2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
25 import java.awt.datatransfer.*;
26 import java.awt.dnd.*;
27 import java.awt.event.*;
28 import java.awt.print.*;
30 import javax.swing.event.MenuEvent;
32 import jalview.analysis.*;
33 import jalview.bin.Cache;
34 import jalview.commands.*;
35 import jalview.datamodel.*;
37 import jalview.jbgui.*;
38 import jalview.schemes.*;
40 import jalview.ws.jws1.Discoverer;
41 import jalview.ws.jws2.Jws2Discoverer;
49 public class AlignFrame extends GAlignFrame implements DropTargetListener,
54 public static final int DEFAULT_WIDTH = 700;
57 public static final int DEFAULT_HEIGHT = 500;
59 public AlignmentPanel alignPanel;
61 AlignViewport viewport;
63 Vector alignPanels = new Vector();
66 * Last format used to load or save alignments in this window
68 String currentFileFormat = null;
71 * Current filename for this alignment
73 String fileName = null;
76 * Creates a new AlignFrame object with specific width and height.
82 public AlignFrame(AlignmentI al, int width, int height)
84 this(al, null, width, height);
88 * Creates a new AlignFrame object with specific width, height and
94 * @param sequenceSetId
96 public AlignFrame(AlignmentI al, int width, int height,
99 this(al, null, width, height, sequenceSetId);
103 * Creates a new AlignFrame object with specific width, height and
109 * @param sequenceSetId
112 public AlignFrame(AlignmentI al, int width, int height,
113 String sequenceSetId, String viewId)
115 this(al, null, width, height, sequenceSetId, viewId);
119 * new alignment window with hidden columns
123 * @param hiddenColumns
124 * ColumnSelection or null
126 * Width of alignment frame
130 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
131 int width, int height)
133 this(al, hiddenColumns, width, height, null);
137 * Create alignment frame for al with hiddenColumns, a specific width and
138 * height, and specific sequenceId
141 * @param hiddenColumns
144 * @param sequenceSetId
147 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
148 int width, int height, String sequenceSetId)
150 this(al, hiddenColumns, width, height, sequenceSetId, null);
154 * Create alignment frame for al with hiddenColumns, a specific width and
155 * height, and specific sequenceId
158 * @param hiddenColumns
161 * @param sequenceSetId
166 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
167 int width, int height, String sequenceSetId, String viewId)
169 setSize(width, height);
170 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
172 alignPanel = new AlignmentPanel(this, viewport);
174 if (al.getDataset() == null)
179 addAlignmentPanel(alignPanel, true);
184 * Make a new AlignFrame from exisiting alignmentPanels
191 public AlignFrame(AlignmentPanel ap)
195 addAlignmentPanel(ap, false);
200 * initalise the alignframe from the underlying viewport data and the
205 if (viewport.conservation == null)
207 BLOSUM62Colour.setEnabled(false);
208 conservationMenuItem.setEnabled(false);
209 modifyConservation.setEnabled(false);
210 // PIDColour.setEnabled(false);
211 // abovePIDThreshold.setEnabled(false);
212 // modifyPID.setEnabled(false);
215 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
218 if (sortby.equals("Id"))
220 sortIDMenuItem_actionPerformed(null);
222 else if (sortby.equals("Pairwise Identity"))
224 sortPairwiseMenuItem_actionPerformed(null);
227 if (Desktop.desktop != null)
229 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
230 addServiceListeners();
231 setGUINucleotide(viewport.alignment.isNucleotide());
234 setMenusFromViewport(viewport);
235 buildSortByAnnotationScoresMenu();
236 if (viewport.wrapAlignment)
238 wrapMenuItem_actionPerformed(null);
241 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
243 this.overviewMenuItem_actionPerformed(null);
251 * Change the filename and format for the alignment, and enable the 'reload'
252 * button functionality.
259 public void setFileName(String file, String format)
262 currentFileFormat = format;
263 reload.setEnabled(true);
266 void addKeyListener()
268 addKeyListener(new KeyAdapter()
270 public void keyPressed(KeyEvent evt)
272 if (viewport.cursorMode
273 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
274 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
275 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
276 && Character.isDigit(evt.getKeyChar()))
277 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
279 switch (evt.getKeyCode())
282 case 27: // escape key
283 deselectAllSequenceMenuItem_actionPerformed(null);
287 case KeyEvent.VK_DOWN:
288 if (evt.isAltDown() || !viewport.cursorMode)
289 moveSelectedSequences(false);
290 if (viewport.cursorMode)
291 alignPanel.seqPanel.moveCursor(0, 1);
295 if (evt.isAltDown() || !viewport.cursorMode)
296 moveSelectedSequences(true);
297 if (viewport.cursorMode)
298 alignPanel.seqPanel.moveCursor(0, -1);
302 case KeyEvent.VK_LEFT:
303 if (evt.isAltDown() || !viewport.cursorMode)
304 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
306 alignPanel.seqPanel.moveCursor(-1, 0);
310 case KeyEvent.VK_RIGHT:
311 if (evt.isAltDown() || !viewport.cursorMode)
312 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
314 alignPanel.seqPanel.moveCursor(1, 0);
317 case KeyEvent.VK_SPACE:
318 if (viewport.cursorMode)
320 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
321 || evt.isShiftDown() || evt.isAltDown());
325 case KeyEvent.VK_DELETE:
326 case KeyEvent.VK_BACK_SPACE:
327 if (!viewport.cursorMode)
329 cut_actionPerformed(null);
333 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
334 || evt.isShiftDown() || evt.isAltDown());
340 if (viewport.cursorMode)
342 alignPanel.seqPanel.setCursorRow();
346 if (viewport.cursorMode && !evt.isControlDown())
348 alignPanel.seqPanel.setCursorColumn();
352 if (viewport.cursorMode)
354 alignPanel.seqPanel.setCursorPosition();
358 case KeyEvent.VK_ENTER:
359 case KeyEvent.VK_COMMA:
360 if (viewport.cursorMode)
362 alignPanel.seqPanel.setCursorRowAndColumn();
367 if (viewport.cursorMode)
369 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
373 if (viewport.cursorMode)
375 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
380 viewport.cursorMode = !viewport.cursorMode;
381 statusBar.setText("Keyboard editing mode is "
382 + (viewport.cursorMode ? "on" : "off"));
383 if (viewport.cursorMode)
385 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
386 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
388 alignPanel.seqPanel.seqCanvas.repaint();
394 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
395 java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
397 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
399 javax.help.HelpBroker hb = hs.createHelpBroker();
400 hb.setCurrentID("home");
401 hb.setDisplayed(true);
402 } catch (Exception ex)
404 ex.printStackTrace();
409 boolean toggleSeqs = !evt.isControlDown();
410 boolean toggleCols = !evt.isShiftDown();
411 toggleHiddenRegions(toggleSeqs, toggleCols);
414 case KeyEvent.VK_PAGE_UP:
415 if (viewport.wrapAlignment)
417 alignPanel.scrollUp(true);
421 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
422 - viewport.endSeq + viewport.startSeq);
425 case KeyEvent.VK_PAGE_DOWN:
426 if (viewport.wrapAlignment)
428 alignPanel.scrollUp(false);
432 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
433 + viewport.endSeq - viewport.startSeq);
439 public void keyReleased(KeyEvent evt)
441 switch (evt.getKeyCode())
443 case KeyEvent.VK_LEFT:
444 if (evt.isAltDown() || !viewport.cursorMode)
445 viewport.firePropertyChange("alignment", null, viewport
446 .getAlignment().getSequences());
449 case KeyEvent.VK_RIGHT:
450 if (evt.isAltDown() || !viewport.cursorMode)
451 viewport.firePropertyChange("alignment", null, viewport
452 .getAlignment().getSequences());
459 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
461 ap.alignFrame = this;
463 alignPanels.addElement(ap);
465 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
467 int aSize = alignPanels.size();
469 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
471 if (aSize == 1 && ap.av.viewName == null)
473 this.getContentPane().add(ap, BorderLayout.CENTER);
479 setInitialTabVisible();
482 expandViews.setEnabled(true);
483 gatherViews.setEnabled(true);
484 tabbedPane.addTab(ap.av.viewName, ap);
486 ap.setVisible(false);
493 ap.av.alignment.padGaps();
495 ap.av.updateConservation(ap);
496 ap.av.updateConsensus(ap);
500 public void setInitialTabVisible()
502 expandViews.setEnabled(true);
503 gatherViews.setEnabled(true);
504 tabbedPane.setVisible(true);
505 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
506 tabbedPane.addTab(first.av.viewName, first);
507 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
510 public AlignViewport getViewport()
515 /* Set up intrinsic listeners for dynamically generated GUI bits. */
516 private void addServiceListeners()
518 final java.beans.PropertyChangeListener thisListener;
519 Desktop.instance.addJalviewPropertyChangeListener("services",
520 thisListener = new java.beans.PropertyChangeListener()
522 public void propertyChange(PropertyChangeEvent evt)
524 // // System.out.println("Discoverer property change.");
525 // if (evt.getPropertyName().equals("services"))
527 SwingUtilities.invokeLater(new Runnable()
534 .println("Rebuild WS Menu for service change");
535 BuildWebServiceMenu();
542 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
544 public void internalFrameClosed(
545 javax.swing.event.InternalFrameEvent evt)
547 System.out.println("deregistering discoverer listener");
548 Desktop.instance.removeJalviewPropertyChangeListener("services",
550 closeMenuItem_actionPerformed(true);
553 // Finally, build the menu once to get current service state
554 BuildWebServiceMenu();
557 public void setGUINucleotide(boolean nucleotide)
559 showTranslation.setVisible(nucleotide);
560 conservationMenuItem.setEnabled(!nucleotide);
561 modifyConservation.setEnabled(!nucleotide);
562 showGroupConservation.setEnabled(!nucleotide);
563 // Remember AlignFrame always starts as protein
566 calculateMenu.remove(calculateMenu.getItemCount() - 2);
571 * set up menus for the currently viewport. This may be called after any
572 * operation that affects the data in the current view (selection changed,
573 * etc) to update the menus to reflect the new state.
575 public void setMenusForViewport()
577 setMenusFromViewport(viewport);
581 * Need to call this method when tabs are selected for multiple views, or when
582 * loading from Jalview2XML.java
587 void setMenusFromViewport(AlignViewport av)
589 padGapsMenuitem.setSelected(av.padGaps);
590 colourTextMenuItem.setSelected(av.showColourText);
591 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
592 conservationMenuItem.setSelected(av.getConservationSelected());
593 seqLimits.setSelected(av.getShowJVSuffix());
594 idRightAlign.setSelected(av.rightAlignIds);
595 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
596 renderGapsMenuItem.setSelected(av.renderGaps);
597 wrapMenuItem.setSelected(av.wrapAlignment);
598 scaleAbove.setVisible(av.wrapAlignment);
599 scaleLeft.setVisible(av.wrapAlignment);
600 scaleRight.setVisible(av.wrapAlignment);
601 annotationPanelMenuItem.setState(av.showAnnotation);
602 viewBoxesMenuItem.setSelected(av.showBoxes);
603 viewTextMenuItem.setSelected(av.showText);
604 showNonconservedMenuItem.setSelected(av.showUnconserved);
605 showGroupConsensus.setSelected(av.showGroupConsensus);
606 showGroupConservation.setSelected(av.showGroupConservation);
607 showConsensusHistogram.setSelected(av.showConsensusHistogram);
608 showSequenceLogo.setSelected(av.showSequenceLogo);
609 setColourSelected(ColourSchemeProperty.getColourName(av
610 .getGlobalColourScheme()));
612 showSeqFeatures.setSelected(av.showSequenceFeatures);
613 hiddenMarkers.setState(av.showHiddenMarkers);
614 applyToAllGroups.setState(av.colourAppliesToAllGroups);
615 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
616 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
618 setShowProductsEnabled();
623 Hashtable progressBars, progressBarHandlers;
628 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
630 public void setProgressBar(String message, long id)
632 if (progressBars == null)
634 progressBars = new Hashtable();
635 progressBarHandlers = new Hashtable();
638 JPanel progressPanel;
639 Long lId = new Long(id);
640 GridLayout layout = (GridLayout) statusPanel.getLayout();
641 if (progressBars.get(lId) != null)
643 progressPanel = (JPanel) progressBars.get(new Long(id));
644 statusPanel.remove(progressPanel);
645 progressBars.remove(lId);
646 progressPanel = null;
649 statusBar.setText(message);
651 if (progressBarHandlers.contains(lId))
653 progressBarHandlers.remove(lId);
655 layout.setRows(layout.getRows() - 1);
659 progressPanel = new JPanel(new BorderLayout(10, 5));
661 JProgressBar progressBar = new JProgressBar();
662 progressBar.setIndeterminate(true);
664 progressPanel.add(new JLabel(message), BorderLayout.WEST);
665 progressPanel.add(progressBar, BorderLayout.CENTER);
667 layout.setRows(layout.getRows() + 1);
668 statusPanel.add(progressPanel);
670 progressBars.put(lId, progressPanel);
673 setMenusForViewport();
677 public void registerHandler(final long id,
678 final IProgressIndicatorHandler handler)
680 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
683 "call setProgressBar before registering the progress bar's handler.");
685 progressBarHandlers.put(new Long(id), handler);
686 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
687 if (handler.canCancel())
689 JButton cancel = new JButton("Cancel");
690 final IProgressIndicator us = this;
691 cancel.addActionListener(new ActionListener()
694 public void actionPerformed(ActionEvent e)
696 handler.cancelActivity(id);
697 us.setProgressBar("Cancelled "
698 + ((JLabel) progressPanel.getComponent(0)).getText(), id);
701 progressPanel.add(cancel, BorderLayout.EAST);
707 * @return true if any progress bars are still active
709 public boolean operationInProgress()
711 if (progressBars != null && progressBars.size() > 0)
719 * Added so Castor Mapping file can obtain Jalview Version
721 public String getVersion()
723 return jalview.bin.Cache.getProperty("VERSION");
726 public FeatureRenderer getFeatureRenderer()
728 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
731 public void fetchSequence_actionPerformed(ActionEvent e)
733 new SequenceFetcher(this);
736 public void addFromFile_actionPerformed(ActionEvent e)
738 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
741 public void reload_actionPerformed(ActionEvent e)
743 if (fileName != null)
745 // TODO: work out how to recover feature settings for correct view(s) when
747 if (currentFileFormat.equals("Jalview"))
749 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
750 for (int i = 0; i < frames.length; i++)
752 if (frames[i] instanceof AlignFrame && frames[i] != this
753 && ((AlignFrame) frames[i]).fileName.equals(fileName))
757 frames[i].setSelected(true);
758 Desktop.instance.closeAssociatedWindows();
759 } catch (java.beans.PropertyVetoException ex)
765 Desktop.instance.closeAssociatedWindows();
767 FileLoader loader = new FileLoader();
768 String protocol = fileName.startsWith("http:") ? "URL" : "File";
769 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
773 Rectangle bounds = this.getBounds();
775 FileLoader loader = new FileLoader();
776 String protocol = fileName.startsWith("http:") ? "URL" : "File";
777 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
778 protocol, currentFileFormat);
780 newframe.setBounds(bounds);
781 if (featureSettings != null && featureSettings.isShowing())
783 final Rectangle fspos = featureSettings.frame.getBounds();
784 // TODO: need a 'show feature settings' function that takes bounds -
785 // need to refactor Desktop.addFrame
786 newframe.featureSettings_actionPerformed(null);
787 final FeatureSettings nfs = newframe.featureSettings;
788 SwingUtilities.invokeLater(new Runnable()
792 nfs.frame.setBounds(fspos);
795 this.featureSettings.close();
796 this.featureSettings = null;
798 this.closeMenuItem_actionPerformed(true);
803 public void addFromText_actionPerformed(ActionEvent e)
805 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
808 public void addFromURL_actionPerformed(ActionEvent e)
810 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
813 public void save_actionPerformed(ActionEvent e)
816 || (currentFileFormat == null || !jalview.io.FormatAdapter
817 .isValidIOFormat(currentFileFormat, true))
818 || fileName.startsWith("http"))
820 saveAs_actionPerformed(null);
824 saveAlignment(fileName, currentFileFormat);
834 public void saveAs_actionPerformed(ActionEvent e)
836 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
837 .getProperty("LAST_DIRECTORY"),
838 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
839 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
840 currentFileFormat, false);
842 chooser.setFileView(new JalviewFileView());
843 chooser.setDialogTitle("Save Alignment to file");
844 chooser.setToolTipText("Save");
846 int value = chooser.showSaveDialog(this);
848 if (value == JalviewFileChooser.APPROVE_OPTION)
850 currentFileFormat = chooser.getSelectedFormat();
851 if (currentFileFormat == null)
853 JOptionPane.showInternalMessageDialog(Desktop.desktop,
854 "You must select a file format before saving!",
855 "File format not specified", JOptionPane.WARNING_MESSAGE);
856 value = chooser.showSaveDialog(this);
860 fileName = chooser.getSelectedFile().getPath();
862 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
865 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
866 if (currentFileFormat.indexOf(" ") > -1)
868 currentFileFormat = currentFileFormat.substring(0,
869 currentFileFormat.indexOf(" "));
871 saveAlignment(fileName, currentFileFormat);
875 public boolean saveAlignment(String file, String format)
877 boolean success = true;
879 if (format.equalsIgnoreCase("Jalview"))
881 String shortName = title;
883 if (shortName.indexOf(java.io.File.separatorChar) > -1)
885 shortName = shortName.substring(shortName
886 .lastIndexOf(java.io.File.separatorChar) + 1);
889 success = new Jalview2XML().SaveAlignment(this, file, shortName);
891 statusBar.setText("Successfully saved to file: " + fileName + " in "
892 + format + " format.");
897 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
899 warningMessage("Cannot save file " + fileName + " using format "
900 + format, "Alignment output format not supported");
901 saveAs_actionPerformed(null);
902 // JBPNote need to have a raise_gui flag here
906 String[] omitHidden = null;
908 if (viewport.hasHiddenColumns)
910 int reply = JOptionPane
911 .showInternalConfirmDialog(
913 "The Alignment contains hidden columns."
914 + "\nDo you want to save only the visible alignment?",
915 "Save / Omit Hidden Columns",
916 JOptionPane.YES_NO_OPTION,
917 JOptionPane.QUESTION_MESSAGE);
919 if (reply == JOptionPane.YES_OPTION)
921 omitHidden = viewport.getViewAsString(false);
924 FormatAdapter f = new FormatAdapter();
925 String output = f.formatSequences(format,
926 (Alignment) viewport.alignment, // class cast exceptions will
927 // occur in the distant future
928 omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
938 java.io.PrintWriter out = new java.io.PrintWriter(
939 new java.io.FileWriter(file));
944 statusBar.setText("Successfully saved to file: " + fileName
945 + " in " + format + " format.");
946 } catch (Exception ex)
949 ex.printStackTrace();
956 JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
957 + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
963 private void warningMessage(String warning, String title)
965 if (new jalview.util.Platform().isHeadless())
967 System.err.println("Warning: " + title + "\nWarning: " + warning);
972 JOptionPane.showInternalMessageDialog(this, warning, title,
973 JOptionPane.WARNING_MESSAGE);
984 protected void outputText_actionPerformed(ActionEvent e)
986 String[] omitHidden = null;
988 if (viewport.hasHiddenColumns)
990 int reply = JOptionPane
991 .showInternalConfirmDialog(
993 "The Alignment contains hidden columns."
994 + "\nDo you want to output only the visible alignment?",
995 "Save / Omit Hidden Columns",
996 JOptionPane.YES_NO_OPTION,
997 JOptionPane.QUESTION_MESSAGE);
999 if (reply == JOptionPane.YES_OPTION)
1001 omitHidden = viewport.getViewAsString(false);
1005 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1006 cap.setForInput(null);
1007 Desktop.addInternalFrame(cap, "Alignment output - "
1008 + e.getActionCommand(), 600, 500);
1010 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1011 viewport.alignment, omitHidden, viewport.colSel));
1020 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1022 new HTMLOutput(alignPanel, alignPanel.seqPanel.seqCanvas
1023 .getSequenceRenderer(), alignPanel.seqPanel.seqCanvas
1024 .getFeatureRenderer());
1027 public void createImageMap(File file, String image)
1029 alignPanel.makePNGImageMap(file, image);
1038 public void createPNG(File f)
1040 alignPanel.makePNG(f);
1049 public void createEPS(File f)
1051 alignPanel.makeEPS(f);
1054 public void pageSetup_actionPerformed(ActionEvent e)
1056 PrinterJob printJob = PrinterJob.getPrinterJob();
1057 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1066 public void printMenuItem_actionPerformed(ActionEvent e)
1068 // Putting in a thread avoids Swing painting problems
1069 PrintThread thread = new PrintThread(alignPanel);
1073 public void exportFeatures_actionPerformed(ActionEvent e)
1075 new AnnotationExporter().exportFeatures(alignPanel);
1078 public void exportAnnotations_actionPerformed(ActionEvent e)
1080 new AnnotationExporter().exportAnnotations(alignPanel,
1081 viewport.showAnnotation ? viewport.alignment
1082 .getAlignmentAnnotation() : null, viewport.alignment
1084 ((Alignment) viewport.alignment).alignmentProperties);
1087 public void associatedData_actionPerformed(ActionEvent e)
1089 // Pick the tree file
1090 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
1091 .getProperty("LAST_DIRECTORY"));
1092 chooser.setFileView(new JalviewFileView());
1093 chooser.setDialogTitle("Load Jalview Annotations or Features File");
1094 chooser.setToolTipText("Load Jalview Annotations / Features file");
1096 int value = chooser.showOpenDialog(null);
1098 if (value == JalviewFileChooser.APPROVE_OPTION)
1100 String choice = chooser.getSelectedFile().getPath();
1101 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1102 loadJalviewDataFile(choice);
1108 * Close the current view or all views in the alignment frame. If the frame
1109 * only contains one view then the alignment will be removed from memory.
1111 * @param closeAllTabs
1113 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1115 if (alignPanels != null && alignPanels.size() < 2)
1117 closeAllTabs = true;
1122 if (alignPanels != null)
1126 if (this.isClosed())
1128 // really close all the windows - otherwise wait till
1129 // setClosed(true) is called
1130 for (int i = 0; i < alignPanels.size(); i++)
1132 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1139 closeView(alignPanel);
1145 this.setClosed(true);
1147 } catch (Exception ex)
1149 ex.printStackTrace();
1154 * close alignPanel2 and shuffle tabs appropriately.
1156 * @param alignPanel2
1158 public void closeView(AlignmentPanel alignPanel2)
1160 int index = tabbedPane.getSelectedIndex();
1161 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1162 alignPanels.removeElement(alignPanel2);
1164 // if (viewport == alignPanel2.av)
1168 alignPanel2.closePanel();
1171 tabbedPane.removeTabAt(closedindex);
1172 tabbedPane.validate();
1174 if (index > closedindex || index == tabbedPane.getTabCount())
1176 // modify currently selected tab index if necessary.
1180 this.tabSelectionChanged(index);
1186 void updateEditMenuBar()
1189 if (viewport.historyList.size() > 0)
1191 undoMenuItem.setEnabled(true);
1192 CommandI command = (CommandI) viewport.historyList.peek();
1193 undoMenuItem.setText("Undo " + command.getDescription());
1197 undoMenuItem.setEnabled(false);
1198 undoMenuItem.setText("Undo");
1201 if (viewport.redoList.size() > 0)
1203 redoMenuItem.setEnabled(true);
1205 CommandI command = (CommandI) viewport.redoList.peek();
1206 redoMenuItem.setText("Redo " + command.getDescription());
1210 redoMenuItem.setEnabled(false);
1211 redoMenuItem.setText("Redo");
1215 public void addHistoryItem(CommandI command)
1217 if (command.getSize() > 0)
1219 viewport.historyList.push(command);
1220 viewport.redoList.clear();
1221 updateEditMenuBar();
1222 viewport.hasHiddenColumns = (viewport.colSel != null
1223 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1224 .getHiddenColumns().size() > 0);
1230 * @return alignment objects for all views
1232 AlignmentI[] getViewAlignments()
1234 if (alignPanels != null)
1236 Enumeration e = alignPanels.elements();
1237 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1238 for (int i = 0; e.hasMoreElements(); i++)
1240 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1244 if (viewport != null)
1246 return new AlignmentI[]
1247 { viewport.alignment };
1258 protected void undoMenuItem_actionPerformed(ActionEvent e)
1260 if (viewport.historyList.empty())
1262 CommandI command = (CommandI) viewport.historyList.pop();
1263 viewport.redoList.push(command);
1264 command.undoCommand(getViewAlignments());
1266 AlignViewport originalSource = getOriginatingSource(command);
1267 updateEditMenuBar();
1269 if (originalSource != null)
1271 originalSource.hasHiddenColumns = (viewport.colSel != null
1272 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1273 .getHiddenColumns().size() > 0);
1274 originalSource.firePropertyChange("alignment", null,
1275 originalSource.alignment.getSequences());
1285 protected void redoMenuItem_actionPerformed(ActionEvent e)
1287 if (viewport.redoList.size() < 1)
1292 CommandI command = (CommandI) viewport.redoList.pop();
1293 viewport.historyList.push(command);
1294 command.doCommand(getViewAlignments());
1296 AlignViewport originalSource = getOriginatingSource(command);
1297 updateEditMenuBar();
1299 if (originalSource != null)
1301 originalSource.hasHiddenColumns = (viewport.colSel != null
1302 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1303 .getHiddenColumns().size() > 0);
1304 originalSource.firePropertyChange("alignment", null,
1305 originalSource.alignment.getSequences());
1309 AlignViewport getOriginatingSource(CommandI command)
1311 AlignViewport originalSource = null;
1312 // For sequence removal and addition, we need to fire
1313 // the property change event FROM the viewport where the
1314 // original alignment was altered
1315 AlignmentI al = null;
1316 if (command instanceof EditCommand)
1318 EditCommand editCommand = (EditCommand) command;
1319 al = editCommand.getAlignment();
1320 Vector comps = (Vector) PaintRefresher.components.get(viewport
1321 .getSequenceSetId());
1323 for (int i = 0; i < comps.size(); i++)
1325 if (comps.elementAt(i) instanceof AlignmentPanel)
1327 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
1329 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1336 if (originalSource == null)
1338 // The original view is closed, we must validate
1339 // the current view against the closed view first
1342 PaintRefresher.validateSequences(al, viewport.alignment);
1345 originalSource = viewport;
1348 return originalSource;
1357 public void moveSelectedSequences(boolean up)
1359 SequenceGroup sg = viewport.getSelectionGroup();
1368 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1370 SequenceI seq = viewport.alignment.getSequenceAt(i);
1372 if (!sg.getSequences(null).contains(seq))
1377 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1379 if (sg.getSequences(null).contains(temp))
1384 viewport.alignment.getSequences().setElementAt(temp, i);
1385 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1390 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1392 SequenceI seq = viewport.alignment.getSequenceAt(i);
1394 if (!sg.getSequences(null).contains(seq))
1399 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1401 if (sg.getSequences(null).contains(temp))
1406 viewport.alignment.getSequences().setElementAt(temp, i);
1407 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1411 alignPanel.paintAlignment(true);
1414 synchronized void slideSequences(boolean right, int size)
1416 Vector sg = new Vector();
1417 if (viewport.cursorMode)
1419 sg.addElement(viewport.alignment
1420 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1422 else if (viewport.getSelectionGroup() != null
1423 && viewport.getSelectionGroup().getSize() != viewport.alignment
1426 sg = viewport.getSelectionGroup().getSequences(
1427 viewport.hiddenRepSequences);
1435 Vector invertGroup = new Vector();
1437 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1439 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
1440 invertGroup.add(viewport.alignment.getSequenceAt(i));
1443 SequenceI[] seqs1 = new SequenceI[sg.size()];
1444 for (int i = 0; i < sg.size(); i++)
1445 seqs1[i] = (SequenceI) sg.elementAt(i);
1447 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1448 for (int i = 0; i < invertGroup.size(); i++)
1449 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1451 SlideSequencesCommand ssc;
1453 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1454 size, viewport.getGapCharacter());
1456 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1457 size, viewport.getGapCharacter());
1459 int groupAdjustment = 0;
1460 if (ssc.getGapsInsertedBegin() && right)
1462 if (viewport.cursorMode)
1463 alignPanel.seqPanel.moveCursor(size, 0);
1465 groupAdjustment = size;
1467 else if (!ssc.getGapsInsertedBegin() && !right)
1469 if (viewport.cursorMode)
1470 alignPanel.seqPanel.moveCursor(-size, 0);
1472 groupAdjustment = -size;
1475 if (groupAdjustment != 0)
1477 viewport.getSelectionGroup().setStartRes(
1478 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1479 viewport.getSelectionGroup().setEndRes(
1480 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1483 boolean appendHistoryItem = false;
1484 if (viewport.historyList != null && viewport.historyList.size() > 0
1485 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1487 appendHistoryItem = ssc
1488 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1492 if (!appendHistoryItem)
1493 addHistoryItem(ssc);
1504 protected void copy_actionPerformed(ActionEvent e)
1507 if (viewport.getSelectionGroup() == null)
1511 // TODO: preserve the ordering of displayed alignment annotation in any
1512 // internal paste (particularly sequence associated annotation)
1513 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1514 String[] omitHidden = null;
1516 if (viewport.hasHiddenColumns)
1518 omitHidden = viewport.getViewAsString(true);
1521 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1524 StringSelection ss = new StringSelection(output);
1528 jalview.gui.Desktop.internalCopy = true;
1529 // Its really worth setting the clipboard contents
1530 // to empty before setting the large StringSelection!!
1531 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
1532 new StringSelection(""), null);
1534 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1536 } catch (OutOfMemoryError er)
1538 new OOMWarning("copying region", er);
1542 Vector hiddenColumns = null;
1543 if (viewport.hasHiddenColumns)
1545 hiddenColumns = new Vector();
1546 int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1547 .getSelectionGroup().getEndRes();
1548 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1551 int[] region = (int[]) viewport.getColumnSelection()
1552 .getHiddenColumns().elementAt(i);
1553 if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1555 hiddenColumns.addElement(new int[]
1556 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1561 Desktop.jalviewClipboard = new Object[]
1562 { seqs, viewport.alignment.getDataset(), hiddenColumns };
1563 statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
1572 protected void pasteNew_actionPerformed(ActionEvent e)
1583 protected void pasteThis_actionPerformed(ActionEvent e)
1589 * Paste contents of Jalview clipboard
1591 * @param newAlignment
1592 * true to paste to a new alignment, otherwise add to this.
1594 void paste(boolean newAlignment)
1596 boolean externalPaste = true;
1599 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1600 Transferable contents = c.getContents(this);
1602 if (contents == null)
1610 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1611 if (str.length() < 1)
1616 format = new IdentifyFile().Identify(str, "Paste");
1618 } catch (OutOfMemoryError er)
1620 new OOMWarning("Out of memory pasting sequences!!", er);
1624 SequenceI[] sequences;
1625 boolean annotationAdded = false;
1626 AlignmentI alignment = null;
1628 if (Desktop.jalviewClipboard != null)
1630 // The clipboard was filled from within Jalview, we must use the
1632 // And dataset from the copied alignment
1633 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1634 // be doubly sure that we create *new* sequence objects.
1635 sequences = new SequenceI[newseq.length];
1636 for (int i = 0; i < newseq.length; i++)
1638 sequences[i] = new Sequence(newseq[i]);
1640 alignment = new Alignment(sequences);
1641 externalPaste = false;
1645 // parse the clipboard as an alignment.
1646 alignment = new FormatAdapter().readFile(str, "Paste", format);
1647 sequences = alignment.getSequencesArray();
1655 if (Desktop.jalviewClipboard != null)
1657 // dataset is inherited
1658 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1662 // new dataset is constructed
1663 alignment.setDataset(null);
1665 alwidth = alignment.getWidth() + 1;
1669 AlignmentI pastedal = alignment; // preserve pasted alignment object
1670 // Add pasted sequences and dataset into existing alignment.
1671 alignment = viewport.getAlignment();
1672 alwidth = alignment.getWidth() + 1;
1673 // decide if we need to import sequences from an existing dataset
1674 boolean importDs = Desktop.jalviewClipboard != null
1675 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1676 // importDs==true instructs us to copy over new dataset sequences from
1677 // an existing alignment
1678 Vector newDs = (importDs) ? new Vector() : null; // used to create
1679 // minimum dataset set
1681 for (int i = 0; i < sequences.length; i++)
1685 newDs.addElement(null);
1687 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1689 if (importDs && ds != null)
1691 if (!newDs.contains(ds))
1693 newDs.setElementAt(ds, i);
1694 ds = new Sequence(ds);
1695 // update with new dataset sequence
1696 sequences[i].setDatasetSequence(ds);
1700 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1705 // copy and derive new dataset sequence
1706 sequences[i] = sequences[i].deriveSequence();
1707 alignment.getDataset().addSequence(
1708 sequences[i].getDatasetSequence());
1709 // TODO: avoid creation of duplicate dataset sequences with a
1710 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1712 alignment.addSequence(sequences[i]); // merges dataset
1716 newDs.clear(); // tidy up
1718 if (pastedal.getAlignmentAnnotation() != null)
1720 // Add any annotation attached to alignment.
1721 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1722 for (int i = 0; i < alann.length; i++)
1724 annotationAdded = true;
1725 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1727 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1728 newann.padAnnotation(alwidth);
1729 alignment.addAnnotation(newann);
1739 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1740 sequences, 0, alignment.getWidth(), alignment));
1742 // Add any annotations attached to sequences
1743 for (int i = 0; i < sequences.length; i++)
1745 if (sequences[i].getAnnotation() != null)
1747 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1749 annotationAdded = true;
1750 sequences[i].getAnnotation()[a].adjustForAlignment();
1751 sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1752 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1757 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1764 // propagate alignment changed.
1765 viewport.setEndSeq(alignment.getHeight());
1766 if (annotationAdded)
1768 // Duplicate sequence annotation in all views.
1769 AlignmentI[] alview = this.getViewAlignments();
1770 for (int i = 0; i < sequences.length; i++)
1772 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1775 for (int avnum = 0; avnum < alview.length; avnum++)
1777 if (alview[avnum] != alignment)
1779 // duplicate in a view other than the one with input focus
1780 int avwidth = alview[avnum].getWidth() + 1;
1781 // this relies on sann being preserved after we
1782 // modify the sequence's annotation array for each duplication
1783 for (int a = 0; a < sann.length; a++)
1785 AlignmentAnnotation newann = new AlignmentAnnotation(
1787 sequences[i].addAlignmentAnnotation(newann);
1788 newann.padAnnotation(avwidth);
1789 alview[avnum].addAnnotation(newann); // annotation was
1790 // duplicated earlier
1791 alview[avnum].setAnnotationIndex(newann, a);
1796 buildSortByAnnotationScoresMenu();
1798 viewport.firePropertyChange("alignment", null, alignment
1804 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
1806 String newtitle = new String("Copied sequences");
1808 if (Desktop.jalviewClipboard != null
1809 && Desktop.jalviewClipboard[2] != null)
1811 Vector hc = (Vector) Desktop.jalviewClipboard[2];
1812 for (int i = 0; i < hc.size(); i++)
1814 int[] region = (int[]) hc.elementAt(i);
1815 af.viewport.hideColumns(region[0], region[1]);
1819 // >>>This is a fix for the moment, until a better solution is
1821 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
1823 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1825 // TODO: maintain provenance of an alignment, rather than just make the
1826 // title a concatenation of operations.
1829 if (title.startsWith("Copied sequences"))
1835 newtitle = newtitle.concat("- from " + title);
1840 newtitle = new String("Pasted sequences");
1843 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1848 } catch (Exception ex)
1850 ex.printStackTrace();
1851 System.out.println("Exception whilst pasting: " + ex);
1852 // could be anything being pasted in here
1863 protected void cut_actionPerformed(ActionEvent e)
1865 copy_actionPerformed(null);
1866 delete_actionPerformed(null);
1875 protected void delete_actionPerformed(ActionEvent evt)
1878 SequenceGroup sg = viewport.getSelectionGroup();
1884 Vector seqs = new Vector();
1886 for (int i = 0; i < sg.getSize(); i++)
1888 seq = sg.getSequenceAt(i);
1889 seqs.addElement(seq);
1892 // If the cut affects all sequences, remove highlighted columns
1893 if (sg.getSize() == viewport.alignment.getHeight())
1895 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1896 sg.getEndRes() + 1);
1899 SequenceI[] cut = new SequenceI[seqs.size()];
1900 for (int i = 0; i < seqs.size(); i++)
1902 cut[i] = (SequenceI) seqs.elementAt(i);
1906 * //ADD HISTORY ITEM
1908 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1909 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1910 viewport.alignment));
1912 viewport.setSelectionGroup(null);
1913 viewport.sendSelection();
1914 viewport.alignment.deleteGroup(sg);
1916 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1918 if (viewport.getAlignment().getHeight() < 1)
1922 this.setClosed(true);
1923 } catch (Exception ex)
1935 protected void deleteGroups_actionPerformed(ActionEvent e)
1937 viewport.alignment.deleteAllGroups();
1938 viewport.sequenceColours = null;
1939 viewport.setSelectionGroup(null);
1940 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1941 alignPanel.updateAnnotation();
1942 alignPanel.paintAlignment(true);
1951 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1953 SequenceGroup sg = new SequenceGroup();
1955 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1957 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1960 sg.setEndRes(viewport.alignment.getWidth() - 1);
1961 viewport.setSelectionGroup(sg);
1962 viewport.sendSelection();
1963 alignPanel.paintAlignment(true);
1964 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1973 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1975 if (viewport.cursorMode)
1977 alignPanel.seqPanel.keyboardNo1 = null;
1978 alignPanel.seqPanel.keyboardNo2 = null;
1980 viewport.setSelectionGroup(null);
1981 viewport.getColumnSelection().clear();
1982 viewport.setSelectionGroup(null);
1983 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1984 alignPanel.idPanel.idCanvas.searchResults = null;
1985 alignPanel.paintAlignment(true);
1986 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1995 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1997 SequenceGroup sg = viewport.getSelectionGroup();
2001 selectAllSequenceMenuItem_actionPerformed(null);
2006 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2008 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2011 alignPanel.paintAlignment(true);
2012 viewport.sendSelection();
2013 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2016 public void invertColSel_actionPerformed(ActionEvent e)
2018 viewport.invertColumnSelection();
2019 alignPanel.paintAlignment(true);
2028 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2030 trimAlignment(true);
2039 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2041 trimAlignment(false);
2044 void trimAlignment(boolean trimLeft)
2046 ColumnSelection colSel = viewport.getColumnSelection();
2049 if (colSel.size() > 0)
2053 column = colSel.getMin();
2057 column = colSel.getMax();
2061 if (viewport.getSelectionGroup() != null)
2063 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2064 viewport.hiddenRepSequences);
2068 seqs = viewport.alignment.getSequencesArray();
2071 TrimRegionCommand trimRegion;
2074 trimRegion = new TrimRegionCommand("Remove Left",
2075 TrimRegionCommand.TRIM_LEFT, seqs, column,
2076 viewport.alignment, viewport.colSel,
2077 viewport.selectionGroup);
2078 viewport.setStartRes(0);
2082 trimRegion = new TrimRegionCommand("Remove Right",
2083 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2084 viewport.alignment, viewport.colSel,
2085 viewport.selectionGroup);
2088 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2090 addHistoryItem(trimRegion);
2092 Vector groups = viewport.alignment.getGroups();
2094 for (int i = 0; i < groups.size(); i++)
2096 SequenceGroup sg = (SequenceGroup) groups.get(i);
2098 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2099 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2101 viewport.alignment.deleteGroup(sg);
2105 viewport.firePropertyChange("alignment", null, viewport
2106 .getAlignment().getSequences());
2116 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2118 int start = 0, end = viewport.alignment.getWidth() - 1;
2121 if (viewport.getSelectionGroup() != null)
2123 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2124 viewport.hiddenRepSequences);
2125 start = viewport.getSelectionGroup().getStartRes();
2126 end = viewport.getSelectionGroup().getEndRes();
2130 seqs = viewport.alignment.getSequencesArray();
2133 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2134 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
2136 addHistoryItem(removeGapCols);
2138 statusBar.setText("Removed " + removeGapCols.getSize()
2139 + " empty columns.");
2141 // This is to maintain viewport position on first residue
2142 // of first sequence
2143 SequenceI seq = viewport.alignment.getSequenceAt(0);
2144 int startRes = seq.findPosition(viewport.startRes);
2145 // ShiftList shifts;
2146 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2147 // edit.alColumnChanges=shifts.getInverse();
2148 // if (viewport.hasHiddenColumns)
2149 // viewport.getColumnSelection().compensateForEdits(shifts);
2150 viewport.setStartRes(seq.findIndex(startRes) - 1);
2151 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2162 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2164 int start = 0, end = viewport.alignment.getWidth() - 1;
2167 if (viewport.getSelectionGroup() != null)
2169 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2170 viewport.hiddenRepSequences);
2171 start = viewport.getSelectionGroup().getStartRes();
2172 end = viewport.getSelectionGroup().getEndRes();
2176 seqs = viewport.alignment.getSequencesArray();
2179 // This is to maintain viewport position on first residue
2180 // of first sequence
2181 SequenceI seq = viewport.alignment.getSequenceAt(0);
2182 int startRes = seq.findPosition(viewport.startRes);
2184 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2185 viewport.alignment));
2187 viewport.setStartRes(seq.findIndex(startRes) - 1);
2189 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2200 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2202 viewport.padGaps = padGapsMenuitem.isSelected();
2203 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2209 // if (justifySeqs>0)
2211 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2223 public void findMenuItem_actionPerformed(ActionEvent e)
2228 public void newView_actionPerformed(ActionEvent e)
2230 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2233 newap.av.gatherViewsHere = false;
2235 if (viewport.viewName == null)
2237 viewport.viewName = "Original";
2240 newap.av.historyList = viewport.historyList;
2241 newap.av.redoList = viewport.redoList;
2243 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2244 String newViewName = "View " + index;
2246 Vector comps = (Vector) PaintRefresher.components.get(viewport
2247 .getSequenceSetId());
2248 Vector existingNames = new Vector();
2249 for (int i = 0; i < comps.size(); i++)
2251 if (comps.elementAt(i) instanceof AlignmentPanel)
2253 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2254 if (!existingNames.contains(ap.av.viewName))
2256 existingNames.addElement(ap.av.viewName);
2261 while (existingNames.contains(newViewName))
2263 newViewName = "View " + (++index);
2266 newap.av.viewName = newViewName;
2268 addAlignmentPanel(newap, true);
2270 if (alignPanels.size() == 2)
2272 viewport.gatherViewsHere = true;
2274 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2277 public void expandViews_actionPerformed(ActionEvent e)
2279 Desktop.instance.explodeViews(this);
2282 public void gatherViews_actionPerformed(ActionEvent e)
2284 Desktop.instance.gatherViews(this);
2293 public void font_actionPerformed(ActionEvent e)
2295 new FontChooser(alignPanel);
2304 protected void seqLimit_actionPerformed(ActionEvent e)
2306 viewport.setShowJVSuffix(seqLimits.isSelected());
2308 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2309 .calculateIdWidth());
2310 alignPanel.paintAlignment(true);
2313 public void idRightAlign_actionPerformed(ActionEvent e)
2315 viewport.rightAlignIds = idRightAlign.isSelected();
2316 alignPanel.paintAlignment(true);
2319 public void centreColumnLabels_actionPerformed(ActionEvent e)
2321 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2322 alignPanel.paintAlignment(true);
2328 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2330 protected void followHighlight_actionPerformed()
2332 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2334 alignPanel.scrollToPosition(
2335 alignPanel.seqPanel.seqCanvas.searchResults, false);
2345 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2347 viewport.setColourText(colourTextMenuItem.isSelected());
2348 alignPanel.paintAlignment(true);
2357 public void wrapMenuItem_actionPerformed(ActionEvent e)
2359 scaleAbove.setVisible(wrapMenuItem.isSelected());
2360 scaleLeft.setVisible(wrapMenuItem.isSelected());
2361 scaleRight.setVisible(wrapMenuItem.isSelected());
2362 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2363 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2366 public void showAllSeqs_actionPerformed(ActionEvent e)
2368 viewport.showAllHiddenSeqs();
2371 public void showAllColumns_actionPerformed(ActionEvent e)
2373 viewport.showAllHiddenColumns();
2377 public void hideSelSequences_actionPerformed(ActionEvent e)
2379 viewport.hideAllSelectedSeqs();
2380 alignPanel.paintAlignment(true);
2384 * called by key handler and the hide all/show all menu items
2389 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2392 boolean hide = false;
2393 SequenceGroup sg = viewport.getSelectionGroup();
2394 if (!toggleSeqs && !toggleCols)
2396 // Hide everything by the current selection - this is a hack - we do the
2397 // invert and then hide
2398 // first check that there will be visible columns after the invert.
2399 if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
2400 .getSelected().size() > 0)
2401 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2404 // now invert the sequence set, if required - empty selection implies
2405 // that no hiding is required.
2408 invertSequenceMenuItem_actionPerformed(null);
2409 sg = viewport.getSelectionGroup();
2413 viewport.expandColSelection(sg, true);
2414 // finally invert the column selection and get the new sequence
2416 invertColSel_actionPerformed(null);
2423 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
2425 hideSelSequences_actionPerformed(null);
2428 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
2430 showAllSeqs_actionPerformed(null);
2436 if (viewport.colSel.getSelected().size() > 0)
2438 hideSelColumns_actionPerformed(null);
2441 viewport.selectionGroup = sg;
2446 showAllColumns_actionPerformed(null);
2455 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2456 * event.ActionEvent)
2458 public void hideAllButSelection_actionPerformed(ActionEvent e)
2460 toggleHiddenRegions(false, false);
2467 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2470 public void hideAllSelection_actionPerformed(ActionEvent e)
2472 SequenceGroup sg = viewport.getSelectionGroup();
2473 viewport.expandColSelection(sg, false);
2474 viewport.hideAllSelectedSeqs();
2475 viewport.hideSelectedColumns();
2476 alignPanel.paintAlignment(true);
2483 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2486 public void showAllhidden_actionPerformed(ActionEvent e)
2488 viewport.showAllHiddenColumns();
2489 viewport.showAllHiddenSeqs();
2490 alignPanel.paintAlignment(true);
2493 public void hideSelColumns_actionPerformed(ActionEvent e)
2495 viewport.hideSelectedColumns();
2496 alignPanel.paintAlignment(true);
2499 public void hiddenMarkers_actionPerformed(ActionEvent e)
2501 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2511 protected void scaleAbove_actionPerformed(ActionEvent e)
2513 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2514 alignPanel.paintAlignment(true);
2523 protected void scaleLeft_actionPerformed(ActionEvent e)
2525 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2526 alignPanel.paintAlignment(true);
2535 protected void scaleRight_actionPerformed(ActionEvent e)
2537 viewport.setScaleRightWrapped(scaleRight.isSelected());
2538 alignPanel.paintAlignment(true);
2547 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2549 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2550 alignPanel.paintAlignment(true);
2559 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2561 viewport.setShowText(viewTextMenuItem.isSelected());
2562 alignPanel.paintAlignment(true);
2571 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2573 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2574 alignPanel.paintAlignment(true);
2577 public FeatureSettings featureSettings;
2579 public void featureSettings_actionPerformed(ActionEvent e)
2581 if (featureSettings != null)
2583 featureSettings.close();
2584 featureSettings = null;
2586 if (!showSeqFeatures.isSelected())
2588 // make sure features are actually displayed
2589 showSeqFeatures.setSelected(true);
2590 showSeqFeatures_actionPerformed(null);
2592 featureSettings = new FeatureSettings(this);
2596 * Set or clear 'Show Sequence Features'
2601 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2603 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2604 alignPanel.paintAlignment(true);
2605 if (alignPanel.getOverviewPanel() != null)
2607 alignPanel.getOverviewPanel().updateOverviewImage();
2612 * Set or clear 'Show Sequence Features'
2617 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2619 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2621 if (viewport.getShowSequenceFeaturesHeight())
2623 // ensure we're actually displaying features
2624 viewport.setShowSequenceFeatures(true);
2625 showSeqFeatures.setSelected(true);
2627 alignPanel.paintAlignment(true);
2628 if (alignPanel.getOverviewPanel() != null)
2630 alignPanel.getOverviewPanel().updateOverviewImage();
2640 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2642 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2643 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2646 public void alignmentProperties()
2648 JEditorPane editPane = new JEditorPane("text/html", "");
2649 editPane.setEditable(false);
2650 StringBuffer contents = new StringBuffer("<html>");
2653 int min = Integer.MAX_VALUE, max = 0;
2654 for (int i = 0; i < viewport.alignment.getHeight(); i++)
2656 int size = viewport.alignment.getSequenceAt(i).getEnd()
2657 - viewport.alignment.getSequenceAt(i).getStart();
2664 avg = avg / (float) viewport.alignment.getHeight();
2666 contents.append("<br>Sequences: " + viewport.alignment.getHeight());
2667 contents.append("<br>Minimum Sequence Length: " + min);
2668 contents.append("<br>Maximum Sequence Length: " + max);
2669 contents.append("<br>Average Length: " + (int) avg);
2671 if (((Alignment) viewport.alignment).getProperties() != null)
2673 Hashtable props = ((Alignment) viewport.alignment).getProperties();
2674 Enumeration en = props.keys();
2675 contents.append("<br><br><table border=\"1\">");
2676 while (en.hasMoreElements())
2678 String key = en.nextElement().toString();
2679 StringBuffer val = new StringBuffer();
2680 String vals = props.get(key).toString();
2684 npos = vals.indexOf("\n", pos);
2687 val.append(vals.substring(pos));
2691 val.append(vals.substring(pos, npos));
2695 } while (npos != -1);
2697 .append("<tr><td>" + key + "</td><td>" + val + "</td></tr>");
2699 contents.append("</table>");
2701 editPane.setText(contents.toString() + "</html>");
2702 JInternalFrame frame = new JInternalFrame();
2703 frame.getContentPane().add(new JScrollPane(editPane));
2705 Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
2706 + getTitle(), 500, 400);
2715 public void overviewMenuItem_actionPerformed(ActionEvent e)
2717 if (alignPanel.overviewPanel != null)
2722 JInternalFrame frame = new JInternalFrame();
2723 OverviewPanel overview = new OverviewPanel(alignPanel);
2724 frame.setContentPane(overview);
2725 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(), frame
2726 .getWidth(), frame.getHeight());
2728 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2730 .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2732 public void internalFrameClosed(
2733 javax.swing.event.InternalFrameEvent evt)
2735 alignPanel.setOverviewPanel(null);
2739 alignPanel.setOverviewPanel(overview);
2742 public void textColour_actionPerformed(ActionEvent e)
2744 new TextColourChooser().chooseColour(alignPanel, null);
2753 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2764 public void clustalColour_actionPerformed(ActionEvent e)
2766 changeColour(new ClustalxColourScheme(
2767 viewport.alignment.getSequences(), viewport.alignment
2777 public void zappoColour_actionPerformed(ActionEvent e)
2779 changeColour(new ZappoColourScheme());
2788 public void taylorColour_actionPerformed(ActionEvent e)
2790 changeColour(new TaylorColourScheme());
2799 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2801 changeColour(new HydrophobicColourScheme());
2810 public void helixColour_actionPerformed(ActionEvent e)
2812 changeColour(new HelixColourScheme());
2821 public void strandColour_actionPerformed(ActionEvent e)
2823 changeColour(new StrandColourScheme());
2832 public void turnColour_actionPerformed(ActionEvent e)
2834 changeColour(new TurnColourScheme());
2843 public void buriedColour_actionPerformed(ActionEvent e)
2845 changeColour(new BuriedColourScheme());
2854 public void nucleotideColour_actionPerformed(ActionEvent e)
2856 changeColour(new NucleotideColourScheme());
2859 public void annotationColour_actionPerformed(ActionEvent e)
2861 new AnnotationColourChooser(viewport, alignPanel);
2870 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2872 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2881 public void changeColour(ColourSchemeI cs)
2887 if (viewport.getAbovePIDThreshold())
2889 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2892 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2894 viewport.setGlobalColourScheme(cs);
2898 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2901 if (viewport.getConservationSelected())
2904 Alignment al = (Alignment) viewport.alignment;
2905 Conservation c = new Conservation("All",
2906 ResidueProperties.propHash, 3, al.getSequences(), 0, al
2910 c.verdict(false, viewport.ConsPercGaps);
2912 cs.setConservation(c);
2914 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
2919 cs.setConservation(null);
2922 cs.setConsensus(viewport.hconsensus);
2925 viewport.setGlobalColourScheme(cs);
2927 if (viewport.getColourAppliesToAllGroups())
2929 Vector groups = viewport.alignment.getGroups();
2931 for (int i = 0; i < groups.size(); i++)
2933 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2941 if (cs instanceof ClustalxColourScheme)
2943 sg.cs = new ClustalxColourScheme(sg
2944 .getSequences(viewport.hiddenRepSequences), sg.getWidth());
2946 else if (cs instanceof UserColourScheme)
2948 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
2954 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2955 } catch (Exception ex)
2960 if (viewport.getAbovePIDThreshold()
2961 || cs instanceof PIDColourScheme
2962 || cs instanceof Blosum62ColourScheme)
2964 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2966 sg.cs.setConsensus(AAFrequency.calculate(sg
2967 .getSequences(viewport.hiddenRepSequences), sg
2968 .getStartRes(), sg.getEndRes() + 1));
2972 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2975 if (viewport.getConservationSelected())
2977 Conservation c = new Conservation("Group",
2978 ResidueProperties.propHash, 3, sg
2979 .getSequences(viewport.hiddenRepSequences), sg
2980 .getStartRes(), sg.getEndRes() + 1);
2982 c.verdict(false, viewport.ConsPercGaps);
2983 sg.cs.setConservation(c);
2987 sg.cs.setConservation(null);
2992 if (alignPanel.getOverviewPanel() != null)
2994 alignPanel.getOverviewPanel().updateOverviewImage();
2997 alignPanel.paintAlignment(true);
3006 protected void modifyPID_actionPerformed(ActionEvent e)
3008 if (viewport.getAbovePIDThreshold()
3009 && viewport.globalColourScheme != null)
3011 SliderPanel.setPIDSliderSource(alignPanel, viewport
3012 .getGlobalColourScheme(), "Background");
3013 SliderPanel.showPIDSlider();
3023 protected void modifyConservation_actionPerformed(ActionEvent e)
3025 if (viewport.getConservationSelected()
3026 && viewport.globalColourScheme != null)
3028 SliderPanel.setConservationSlider(alignPanel,
3029 viewport.globalColourScheme, "Background");
3030 SliderPanel.showConservationSlider();
3040 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3042 viewport.setConservationSelected(conservationMenuItem.isSelected());
3044 viewport.setAbovePIDThreshold(false);
3045 abovePIDThreshold.setSelected(false);
3047 changeColour(viewport.getGlobalColourScheme());
3049 modifyConservation_actionPerformed(null);
3058 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3060 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3062 conservationMenuItem.setSelected(false);
3063 viewport.setConservationSelected(false);
3065 changeColour(viewport.getGlobalColourScheme());
3067 modifyPID_actionPerformed(null);
3076 public void userDefinedColour_actionPerformed(ActionEvent e)
3078 if (e.getActionCommand().equals("User Defined..."))
3080 new UserDefinedColours(alignPanel, null);
3084 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3085 .getUserColourSchemes().get(e.getActionCommand());
3091 public void updateUserColourMenu()
3094 Component[] menuItems = colourMenu.getMenuComponents();
3095 int i, iSize = menuItems.length;
3096 for (i = 0; i < iSize; i++)
3098 if (menuItems[i].getName() != null
3099 && menuItems[i].getName().equals("USER_DEFINED"))
3101 colourMenu.remove(menuItems[i]);
3105 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3107 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3108 .getUserColourSchemes().keys();
3110 while (userColours.hasMoreElements())
3112 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3113 userColours.nextElement().toString());
3114 radioItem.setName("USER_DEFINED");
3115 radioItem.addMouseListener(new MouseAdapter()
3117 public void mousePressed(MouseEvent evt)
3119 if (evt.isControlDown()
3120 || SwingUtilities.isRightMouseButton(evt))
3123 .removeActionListener(radioItem.getActionListeners()[0]);
3125 int option = JOptionPane.showInternalConfirmDialog(
3126 jalview.gui.Desktop.desktop,
3127 "Remove from default list?",
3128 "Remove user defined colour",
3129 JOptionPane.YES_NO_OPTION);
3130 if (option == JOptionPane.YES_OPTION)
3132 jalview.gui.UserDefinedColours
3133 .removeColourFromDefaults(radioItem.getText());
3134 colourMenu.remove(radioItem);
3138 radioItem.addActionListener(new ActionListener()
3140 public void actionPerformed(ActionEvent evt)
3142 userDefinedColour_actionPerformed(evt);
3149 radioItem.addActionListener(new ActionListener()
3151 public void actionPerformed(ActionEvent evt)
3153 userDefinedColour_actionPerformed(evt);
3157 colourMenu.insert(radioItem, 15);
3158 colours.add(radioItem);
3169 public void PIDColour_actionPerformed(ActionEvent e)
3171 changeColour(new PIDColourScheme());
3180 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3182 changeColour(new Blosum62ColourScheme());
3191 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3193 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3194 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3195 .getAlignment().getSequenceAt(0), null);
3196 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3197 viewport.alignment));
3198 alignPanel.paintAlignment(true);
3207 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3209 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3210 AlignmentSorter.sortByID(viewport.getAlignment());
3211 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
3212 alignPanel.paintAlignment(true);
3221 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3223 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3224 AlignmentSorter.sortByLength(viewport.getAlignment());
3225 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3226 viewport.alignment));
3227 alignPanel.paintAlignment(true);
3236 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3238 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3239 AlignmentSorter.sortByGroup(viewport.getAlignment());
3240 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3241 viewport.alignment));
3243 alignPanel.paintAlignment(true);
3252 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3254 new RedundancyPanel(alignPanel, this);
3263 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3265 if ((viewport.getSelectionGroup() == null)
3266 || (viewport.getSelectionGroup().getSize() < 2))
3268 JOptionPane.showInternalMessageDialog(this,
3269 "You must select at least 2 sequences.", "Invalid Selection",
3270 JOptionPane.WARNING_MESSAGE);
3274 JInternalFrame frame = new JInternalFrame();
3275 frame.setContentPane(new PairwiseAlignPanel(viewport));
3276 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
3286 public void PCAMenuItem_actionPerformed(ActionEvent e)
3288 if (((viewport.getSelectionGroup() != null)
3289 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3290 .getSelectionGroup().getSize() > 0))
3291 || (viewport.getAlignment().getHeight() < 4))
3293 JOptionPane.showInternalMessageDialog(this,
3294 "Principal component analysis must take\n"
3295 + "at least 4 input sequences.",
3296 "Sequence selection insufficient",
3297 JOptionPane.WARNING_MESSAGE);
3302 new PCAPanel(alignPanel);
3305 public void autoCalculate_actionPerformed(ActionEvent e)
3307 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3308 if (viewport.autoCalculateConsensus)
3310 viewport.firePropertyChange("alignment", null, viewport
3311 .getAlignment().getSequences());
3321 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3323 NewTreePanel("AV", "PID", "Average distance tree using PID");
3332 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3334 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3343 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3345 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3354 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3356 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3369 void NewTreePanel(String type, String pwType, String title)
3373 if (viewport.getSelectionGroup() != null)
3375 if (viewport.getSelectionGroup().getSize() < 3)
3380 "You need to have more than two sequences selected to build a tree!",
3381 "Not enough sequences", JOptionPane.WARNING_MESSAGE);
3386 SequenceGroup sg = viewport.getSelectionGroup();
3388 /* Decide if the selection is a column region */
3389 while (s < sg.getSize())
3391 if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
3397 "The selected region to create a tree may\nonly contain residues or gaps.\n"
3398 + "Try using the Pad function in the edit menu,\n"
3399 + "or one of the multiple sequence alignment web services.",
3400 "Sequences in selection are not aligned",
3401 JOptionPane.WARNING_MESSAGE);
3407 title = title + " on region";
3408 tp = new TreePanel(alignPanel, type, pwType);
3412 // are the visible sequences aligned?
3413 if (!viewport.alignment.isAligned(false))
3418 "The sequences must be aligned before creating a tree.\n"
3419 + "Try using the Pad function in the edit menu,\n"
3420 + "or one of the multiple sequence alignment web services.",
3421 "Sequences not aligned",
3422 JOptionPane.WARNING_MESSAGE);
3427 if (viewport.alignment.getHeight() < 2)
3432 tp = new TreePanel(alignPanel, type, pwType);
3437 if (viewport.viewName != null)
3439 title += viewport.viewName + " of ";
3442 title += this.title;
3444 Desktop.addInternalFrame(tp, title, 600, 500);
3455 public void addSortByOrderMenuItem(String title,
3456 final AlignmentOrder order)
3458 final JMenuItem item = new JMenuItem("by " + title);
3460 item.addActionListener(new java.awt.event.ActionListener()
3462 public void actionPerformed(ActionEvent e)
3464 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3466 // TODO: JBPNote - have to map order entries to curent SequenceI
3468 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3470 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3471 viewport.alignment));
3473 alignPanel.paintAlignment(true);
3479 * Add a new sort by annotation score menu item
3482 * the menu to add the option to
3484 * the label used to retrieve scores for each sequence on the
3487 public void addSortByAnnotScoreMenuItem(JMenu sort,
3488 final String scoreLabel)
3490 final JMenuItem item = new JMenuItem(scoreLabel);
3492 item.addActionListener(new java.awt.event.ActionListener()
3494 public void actionPerformed(ActionEvent e)
3496 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3497 AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport
3498 .getAlignment());// ,viewport.getSelectionGroup());
3499 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3500 viewport.alignment));
3501 alignPanel.paintAlignment(true);
3507 * last hash for alignment's annotation array - used to minimise cost of
3510 protected int _annotationScoreVectorHash;
3513 * search the alignment and rebuild the sort by annotation score submenu the
3514 * last alignment annotation vector hash is stored to minimize cost of
3515 * rebuilding in subsequence calls.
3518 public void buildSortByAnnotationScoresMenu()
3520 if (viewport.alignment.getAlignmentAnnotation() == null)
3525 if (viewport.alignment.getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3527 sortByAnnotScore.removeAll();
3528 // almost certainly a quicker way to do this - but we keep it simple
3529 Hashtable scoreSorts = new Hashtable();
3530 AlignmentAnnotation aann[];
3531 Enumeration sq = viewport.alignment.getSequences().elements();
3532 while (sq.hasMoreElements())
3534 aann = ((SequenceI) sq.nextElement()).getAnnotation();
3535 for (int i = 0; aann != null && i < aann.length; i++)
3537 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3539 scoreSorts.put(aann[i].label, aann[i].label);
3543 Enumeration labels = scoreSorts.keys();
3544 while (labels.hasMoreElements())
3546 addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels
3549 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3552 _annotationScoreVectorHash = viewport.alignment
3553 .getAlignmentAnnotation().hashCode();
3558 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3559 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3560 * call. Listeners are added to remove the menu item when the treePanel is
3561 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3565 * Displayed tree window.
3567 * SortBy menu item title.
3569 public void buildTreeMenu()
3571 sortByTreeMenu.removeAll();
3573 Vector comps = (Vector) PaintRefresher.components.get(viewport
3574 .getSequenceSetId());
3575 Vector treePanels = new Vector();
3576 int i, iSize = comps.size();
3577 for (i = 0; i < iSize; i++)
3579 if (comps.elementAt(i) instanceof TreePanel)
3581 treePanels.add(comps.elementAt(i));
3585 iSize = treePanels.size();
3589 sortByTreeMenu.setVisible(false);
3593 sortByTreeMenu.setVisible(true);
3595 for (i = 0; i < treePanels.size(); i++)
3597 TreePanel tp = (TreePanel) treePanels.elementAt(i);
3598 final JMenuItem item = new JMenuItem(tp.getTitle());
3599 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3600 item.addActionListener(new java.awt.event.ActionListener()
3602 public void actionPerformed(ActionEvent e)
3604 SequenceI[] oldOrder = viewport.getAlignment()
3605 .getSequencesArray();
3606 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
3608 addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
3609 viewport.alignment));
3611 alignPanel.paintAlignment(true);
3615 sortByTreeMenu.add(item);
3620 * Work out whether the whole set of sequences or just the selected set will
3621 * be submitted for multiple alignment.
3624 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3626 // Now, check we have enough sequences
3627 AlignmentView msa = null;
3629 if ((viewport.getSelectionGroup() != null)
3630 && (viewport.getSelectionGroup().getSize() > 1))
3632 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3633 // some common interface!
3635 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3636 * SequenceI[sz = seqs.getSize(false)];
3638 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3639 * seqs.getSequenceAt(i); }
3641 msa = viewport.getAlignmentView(true);
3646 * Vector seqs = viewport.getAlignment().getSequences();
3648 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3650 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3651 * seqs.elementAt(i); } }
3653 msa = viewport.getAlignmentView(false);
3659 * Decides what is submitted to a secondary structure prediction service: the
3660 * first sequence in the alignment, or in the current selection, or, if the
3661 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3662 * region or the whole alignment. (where the first sequence in the set is the
3663 * one that the prediction will be for).
3665 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3667 AlignmentView seqs = null;
3669 if ((viewport.getSelectionGroup() != null)
3670 && (viewport.getSelectionGroup().getSize() > 0))
3672 seqs = viewport.getAlignmentView(true);
3676 seqs = viewport.getAlignmentView(false);
3678 // limit sequences - JBPNote in future - could spawn multiple prediction
3680 // TODO: viewport.alignment.isAligned is a global state - the local
3681 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3682 if (!viewport.alignment.isAligned(false))
3684 seqs.setSequences(new SeqCigar[]
3685 { seqs.getSequences()[0] });
3686 // TODO: if seqs.getSequences().length>1 then should really have warned
3699 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3701 // Pick the tree file
3702 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
3703 .getProperty("LAST_DIRECTORY"));
3704 chooser.setFileView(new JalviewFileView());
3705 chooser.setDialogTitle("Select a newick-like tree file");
3706 chooser.setToolTipText("Load a tree file");
3708 int value = chooser.showOpenDialog(null);
3710 if (value == JalviewFileChooser.APPROVE_OPTION)
3712 String choice = chooser.getSelectedFile().getPath();
3713 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3714 jalview.io.NewickFile fin = null;
3717 fin = new jalview.io.NewickFile(choice, "File");
3718 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3719 } catch (Exception ex)
3721 JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3722 "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
3723 ex.printStackTrace();
3725 if (fin != null && fin.hasWarningMessage())
3727 JOptionPane.showMessageDialog(Desktop.desktop, fin
3728 .getWarningMessage(), "Possible problem with tree file",
3729 JOptionPane.WARNING_MESSAGE);
3734 public TreePanel ShowNewickTree(NewickFile nf, String title)
3736 return ShowNewickTree(nf, title, 600, 500, 4, 5);
3739 public TreePanel ShowNewickTree(NewickFile nf, String title,
3740 AlignmentView input)
3742 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
3745 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
3746 int h, int x, int y)
3748 return ShowNewickTree(nf, title, null, w, h, x, y);
3752 * Add a treeviewer for the tree extracted from a newick file object to the
3753 * current alignment view
3760 * Associated alignment input data (or null)
3769 * @return TreePanel handle
3771 public TreePanel ShowNewickTree(NewickFile nf, String title,
3772 AlignmentView input, int w, int h, int x, int y)
3774 TreePanel tp = null;
3780 if (nf.getTree() != null)
3782 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
3788 tp.setLocation(x, y);
3791 Desktop.addInternalFrame(tp, title, w, h);
3793 } catch (Exception ex)
3795 ex.printStackTrace();
3801 private boolean buildingMenu = false;
3804 * Generates menu items and listener event actions for web service clients
3807 public void BuildWebServiceMenu()
3809 while (buildingMenu)
3813 System.err.println("Waiting for building menu to finish.");
3815 } catch (Exception e)
3820 buildingMenu = true;
3824 .println("Building ws menu again " + Thread.currentThread());
3825 // TODO: add support for context dependent disabling of services based on
3826 // alignment and current selection
3827 // TODO: add additional serviceHandle parameter to specify abstract
3829 // class independently of AbstractName
3830 // TODO: add in rediscovery GUI function to restart discoverer
3831 // TODO: group services by location as well as function and/or introduce
3832 // object broker mechanism.
3833 Vector wsmenu = new Vector();
3834 final IProgressIndicator af = this;
3835 if (Cache.getDefault("SHOW_JWS1_SERVICES", true)
3836 && Discoverer.services != null
3837 && (Discoverer.services.size() > 0))
3839 // TODO: refactor to allow list of AbstractName/Handler bindings to be
3840 // stored or retrieved from elsewhere
3841 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
3842 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
3843 Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
3844 // TODO: move GUI generation code onto service implementation - so a
3845 // client instance attaches itself to the GUI with method call like
3846 // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
3850 // Add any Multiple Sequence Alignment Services
3851 final JMenu msawsmenu = new JMenu("Alignment");
3852 for (int i = 0, j = msaws.size(); i < j; i++)
3854 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
3856 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
3857 .getServiceClient(sh);
3858 impl.attachWSMenuEntry(msawsmenu, this);
3861 wsmenu.add(msawsmenu);
3863 if (secstrpr != null)
3865 // Add any secondary structure prediction services
3866 final JMenu secstrmenu = new JMenu(
3867 "Secondary Structure Prediction");
3868 for (int i = 0, j = secstrpr.size(); i < j; i++)
3870 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
3872 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
3873 .getServiceClient(sh);
3874 impl.attachWSMenuEntry(secstrmenu, this);
3876 wsmenu.add(secstrmenu);
3878 if (seqsrch != null)
3880 // Add any sequence search services
3881 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
3882 for (int i = 0, j = seqsrch.size(); i < j; i++)
3884 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
3886 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
3887 .getServiceClient(sh);
3888 impl.attachWSMenuEntry(seqsrchmenu, this);
3890 wsmenu.add(seqsrchmenu);
3894 // TODO: move into separate menu builder class.
3895 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
3897 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
3898 if (jws2servs != null)
3900 if (jws2servs.hasServices())
3902 JMenu jws2men = new JMenu("Jalview 2 Services");
3903 jws2servs.attachWSMenuEntry(jws2men, this);
3904 for (int i = 0, iSize = jws2men.getMenuComponentCount(); i < iSize; i++)
3906 wsmenu.add(jws2men.getMenuComponent(i));
3911 resetWebServiceMenu();
3912 // finally, add the whole shebang onto the webservices menu
3913 if (wsmenu.size() > 0)
3915 for (int i = 0, j = wsmenu.size(); i < j; i++)
3917 webService.add((JMenu) wsmenu.get(i));
3922 this.webService.add(this.webServiceNoServices);
3924 } catch (Exception e)
3928 buildingMenu = false;
3932 * empty the web service menu and add any ad-hoc functions not dynamically
3936 private void resetWebServiceMenu()
3938 webService.removeAll();
3939 build_fetchdbmenu(webService);
3940 build_urlServiceMenu(webService);
3944 * construct any groupURL type service menu entries.
3948 private void build_urlServiceMenu(JMenu webService)
3950 if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
3952 jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
3958 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
3959 * chooser = new JalviewFileChooser(jalview.bin.Cache.
3960 * getProperty("LAST_DIRECTORY"));
3962 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
3963 * to Vamsas file"); chooser.setToolTipText("Export");
3965 * int value = chooser.showSaveDialog(this);
3967 * if (value == JalviewFileChooser.APPROVE_OPTION) {
3968 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
3969 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
3970 * chooser.getSelectedFile().getAbsolutePath(), this); } }
3973 * prototype of an automatically enabled/disabled analysis function
3976 protected void setShowProductsEnabled()
3978 SequenceI[] selection = viewport.getSequenceSelection();
3979 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
3980 viewport.getAlignment().getDataset()))
3982 showProducts.setEnabled(true);
3987 showProducts.setEnabled(false);
3992 * search selection for sequence xRef products and build the show products
3997 * @return true if showProducts menu should be enabled.
3999 public boolean canShowProducts(SequenceI[] selection,
4000 boolean isRegionSelection, Alignment dataset)
4002 boolean showp = false;
4005 showProducts.removeAll();
4006 final boolean dna = viewport.getAlignment().isNucleotide();
4007 final Alignment ds = dataset;
4008 String[] ptypes = (selection == null || selection.length == 0) ? null
4009 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4011 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4012 // selection, dataset, true);
4013 final SequenceI[] sel = selection;
4014 for (int t = 0; ptypes != null && t < ptypes.length; t++)
4017 final boolean isRegSel = isRegionSelection;
4018 final AlignFrame af = this;
4019 final String source = ptypes[t];
4020 JMenuItem xtype = new JMenuItem(ptypes[t]);
4021 xtype.addActionListener(new ActionListener()
4024 public void actionPerformed(ActionEvent e)
4026 // TODO: new thread for this call with vis-delay
4027 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4028 isRegSel, dna, source);
4032 showProducts.add(xtype);
4034 showProducts.setVisible(showp);
4035 showProducts.setEnabled(showp);
4036 } catch (Exception e)
4038 jalview.bin.Cache.log
4040 "canTranslate threw an exception - please report to help@jalview.org",
4047 protected void showProductsFor(SequenceI[] sel, Alignment ds,
4048 boolean isRegSel, boolean dna, String source)
4050 final boolean fisRegSel = isRegSel;
4051 final boolean fdna = dna;
4052 final String fsrc = source;
4053 final AlignFrame ths = this;
4054 final SequenceI[] fsel = sel;
4055 Runnable foo = new Runnable()
4060 final long sttime = System.currentTimeMillis();
4061 ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4064 Alignment ds = ths.getViewport().alignment.getDataset(); // update
4068 Alignment prods = CrossRef
4069 .findXrefSequences(fsel, fdna, fsrc, ds);
4072 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4073 for (int s = 0; s < sprods.length; s++)
4075 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4076 if (ds.getSequences() == null
4077 || !ds.getSequences().contains(
4078 sprods[s].getDatasetSequence()))
4079 ds.addSequence(sprods[s].getDatasetSequence());
4080 sprods[s].updatePDBIds();
4082 Alignment al = new Alignment(sprods);
4083 AlignedCodonFrame[] cf = prods.getCodonFrames();
4085 for (int s = 0; cf != null && s < cf.length; s++)
4087 al.addCodonFrame(cf[s]);
4090 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4092 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4093 + " for " + ((fisRegSel) ? "selected region of " : "")
4095 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4100 System.err.println("No Sequences generated for xRef type "
4103 } catch (Exception e)
4105 jalview.bin.Cache.log.error(
4106 "Exception when finding crossreferences", e);
4107 } catch (OutOfMemoryError e)
4109 new OOMWarning("whilst fetching crossreferences", e);
4112 jalview.bin.Cache.log.error("Error when finding crossreferences",
4115 ths.setProgressBar("Finished searching for sequences from " + fsrc,
4120 Thread frunner = new Thread(foo);
4124 public boolean canShowTranslationProducts(SequenceI[] selection,
4125 AlignmentI alignment)
4130 return (jalview.analysis.Dna.canTranslate(selection, viewport
4131 .getViewAsVisibleContigs(true)));
4132 } catch (Exception e)
4134 jalview.bin.Cache.log
4136 "canTranslate threw an exception - please report to help@jalview.org",
4142 public void showProducts_actionPerformed(ActionEvent e)
4144 // /////////////////////////////
4145 // Collect Data to be translated/transferred
4147 SequenceI[] selection = viewport.getSequenceSelection();
4148 AlignmentI al = null;
4151 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4152 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4153 viewport.getAlignment().getDataset());
4154 } catch (Exception ex)
4157 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4164 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4165 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4169 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4170 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4171 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4175 public void showTranslation_actionPerformed(ActionEvent e)
4177 // /////////////////////////////
4178 // Collect Data to be translated/transferred
4180 SequenceI[] selection = viewport.getSequenceSelection();
4181 String[] seqstring = viewport.getViewAsString(true);
4182 AlignmentI al = null;
4185 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4186 viewport.getViewAsVisibleContigs(true), viewport
4187 .getGapCharacter(), viewport.alignment
4188 .getAlignmentAnnotation(), viewport.alignment
4189 .getWidth(), viewport.getAlignment().getDataset());
4190 } catch (Exception ex)
4193 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4200 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4201 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4205 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4206 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4207 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4212 * Try to load a features file onto the alignment.
4215 * contents or path to retrieve file
4217 * access mode of file (see jalview.io.AlignFile)
4218 * @return true if features file was parsed corectly.
4220 public boolean parseFeaturesFile(String file, String type)
4222 boolean featuresFile = false;
4225 featuresFile = new FeaturesFile(file, type).parse(viewport.alignment
4226 .getDataset(), alignPanel.seqPanel.seqCanvas
4227 .getFeatureRenderer().featureColours, false);
4228 } catch (Exception ex)
4230 ex.printStackTrace();
4235 viewport.showSequenceFeatures = true;
4236 showSeqFeatures.setSelected(true);
4237 if (alignPanel.seqPanel.seqCanvas.fr != null)
4239 // update the min/max ranges where necessary
4240 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4242 if (featureSettings != null)
4244 featureSettings.setTableData();
4246 alignPanel.paintAlignment(true);
4249 return featuresFile;
4252 public void dragEnter(DropTargetDragEvent evt)
4256 public void dragExit(DropTargetEvent evt)
4260 public void dragOver(DropTargetDragEvent evt)
4264 public void dropActionChanged(DropTargetDragEvent evt)
4268 public void drop(DropTargetDropEvent evt)
4270 Transferable t = evt.getTransferable();
4271 java.util.List files = null;
4275 DataFlavor uriListFlavor = new DataFlavor(
4276 "text/uri-list;class=java.lang.String");
4277 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4279 // Works on Windows and MacOSX
4280 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4281 files = (java.util.List) t
4282 .getTransferData(DataFlavor.javaFileListFlavor);
4284 else if (t.isDataFlavorSupported(uriListFlavor))
4286 // This is used by Unix drag system
4287 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4288 String data = (String) t.getTransferData(uriListFlavor);
4289 files = new java.util.ArrayList(1);
4290 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4291 data, "\r\n"); st.hasMoreTokens();)
4293 String s = st.nextToken();
4294 if (s.startsWith("#"))
4296 // the line is a comment (as per the RFC 2483)
4300 java.net.URI uri = new java.net.URI(s);
4301 // check to see if we can handle this kind of URI
4302 if (uri.getScheme().toLowerCase().startsWith("http"))
4304 files.add(uri.toString());
4308 // otherwise preserve old behaviour: catch all for file objects
4309 java.io.File file = new java.io.File(uri);
4310 files.add(file.toString());
4314 } catch (Exception e)
4316 e.printStackTrace();
4323 for (int i = 0; i < files.size(); i++)
4325 loadJalviewDataFile(files.get(i).toString());
4327 } catch (Exception ex)
4329 ex.printStackTrace();
4335 * Attempt to load a "dropped" file or URL string: First by testing whether
4336 * it's and Annotation file, then a JNet file, and finally a features file. If
4337 * all are false then the user may have dropped an alignment file onto this
4341 * either a filename or a URL string.
4343 public void loadJalviewDataFile(String file)
4347 String protocol = jalview.io.FormatAdapter.FILE;
4348 String f = file.toLowerCase();
4349 if (f.indexOf("http:") == 0 || f.indexOf("https:") == 0
4350 || f.indexOf("file:") == 0)
4352 protocol = jalview.io.FormatAdapter.URL;
4355 boolean isAnnotation = new AnnotationFile().readAnnotationFile(
4356 viewport.alignment, file, protocol);
4360 // try to see if its a JNet 'concise' style annotation file *before* we
4361 // try to parse it as a features file
4362 String format = new IdentifyFile().Identify(file, protocol);
4363 if (format.equalsIgnoreCase("JnetFile"))
4365 jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
4367 new JnetAnnotationMaker().add_annotation(predictions, viewport
4368 .getAlignment(), 0, false);
4369 isAnnotation = true;
4373 // try to parse it as a features file
4374 boolean isGroupsFile = parseFeaturesFile(file, protocol);
4375 // if it wasn't a features file then we just treat it as a general
4376 // alignment file to load into the current view.
4379 new FileLoader().LoadFile(viewport, file, protocol, format);
4383 alignPanel.paintAlignment(true);
4390 alignPanel.adjustAnnotationHeight();
4391 viewport.updateSequenceIdColours();
4392 buildSortByAnnotationScoresMenu();
4393 alignPanel.paintAlignment(true);
4395 } catch (Exception ex)
4397 ex.printStackTrace();
4401 public void tabSelectionChanged(int index)
4405 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
4406 viewport = alignPanel.av;
4407 setMenusFromViewport(viewport);
4411 public void tabbedPane_mousePressed(MouseEvent e)
4413 if (SwingUtilities.isRightMouseButton(e))
4415 String reply = JOptionPane.showInternalInputDialog(this,
4416 "Enter View Name", "Edit View Name",
4417 JOptionPane.QUESTION_MESSAGE);
4421 viewport.viewName = reply;
4422 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4427 public AlignViewport getCurrentView()
4433 * Open the dialog for regex description parsing.
4435 protected void extractScores_actionPerformed(ActionEvent e)
4437 ParseProperties pp = new jalview.analysis.ParseProperties(
4438 viewport.alignment);
4439 // TODO: verify regex and introduce GUI dialog for version 2.5
4440 // if (pp.getScoresFromDescription("col", "score column ",
4441 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4443 if (pp.getScoresFromDescription("description column",
4444 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4446 buildSortByAnnotationScoresMenu();
4454 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4457 protected void showDbRefs_actionPerformed(ActionEvent e)
4459 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
4465 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4468 protected void showNpFeats_actionPerformed(ActionEvent e)
4470 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
4474 * find the viewport amongst the tabs in this alignment frame and close that
4479 public boolean closeView(AlignViewport av)
4483 this.closeMenuItem_actionPerformed(false);
4486 Component[] comp = tabbedPane.getComponents();
4487 for (int i = 0; comp != null && i < comp.length; i++)
4489 if (comp[i] instanceof AlignmentPanel)
4491 if (((AlignmentPanel) comp[i]).av == av)
4494 closeView((AlignmentPanel) comp[i]);
4502 protected void build_fetchdbmenu(JMenu webService)
4504 // Temporary hack - DBRef Fetcher always top level ws entry.
4505 // TODO We probably want to store a sequence database checklist in
4506 // preferences and have checkboxes.. rather than individual sources selected
4508 JMenu rfetch = new JMenu("Fetch DB References");
4510 .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
4511 webService.add(rfetch);
4513 JMenuItem fetchr = new JMenuItem("Standard Databases");
4515 .setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
4516 fetchr.addActionListener(new ActionListener()
4519 public void actionPerformed(ActionEvent e)
4521 new Thread(new Runnable()
4526 new jalview.ws.DBRefFetcher(alignPanel.av
4527 .getSequenceSelection(), alignPanel.alignFrame)
4528 .fetchDBRefs(false);
4536 JMenu dfetch = new JMenu();
4538 jalview.ws.SequenceFetcher sf = SequenceFetcher
4539 .getSequenceFetcherSingleton(this);
4540 String[] otherdb = sf.getOrderedSupportedSources();
4541 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4542 // jalview.util.QuickSort.sort(otherdb, otherdb);
4543 int comp = 0, mcomp = 15;
4544 String mname = null;
4545 if (otherdb != null && otherdb.length > 0)
4547 for (int i = 0; i < otherdb.length; i++)
4549 String dbname = sf.getSourceProxy(otherdb[i]).getDbName();
4552 mname = "from '" + dbname + "'";
4554 fetchr = new JMenuItem(otherdb[i]);
4555 final String[] dassource = new String[]
4557 fetchr.addActionListener(new ActionListener()
4560 public void actionPerformed(ActionEvent e)
4562 new Thread(new Runnable()
4567 new jalview.ws.DBRefFetcher(alignPanel.av
4568 .getSequenceSelection(), alignPanel.alignFrame,
4569 dassource).fetchDBRefs(false);
4575 fetchr.setToolTipText("Retrieve from " + dbname);
4577 if (comp++ == mcomp || i == (otherdb.length - 1))
4579 dfetch.setText(mname + " to '" + dbname + "'");
4581 dfetch = new JMenu();
4590 * Left justify the whole alignment.
4592 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
4594 AlignmentI al = viewport.getAlignment();
4596 viewport.firePropertyChange("alignment", null, al);
4600 * Right justify the whole alignment.
4602 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
4604 AlignmentI al = viewport.getAlignment();
4606 viewport.firePropertyChange("alignment", null, al);
4609 public void setShowSeqFeatures(boolean b)
4611 showSeqFeatures.setSelected(true);
4612 viewport.setShowSequenceFeatures(true);
4619 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
4620 * awt.event.ActionEvent)
4622 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
4624 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
4625 alignPanel.paintAlignment(true);
4632 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
4635 protected void showGroupConsensus_actionPerformed(ActionEvent e)
4637 viewport.setShowGroupConsensus(showGroupConsensus.getState());
4638 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4646 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
4647 * .event.ActionEvent)
4649 protected void showGroupConservation_actionPerformed(ActionEvent e)
4651 viewport.setShowGroupConservation(showGroupConservation.getState());
4652 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4659 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
4660 * .event.ActionEvent)
4662 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
4664 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
4665 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4672 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
4673 * .event.ActionEvent)
4675 protected void showSequenceLogo_actionPerformed(ActionEvent e)
4677 viewport.setShowSequenceLogo(showSequenceLogo.getState());
4678 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4681 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
4683 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4690 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
4691 * .event.ActionEvent)
4693 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
4695 if (viewport.getSelectionGroup() != null)
4697 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
4698 viewport.getSequenceSelection(), viewport.getAlignmentView(
4699 true).getSequenceStrings(viewport.getGapCharacter()),
4700 viewport.alignment.getGroups());
4701 viewport.alignment.deleteAllGroups();
4702 viewport.sequenceColours = null;
4703 viewport.setSelectionGroup(null);
4704 // set view properties for each group
4705 for (int g = 0; g < gps.length; g++)
4707 gps[g].setShowNonconserved(viewport.getShowUnconserved());
4708 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
4709 viewport.alignment.addGroup(gps[g]);
4710 Color col = new Color((int) (Math.random() * 255), (int) (Math
4711 .random() * 255), (int) (Math.random() * 255));
4712 col = col.brighter();
4713 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
4714 .hasMoreElements(); viewport.setSequenceColour(
4715 (SequenceI) sq.nextElement(), col))
4718 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
4719 alignPanel.updateAnnotation();
4720 alignPanel.paintAlignment(true);
4725 class PrintThread extends Thread
4729 public PrintThread(AlignmentPanel ap)
4734 static PageFormat pf;
4738 PrinterJob printJob = PrinterJob.getPrinterJob();
4742 printJob.setPrintable(ap, pf);
4746 printJob.setPrintable(ap);
4749 if (printJob.printDialog())
4754 } catch (Exception PrintException)
4756 PrintException.printStackTrace();