect Data to be translated/transferred
4189 SequenceI[] selection = viewport.getSequenceSelection();
4190 String[] seqstring = viewport.getViewAsString(true);
4191 AlignmentI al = null;
4194 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4195 viewport.getViewAsVisibleContigs(true), viewport
4196 .getGapCharacter(), viewport.alignment
4197 .getAlignmentAnnotation(), viewport.alignment
4198 .getWidth(), viewport.getAlignment().getDataset());
4199 } catch (Exception ex)
4202 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4209 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4210 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4214 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4215 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4216 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4221 * Try to load a features file onto the alignment.
4224 * contents or path to retrieve file
4226 * access mode of file (see jalview.io.AlignFile)
4227 * @return true if features file was parsed corectly.
4229 public boolean parseFeaturesFile(String file, String type)
4231 boolean featuresFile = false;
4234 featuresFile = new FeaturesFile(file, type).parse(viewport.alignment
4235 .getDataset(), alignPanel.seqPanel.seqCanvas
4236 .getFeatureRenderer().featureColours, false);
4237 } catch (Exception ex)
4239 ex.printStackTrace();
4244 viewport.showSequenceFeatures = true;
4245 showSeqFeatures.setSelected(true);
4246 if (alignPanel.seqPanel.seqCanvas.fr != null)
4248 // update the min/max ranges where necessary
4249 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4251 if (featureSettings != null)
4253 featureSettings.setTableData();
4255 alignPanel.paintAlignment(true);
4258 return featuresFile;
4261 public void dragEnter(DropTargetDragEvent evt)
4265 public void dragExit(DropTargetEvent evt)
4269 public void dragOver(DropTargetDragEvent evt)
4273 public void dropActionChanged(DropTargetDragEvent evt)
4277 public void drop(DropTargetDropEvent evt)
4279 Transferable t = evt.getTransferable();
4280 java.util.List files = null;
4284 DataFlavor uriListFlavor = new DataFlavor(
4285 "text/uri-list;class=java.lang.String");
4286 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4288 // Works on Windows and MacOSX
4289 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4290 files = (java.util.List) t
4291 .getTransferData(DataFlavor.javaFileListFlavor);
4293 else if (t.isDataFlavorSupported(uriListFlavor))
4295 // This is used by Unix drag system
4296 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4297 String data = (String) t.getTransferData(uriListFlavor);
4298 files = new java.util.ArrayList(1);
4299 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4300 data, "\r\n"); st.hasMoreTokens();)
4302 String s = st.nextToken();
4303 if (s.startsWith("#"))
4305 // the line is a comment (as per the RFC 2483)
4309 java.net.URI uri = new java.net.URI(s);
4310 // check to see if we can handle this kind of URI
4311 if (uri.getScheme().toLowerCase().startsWith("http"))
4313 files.add(uri.toString());
4317 // otherwise preserve old behaviour: catch all for file objects
4318 java.io.File file = new java.io.File(uri);
4319 files.add(file.toString());
4323 } catch (Exception e)
4325 e.printStackTrace();
4332 for (int i = 0; i < files.size(); i++)
4334 loadJalviewDataFile(files.get(i).toString());
4336 } catch (Exception ex)
4338 ex.printStackTrace();
4344 * Attempt to load a "dropped" file or URL string: First by testing whether
4345 * it's and Annotation file, then a JNet file, and finally a features file. If
4346 * all are false then the user may have dropped an alignment file onto this
4350 * either a filename or a URL string.
4352 public void loadJalviewDataFile(String file)
4356 String protocol = jalview.io.FormatAdapter.FILE;
4357 String f = file.toLowerCase();
4358 if (f.indexOf("http:") == 0 || f.indexOf("https:") == 0
4359 || f.indexOf("file:") == 0)
4361 protocol = jalview.io.FormatAdapter.URL;
4364 boolean isAnnotation = new AnnotationFile().readAnnotationFile(
4365 viewport.alignment, file, protocol);
4369 // try to see if its a JNet 'concise' style annotation file *before* we
4370 // try to parse it as a features file
4371 String format = new IdentifyFile().Identify(file, protocol);
4372 if (format.equalsIgnoreCase("JnetFile"))
4374 jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
4376 new JnetAnnotationMaker().add_annotation(predictions, viewport
4377 .getAlignment(), 0, false);
4378 isAnnotation = true;
4382 // try to parse it as a features file
4383 boolean isGroupsFile = parseFeaturesFile(file, protocol);
4384 // if it wasn't a features file then we just treat it as a general
4385 // alignment file to load into the current view.
4388 new FileLoader().LoadFile(viewport, file, protocol, format);
4392 alignPanel.paintAlignment(true);
4399 alignPanel.adjustAnnotationHeight();
4400 viewport.updateSequenceIdColours();
4401 buildSortByAnnotationScoresMenu();
4402 alignPanel.paintAlignment(true);
4404 } catch (Exception ex)
4406 ex.printStackTrace();
4410 public void tabSelectionChanged(int index)
4414 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
4415 viewport = alignPanel.av;
4416 setMenusFromViewport(viewport);
4420 public void tabbedPane_mousePressed(MouseEvent e)
4422 if (SwingUtilities.isRightMouseButton(e))
4424 String reply = JOptionPane.showInternalInputDialog(this,
4425 "Enter View Name", "Edit View Name",
4426 JOptionPane.QUESTION_MESSAGE);
4430 viewport.viewName = reply;
4431 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4436 public AlignViewport getCurrentView()
4442 * Open the dialog for regex description parsing.
4444 protected void extractScores_actionPerformed(ActionEvent e)
4446 ParseProperties pp = new jalview.analysis.ParseProperties(
4447 viewport.alignment);
4448 // TODO: verify regex and introduce GUI dialog for version 2.5
4449 // if (pp.getScoresFromDescription("col", "score column ",
4450 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4452 if (pp.getScoresFromDescription("description column",
4453 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4455 buildSortByAnnotationScoresMenu();
4463 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4466 protected void showDbRefs_actionPerformed(ActionEvent e)
4468 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
4474 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4477 protected void showNpFeats_actionPerformed(ActionEvent e)
4479 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
4483 * find the viewport amongst the tabs in this alignment frame and close that
4488 public boolean closeView(AlignViewport av)
4492 this.closeMenuItem_actionPerformed(false);
4495 Component[] comp = tabbedPane.getComponents();
4496 for (int i = 0; comp != null && i < comp.length; i++)
4498 if (comp[i] instanceof AlignmentPanel)
4500 if (((AlignmentPanel) comp[i]).av == av)
4503 closeView((AlignmentPanel) comp[i]);
4511 protected void build_fetchdbmenu(JMenu webService)
4513 // Temporary hack - DBRef Fetcher always top level ws entry.
4514 // TODO We probably want to store a sequence database checklist in
4515 // preferences and have checkboxes.. rather than individual sources selected
4517 JMenu rfetch = new JMenu("Fetch DB References");
4519 .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
4520 webService.add(rfetch);
4522 JMenuItem fetchr = new JMenuItem("Standard Databases");
4524 .setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
4525 fetchr.addActionListener(new ActionListener()
4528 public void actionPerformed(ActionEvent e)
4530 new Thread(new Runnable()
4535 new jalview.ws.DBRefFetcher(alignPanel.av
4536 .getSequenceSelection(), alignPanel.alignFrame)
4537 .fetchDBRefs(false);
4545 JMenu dfetch = new JMenu();
4547 jalview.ws.SequenceFetcher sf = SequenceFetcher
4548 .getSequenceFetcherSingleton(this);
4549 String[] otherdb = sf.getOrderedSupportedSources();
4550 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4551 // jalview.util.QuickSort.sort(otherdb, otherdb);
4552 int comp = 0, mcomp = 15;
4553 String mname = null;
4554 if (otherdb != null && otherdb.length > 0)
4556 for (int i = 0; i < otherdb.length; i++)
4558 String dbname = sf.getSourceProxy(otherdb[i]).getDbName();
4561 mname = "from '" + dbname + "'";
4563 fetchr = new JMenuItem(otherdb[i]);
4564 final String[] dassource = new String[]
4566 fetchr.addActionListener(new ActionListener()
4569 public void actionPerformed(ActionEvent e)
4571 new Thread(new Runnable()
4576 new jalview.ws.DBRefFetcher(alignPanel.av
4577 .getSequenceSelection(), alignPanel.alignFrame,
4578 dassource).fetchDBRefs(false);
4584 fetchr.setToolTipText("Retrieve from " + dbname);
4586 if (comp++ == mcomp || i == (otherdb.length - 1))
4588 dfetch.setText(mname + " to '" + dbname + "'");
4590 dfetch = new JMenu();
4599 * Left justify the whole alignment.
4601 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
4603 AlignmentI al = viewport.getAlignment();
4605 viewport.firePropertyChange("alignment", null, al);
4609 * Right justify the whole alignment.
4611 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
4613 AlignmentI al = viewport.getAlignment();
4615 viewport.firePropertyChange("alignment", null, al);
4618 public void setShowSeqFeatures(boolean b)
4620 showSeqFeatures.setSelected(true);
4621 viewport.setShowSequenceFeatures(true);
4628 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
4629 * awt.event.ActionEvent)
4631 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
4633 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
4634 alignPanel.paintAlignment(true);
4641 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
4644 protected void showGroupConsensus_actionPerformed(ActionEvent e)
4646 viewport.setShowGroupConsensus(showGroupConsensus.getState());
4647 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4655 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
4656 * .event.ActionEvent)
4658 protected void showGroupConservation_actionPerformed(ActionEvent e)
4660 viewport.setShowGroupConservation(showGroupConservation.getState());
4661 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4668 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
4669 * .event.ActionEvent)
4671 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
4673 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
4674 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4681 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
4682 * .event.ActionEvent)
4684 protected void showSequenceLogo_actionPerformed(ActionEvent e)
4686 viewport.setShowSequenceLogo(showSequenceLogo.getState());
4687 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4690 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
4692 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4699 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
4700 * .event.ActionEvent)
4702 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
4704 if (viewport.getSelectionGroup() != null)
4706 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
4707 viewport.getSequenceSelection(), viewport.getAlignmentView(
4708 true).getSequenceStrings(viewport.getGapCharacter()),
4709 viewport.alignment.getGroups());
4710 viewport.alignment.deleteAllGroups();
4711 viewport.sequenceColours = null;
4712 viewport.setSelectionGroup(null);
4713 // set view properties for each group
4714 for (int g = 0; g < gps.length; g++)
4716 gps[g].setShowNonconserved(viewport.getShowUnconserved());
4717 gps[g].setIncludeAllConsSymbols(viewport
4718 .isIncludeAllConsensusSymbols());
4719 viewport.alignment.addGroup(gps[g]);
4720 Color col = new Color((int) (Math.random() * 255), (int) (Math
4721 .random() * 255), (int) (Math.random() * 255));
4722 col = col.brighter();
4723 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
4724 .hasMoreElements(); viewport.setSequenceColour(
4725 (SequenceI) sq.nextElement(), col))
4728 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
4729 alignPanel.updateAnnotation();
4730 alignPanel.paintAlignment(true);
4735 class PrintThread extends Thread
4739 public PrintThread(AlignmentPanel ap)
4744 static PageFormat pf;
4748 PrinterJob printJob = PrinterJob.getPrinterJob();
4752 printJob.setPrintable(ap, pf);
4756 printJob.setPrintable(ap);
4759 if (printJob.printDialog())
4764 } catch (Exception PrintException)
4766 PrintException.printStackTrace();