2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
3 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
26 import java.awt.datatransfer.*;
27 import java.awt.dnd.*;
28 import java.awt.event.*;
29 import java.awt.print.*;
31 import javax.swing.event.MenuEvent;
33 import jalview.analysis.*;
34 import jalview.commands.*;
35 import jalview.datamodel.*;
37 import jalview.jbgui.*;
38 import jalview.schemes.*;
47 public class AlignFrame extends GAlignFrame implements DropTargetListener,
52 public static final int DEFAULT_WIDTH = 700;
55 public static final int DEFAULT_HEIGHT = 500;
57 public AlignmentPanel alignPanel;
59 AlignViewport viewport;
61 Vector alignPanels = new Vector();
64 * Last format used to load or save alignments in this window
66 String currentFileFormat = null;
69 * Current filename for this alignment
71 String fileName = null;
74 * Creates a new AlignFrame object with specific width and height.
80 public AlignFrame(AlignmentI al, int width, int height)
82 this(al, null, width, height);
86 * Creates a new AlignFrame object with specific width, height and
92 * @param sequenceSetId
94 public AlignFrame(AlignmentI al, int width, int height,
97 this(al, null, width, height, sequenceSetId);
101 * Creates a new AlignFrame object with specific width, height and
107 * @param sequenceSetId
110 public AlignFrame(AlignmentI al, int width, int height,
111 String sequenceSetId, String viewId)
113 this(al, null, width, height, sequenceSetId, viewId);
117 * new alignment window with hidden columns
121 * @param hiddenColumns
122 * ColumnSelection or null
124 * Width of alignment frame
128 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
129 int width, int height)
131 this(al, hiddenColumns, width, height, null);
135 * Create alignment frame for al with hiddenColumns, a specific width and
136 * height, and specific sequenceId
139 * @param hiddenColumns
142 * @param sequenceSetId
145 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
146 int width, int height, String sequenceSetId)
148 this(al, hiddenColumns, width, height, sequenceSetId, null);
152 * Create alignment frame for al with hiddenColumns, a specific width and
153 * height, and specific sequenceId
156 * @param hiddenColumns
159 * @param sequenceSetId
164 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
165 int width, int height, String sequenceSetId, String viewId)
167 setSize(width, height);
168 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
170 alignPanel = new AlignmentPanel(this, viewport);
172 if (al.getDataset() == null)
177 addAlignmentPanel(alignPanel, true);
182 * Make a new AlignFrame from exisiting alignmentPanels
189 public AlignFrame(AlignmentPanel ap)
193 addAlignmentPanel(ap, false);
198 * initalise the alignframe from the underlying viewport data and the
203 if (viewport.conservation == null)
205 BLOSUM62Colour.setEnabled(false);
206 conservationMenuItem.setEnabled(false);
207 modifyConservation.setEnabled(false);
208 // PIDColour.setEnabled(false);
209 // abovePIDThreshold.setEnabled(false);
210 // modifyPID.setEnabled(false);
213 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
216 if (sortby.equals("Id"))
218 sortIDMenuItem_actionPerformed(null);
220 else if (sortby.equals("Pairwise Identity"))
222 sortPairwiseMenuItem_actionPerformed(null);
225 if (Desktop.desktop != null)
227 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
228 addServiceListeners();
229 setGUINucleotide(viewport.alignment.isNucleotide());
232 setMenusFromViewport(viewport);
233 buildSortByAnnotationScoresMenu();
234 if (viewport.wrapAlignment)
236 wrapMenuItem_actionPerformed(null);
239 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
241 this.overviewMenuItem_actionPerformed(null);
249 * Change the filename and format for the alignment, and enable the 'reload'
250 * button functionality.
257 public void setFileName(String file, String format)
260 currentFileFormat = format;
261 reload.setEnabled(true);
264 void addKeyListener()
266 addKeyListener(new KeyAdapter()
268 public void keyPressed(KeyEvent evt)
270 if (viewport.cursorMode
271 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
272 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
273 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
274 && Character.isDigit(evt.getKeyChar()))
275 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
277 switch (evt.getKeyCode())
280 case 27: // escape key
281 deselectAllSequenceMenuItem_actionPerformed(null);
285 case KeyEvent.VK_DOWN:
286 if (evt.isAltDown() || !viewport.cursorMode)
287 moveSelectedSequences(false);
288 if (viewport.cursorMode)
289 alignPanel.seqPanel.moveCursor(0, 1);
293 if (evt.isAltDown() || !viewport.cursorMode)
294 moveSelectedSequences(true);
295 if (viewport.cursorMode)
296 alignPanel.seqPanel.moveCursor(0, -1);
300 case KeyEvent.VK_LEFT:
301 if (evt.isAltDown() || !viewport.cursorMode)
302 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
304 alignPanel.seqPanel.moveCursor(-1, 0);
308 case KeyEvent.VK_RIGHT:
309 if (evt.isAltDown() || !viewport.cursorMode)
310 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
312 alignPanel.seqPanel.moveCursor(1, 0);
315 case KeyEvent.VK_SPACE:
316 if (viewport.cursorMode)
318 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
319 || evt.isShiftDown() || evt.isAltDown());
323 case KeyEvent.VK_DELETE:
324 case KeyEvent.VK_BACK_SPACE:
325 if (!viewport.cursorMode)
327 cut_actionPerformed(null);
331 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
332 || evt.isShiftDown() || evt.isAltDown());
338 if (viewport.cursorMode)
340 alignPanel.seqPanel.setCursorRow();
344 if (viewport.cursorMode && !evt.isControlDown())
346 alignPanel.seqPanel.setCursorColumn();
350 if (viewport.cursorMode)
352 alignPanel.seqPanel.setCursorPosition();
356 case KeyEvent.VK_ENTER:
357 case KeyEvent.VK_COMMA:
358 if (viewport.cursorMode)
360 alignPanel.seqPanel.setCursorRowAndColumn();
365 if (viewport.cursorMode)
367 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
371 if (viewport.cursorMode)
373 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
378 viewport.cursorMode = !viewport.cursorMode;
379 statusBar.setText("Keyboard editing mode is "
380 + (viewport.cursorMode ? "on" : "off"));
381 if (viewport.cursorMode)
383 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
384 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
386 alignPanel.seqPanel.seqCanvas.repaint();
392 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
393 java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
395 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
397 javax.help.HelpBroker hb = hs.createHelpBroker();
398 hb.setCurrentID("home");
399 hb.setDisplayed(true);
400 } catch (Exception ex)
402 ex.printStackTrace();
407 boolean toggleSeqs = !evt.isControlDown();
408 boolean toggleCols = !evt.isShiftDown();
410 boolean hide = false;
411 SequenceGroup sg = viewport.getSelectionGroup();
412 // TODO: document ctrl-shift-h for show visible selected area and fix hack so columns for the current selected region get transferred.
413 if (!toggleSeqs && !toggleCols)
415 // Hide everything by the current selection - this is a hack - we do the invert and then hide
416 // first check that there will be visible columns after the invert.
417 if ((viewport.colSel!=null && viewport.colSel.getSelected()!=null && viewport.colSel.getSelected().size()>0) || (sg!=null && sg.getSize()>0 && sg.getStartRes()<=sg.getEndRes()))
419 // now invert the sequence set, if required - empty selection implies that no hiding is required.
421 invertSequenceMenuItem_actionPerformed(null);
422 sg = viewport.getSelectionGroup();
427 if (sg!=null && sg.getStartRes()>=0 && sg.getStartRes()<=sg.getEndRes()&& (viewport.colSel==null || viewport.colSel.getSelected()==null || viewport.colSel.getSelected().size()==0))
429 // synthesize a column selection if none exists. this happens if a single region has been selected rather than whole columns.
430 if (viewport.colSel==null)
432 viewport.colSel = new ColumnSelection();
434 for (int cspos = sg.getStartRes(); cspos<=sg.getEndRes(); cspos++) {
435 viewport.colSel.addElement(cspos);
438 // finally invert the column selection and get the new sequence selection.
439 invertColSel_actionPerformed(null);
447 && sg.getSize() != viewport.alignment.getHeight())
449 hideSelSequences_actionPerformed(null);
452 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
454 showAllSeqs_actionPerformed(null);
460 if (viewport.colSel.getSelected().size() > 0)
462 hideSelColumns_actionPerformed(null);
465 viewport.selectionGroup = sg;
470 showAllColumns_actionPerformed(null);
475 case KeyEvent.VK_PAGE_UP:
476 if (viewport.wrapAlignment)
478 alignPanel.scrollUp(true);
482 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
483 - viewport.endSeq + viewport.startSeq);
486 case KeyEvent.VK_PAGE_DOWN:
487 if (viewport.wrapAlignment)
489 alignPanel.scrollUp(false);
493 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
494 + viewport.endSeq - viewport.startSeq);
500 public void keyReleased(KeyEvent evt)
502 switch (evt.getKeyCode())
504 case KeyEvent.VK_LEFT:
505 if (evt.isAltDown() || !viewport.cursorMode)
506 viewport.firePropertyChange("alignment", null, viewport
507 .getAlignment().getSequences());
510 case KeyEvent.VK_RIGHT:
511 if (evt.isAltDown() || !viewport.cursorMode)
512 viewport.firePropertyChange("alignment", null, viewport
513 .getAlignment().getSequences());
520 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
522 ap.alignFrame = this;
524 alignPanels.addElement(ap);
526 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
528 int aSize = alignPanels.size();
530 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
532 if (aSize == 1 && ap.av.viewName == null)
534 this.getContentPane().add(ap, BorderLayout.CENTER);
540 setInitialTabVisible();
543 expandViews.setEnabled(true);
544 gatherViews.setEnabled(true);
545 tabbedPane.addTab(ap.av.viewName, ap);
547 ap.setVisible(false);
554 ap.av.alignment.padGaps();
556 ap.av.updateConservation(ap);
557 ap.av.updateConsensus(ap);
561 public void setInitialTabVisible()
563 expandViews.setEnabled(true);
564 gatherViews.setEnabled(true);
565 tabbedPane.setVisible(true);
566 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
567 tabbedPane.addTab(first.av.viewName, first);
568 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
571 public AlignViewport getViewport()
576 /* Set up intrinsic listeners for dynamically generated GUI bits. */
577 private void addServiceListeners()
579 final java.beans.PropertyChangeListener thisListener;
580 // Do this once to get current state
581 BuildWebServiceMenu();
583 .addPropertyChangeListener(thisListener = new java.beans.PropertyChangeListener()
585 public void propertyChange(PropertyChangeEvent evt)
587 // System.out.println("Discoverer property change.");
588 if (evt.getPropertyName().equals("services"))
590 // System.out.println("Rebuilding web service menu");
591 BuildWebServiceMenu();
596 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
598 public void internalFrameClosed(
599 javax.swing.event.InternalFrameEvent evt)
601 // System.out.println("deregistering discoverer listener");
602 Desktop.discoverer.removePropertyChangeListener(thisListener);
603 closeMenuItem_actionPerformed(true);
608 public void setGUINucleotide(boolean nucleotide)
610 showTranslation.setVisible(nucleotide);
611 conservationMenuItem.setEnabled(!nucleotide);
612 modifyConservation.setEnabled(!nucleotide);
614 // Remember AlignFrame always starts as protein
617 calculateMenu.remove(calculateMenu.getItemCount() - 2);
622 * set up menus for the currently viewport. This may be called after any
623 * operation that affects the data in the current view (selection changed,
624 * etc) to update the menus to reflect the new state.
626 public void setMenusForViewport()
628 setMenusFromViewport(viewport);
632 * Need to call this method when tabs are selected for multiple views, or when
633 * loading from Jalview2XML.java
638 void setMenusFromViewport(AlignViewport av)
640 padGapsMenuitem.setSelected(av.padGaps);
641 colourTextMenuItem.setSelected(av.showColourText);
642 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
643 conservationMenuItem.setSelected(av.getConservationSelected());
644 seqLimits.setSelected(av.getShowJVSuffix());
645 idRightAlign.setSelected(av.rightAlignIds);
646 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
647 renderGapsMenuItem.setSelected(av.renderGaps);
648 wrapMenuItem.setSelected(av.wrapAlignment);
649 scaleAbove.setVisible(av.wrapAlignment);
650 scaleLeft.setVisible(av.wrapAlignment);
651 scaleRight.setVisible(av.wrapAlignment);
652 annotationPanelMenuItem.setState(av.showAnnotation);
653 viewBoxesMenuItem.setSelected(av.showBoxes);
654 viewTextMenuItem.setSelected(av.showText);
655 showUnconservedMenuItem.setSelected(av.showUnconserved);
656 showGroupConsensus.setSelected(av.showGroupConsensus);
657 showGroupConservation.setSelected(av.showGroupConservation);
658 setColourSelected(ColourSchemeProperty.getColourName(av
659 .getGlobalColourScheme()));
661 showSeqFeatures.setSelected(av.showSequenceFeatures);
662 hiddenMarkers.setState(av.showHiddenMarkers);
663 applyToAllGroups.setState(av.colourAppliesToAllGroups);
664 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
665 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
667 setShowProductsEnabled();
672 Hashtable progressBars, progressBarHandlers;
677 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
679 public void setProgressBar(String message, long id)
681 if (progressBars == null)
683 progressBars = new Hashtable();
684 progressBarHandlers = new Hashtable();
687 JPanel progressPanel;
688 GridLayout layout = (GridLayout) statusPanel.getLayout();
689 if (progressBars.get(new Long(id)) != null)
691 progressPanel = (JPanel) progressBars.get(new Long(id));
692 statusPanel.remove(progressPanel);
693 progressBars.remove(progressPanel);
694 progressPanel = null;
697 statusBar.setText(message);
699 if (progressBarHandlers.contains(new Long(id)))
701 progressBarHandlers.remove(new Long(id));
703 layout.setRows(layout.getRows() - 1);
707 progressPanel = new JPanel(new BorderLayout(10, 5));
709 JProgressBar progressBar = new JProgressBar();
710 progressBar.setIndeterminate(true);
712 progressPanel.add(new JLabel(message), BorderLayout.WEST);
713 progressPanel.add(progressBar, BorderLayout.CENTER);
715 layout.setRows(layout.getRows() + 1);
716 statusPanel.add(progressPanel);
718 progressBars.put(new Long(id), progressPanel);
721 setMenusForViewport();
725 public void registerHandler(final long id,
726 final IProgressIndicatorHandler handler)
728 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
731 "call setProgressBar before registering the progress bar's handler.");
733 progressBarHandlers.put(new Long(id), handler);
734 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
735 if (handler.canCancel())
737 JButton cancel = new JButton("Cancel");
738 final IProgressIndicator us = this;
739 cancel.addActionListener(new ActionListener()
742 public void actionPerformed(ActionEvent e)
744 handler.cancelActivity(id);
745 us.setProgressBar("Cancelled "
746 + ((JLabel) progressPanel.getComponent(0)).getText(), id);
749 progressPanel.add(cancel, BorderLayout.EAST);
755 * @return true if any progress bars are still active
757 public boolean operationInProgress()
759 if (progressBars != null && progressBars.size() > 0)
767 * Added so Castor Mapping file can obtain Jalview Version
769 public String getVersion()
771 return jalview.bin.Cache.getProperty("VERSION");
774 public FeatureRenderer getFeatureRenderer()
776 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
779 public void fetchSequence_actionPerformed(ActionEvent e)
781 new SequenceFetcher(this);
784 public void addFromFile_actionPerformed(ActionEvent e)
786 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
789 public void reload_actionPerformed(ActionEvent e)
791 if (fileName != null)
793 if (currentFileFormat.equals("Jalview"))
795 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
796 for (int i = 0; i < frames.length; i++)
798 if (frames[i] instanceof AlignFrame && frames[i] != this
799 && ((AlignFrame) frames[i]).fileName.equals(fileName))
803 frames[i].setSelected(true);
804 Desktop.instance.closeAssociatedWindows();
805 } catch (java.beans.PropertyVetoException ex)
811 Desktop.instance.closeAssociatedWindows();
813 FileLoader loader = new FileLoader();
814 String protocol = fileName.startsWith("http:") ? "URL" : "File";
815 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
819 Rectangle bounds = this.getBounds();
821 FileLoader loader = new FileLoader();
822 String protocol = fileName.startsWith("http:") ? "URL" : "File";
823 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
824 protocol, currentFileFormat);
826 newframe.setBounds(bounds);
828 this.closeMenuItem_actionPerformed(true);
833 public void addFromText_actionPerformed(ActionEvent e)
835 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
838 public void addFromURL_actionPerformed(ActionEvent e)
840 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
843 public void save_actionPerformed(ActionEvent e)
846 || (currentFileFormat == null || !jalview.io.FormatAdapter
847 .isValidIOFormat(currentFileFormat, true))
848 || fileName.startsWith("http"))
850 saveAs_actionPerformed(null);
854 saveAlignment(fileName, currentFileFormat);
864 public void saveAs_actionPerformed(ActionEvent e)
866 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
867 .getProperty("LAST_DIRECTORY"),
868 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
869 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
870 currentFileFormat, false);
872 chooser.setFileView(new JalviewFileView());
873 chooser.setDialogTitle("Save Alignment to file");
874 chooser.setToolTipText("Save");
876 int value = chooser.showSaveDialog(this);
878 if (value == JalviewFileChooser.APPROVE_OPTION)
880 currentFileFormat = chooser.getSelectedFormat();
881 if (currentFileFormat == null)
883 JOptionPane.showInternalMessageDialog(Desktop.desktop,
884 "You must select a file format before saving!",
885 "File format not specified", JOptionPane.WARNING_MESSAGE);
886 value = chooser.showSaveDialog(this);
890 fileName = chooser.getSelectedFile().getPath();
892 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
895 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
896 if (currentFileFormat.indexOf(" ") > -1)
898 currentFileFormat = currentFileFormat.substring(0,
899 currentFileFormat.indexOf(" "));
901 saveAlignment(fileName, currentFileFormat);
905 public boolean saveAlignment(String file, String format)
907 boolean success = true;
909 if (format.equalsIgnoreCase("Jalview"))
911 String shortName = title;
913 if (shortName.indexOf(java.io.File.separatorChar) > -1)
915 shortName = shortName.substring(shortName
916 .lastIndexOf(java.io.File.separatorChar) + 1);
919 success = new Jalview2XML().SaveAlignment(this, file, shortName);
921 statusBar.setText("Successfully saved to file: " + fileName + " in "
922 + format + " format.");
927 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
929 warningMessage("Cannot save file " + fileName + " using format "
930 + format, "Alignment output format not supported");
931 saveAs_actionPerformed(null);
932 // JBPNote need to have a raise_gui flag here
936 String[] omitHidden = null;
938 if (viewport.hasHiddenColumns)
940 int reply = JOptionPane
941 .showInternalConfirmDialog(
943 "The Alignment contains hidden columns."
944 + "\nDo you want to save only the visible alignment?",
945 "Save / Omit Hidden Columns",
946 JOptionPane.YES_NO_OPTION,
947 JOptionPane.QUESTION_MESSAGE);
949 if (reply == JOptionPane.YES_OPTION)
951 omitHidden = viewport.getViewAsString(false);
954 FormatAdapter f = new FormatAdapter();
955 String output = f.formatSequences(format,
956 (Alignment) viewport.alignment, // class cast exceptions will
957 // occur in the distant future
958 omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
968 java.io.PrintWriter out = new java.io.PrintWriter(
969 new java.io.FileWriter(file));
974 statusBar.setText("Successfully saved to file: " + fileName
975 + " in " + format + " format.");
976 } catch (Exception ex)
979 ex.printStackTrace();
986 JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
987 + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
993 private void warningMessage(String warning, String title)
995 if (new jalview.util.Platform().isHeadless())
997 System.err.println("Warning: " + title + "\nWarning: " + warning);
1002 JOptionPane.showInternalMessageDialog(this, warning, title,
1003 JOptionPane.WARNING_MESSAGE);
1014 protected void outputText_actionPerformed(ActionEvent e)
1016 String[] omitHidden = null;
1018 if (viewport.hasHiddenColumns)
1020 int reply = JOptionPane
1021 .showInternalConfirmDialog(
1023 "The Alignment contains hidden columns."
1024 + "\nDo you want to output only the visible alignment?",
1025 "Save / Omit Hidden Columns",
1026 JOptionPane.YES_NO_OPTION,
1027 JOptionPane.QUESTION_MESSAGE);
1029 if (reply == JOptionPane.YES_OPTION)
1031 omitHidden = viewport.getViewAsString(false);
1035 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1036 cap.setForInput(null);
1037 Desktop.addInternalFrame(cap, "Alignment output - "
1038 + e.getActionCommand(), 600, 500);
1040 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1041 viewport.alignment, omitHidden, viewport.colSel));
1050 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1052 new HTMLOutput(alignPanel, alignPanel.seqPanel.seqCanvas
1053 .getSequenceRenderer(), alignPanel.seqPanel.seqCanvas
1054 .getFeatureRenderer());
1057 public void createImageMap(File file, String image)
1059 alignPanel.makePNGImageMap(file, image);
1068 public void createPNG(File f)
1070 alignPanel.makePNG(f);
1079 public void createEPS(File f)
1081 alignPanel.makeEPS(f);
1084 public void pageSetup_actionPerformed(ActionEvent e)
1086 PrinterJob printJob = PrinterJob.getPrinterJob();
1087 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1096 public void printMenuItem_actionPerformed(ActionEvent e)
1098 // Putting in a thread avoids Swing painting problems
1099 PrintThread thread = new PrintThread(alignPanel);
1103 public void exportFeatures_actionPerformed(ActionEvent e)
1105 new AnnotationExporter().exportFeatures(alignPanel);
1108 public void exportAnnotations_actionPerformed(ActionEvent e)
1110 new AnnotationExporter().exportAnnotations(alignPanel,
1111 viewport.showAnnotation ? viewport.alignment
1112 .getAlignmentAnnotation() : null, viewport.alignment
1114 ((Alignment) viewport.alignment).alignmentProperties);
1117 public void associatedData_actionPerformed(ActionEvent e)
1119 // Pick the tree file
1120 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
1121 .getProperty("LAST_DIRECTORY"));
1122 chooser.setFileView(new JalviewFileView());
1123 chooser.setDialogTitle("Load Jalview Annotations or Features File");
1124 chooser.setToolTipText("Load Jalview Annotations / Features file");
1126 int value = chooser.showOpenDialog(null);
1128 if (value == JalviewFileChooser.APPROVE_OPTION)
1130 String choice = chooser.getSelectedFile().getPath();
1131 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1132 loadJalviewDataFile(choice);
1138 * Close the current view or all views in the alignment frame. If the frame
1139 * only contains one view then the alignment will be removed from memory.
1141 * @param closeAllTabs
1143 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1145 if (alignPanels != null && alignPanels.size() < 2)
1147 closeAllTabs = true;
1152 if (alignPanels != null)
1156 if (this.isClosed())
1158 // really close all the windows - otherwise wait till
1159 // setClosed(true) is called
1160 for (int i = 0; i < alignPanels.size(); i++)
1162 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1169 closeView(alignPanel);
1175 this.setClosed(true);
1177 } catch (Exception ex)
1179 ex.printStackTrace();
1184 * close alignPanel2 and shuffle tabs appropriately.
1186 * @param alignPanel2
1188 public void closeView(AlignmentPanel alignPanel2)
1190 int index = tabbedPane.getSelectedIndex();
1191 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1192 alignPanels.removeElement(alignPanel2);
1194 // if (viewport == alignPanel2.av)
1198 alignPanel2.closePanel();
1201 tabbedPane.removeTabAt(closedindex);
1202 tabbedPane.validate();
1204 if (index > closedindex || index == tabbedPane.getTabCount())
1206 // modify currently selected tab index if necessary.
1210 this.tabSelectionChanged(index);
1216 void updateEditMenuBar()
1219 if (viewport.historyList.size() > 0)
1221 undoMenuItem.setEnabled(true);
1222 CommandI command = (CommandI) viewport.historyList.peek();
1223 undoMenuItem.setText("Undo " + command.getDescription());
1227 undoMenuItem.setEnabled(false);
1228 undoMenuItem.setText("Undo");
1231 if (viewport.redoList.size() > 0)
1233 redoMenuItem.setEnabled(true);
1235 CommandI command = (CommandI) viewport.redoList.peek();
1236 redoMenuItem.setText("Redo " + command.getDescription());
1240 redoMenuItem.setEnabled(false);
1241 redoMenuItem.setText("Redo");
1245 public void addHistoryItem(CommandI command)
1247 if (command.getSize() > 0)
1249 viewport.historyList.push(command);
1250 viewport.redoList.clear();
1251 updateEditMenuBar();
1252 viewport.hasHiddenColumns = (viewport.colSel!=null && viewport.colSel.getHiddenColumns() != null && viewport.colSel.getHiddenColumns().size()>0);
1258 * @return alignment objects for all views
1260 AlignmentI[] getViewAlignments()
1262 if (alignPanels != null)
1264 Enumeration e = alignPanels.elements();
1265 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1266 for (int i = 0; e.hasMoreElements(); i++)
1268 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1272 if (viewport != null)
1274 return new AlignmentI[]
1275 { viewport.alignment };
1286 protected void undoMenuItem_actionPerformed(ActionEvent e)
1288 if (viewport.historyList.empty())
1290 CommandI command = (CommandI) viewport.historyList.pop();
1291 viewport.redoList.push(command);
1292 command.undoCommand(getViewAlignments());
1294 AlignViewport originalSource = getOriginatingSource(command);
1295 updateEditMenuBar();
1297 if (originalSource != null)
1299 originalSource.hasHiddenColumns = (viewport.colSel!=null && viewport.colSel.getHiddenColumns() != null && viewport.colSel.getHiddenColumns().size()>0);
1300 originalSource.firePropertyChange("alignment", null,
1301 originalSource.alignment.getSequences());
1311 protected void redoMenuItem_actionPerformed(ActionEvent e)
1313 if (viewport.redoList.size() < 1)
1318 CommandI command = (CommandI) viewport.redoList.pop();
1319 viewport.historyList.push(command);
1320 command.doCommand(getViewAlignments());
1322 AlignViewport originalSource = getOriginatingSource(command);
1323 updateEditMenuBar();
1325 if (originalSource != null)
1327 originalSource.hasHiddenColumns = (viewport.colSel!=null && viewport.colSel.getHiddenColumns() != null && viewport.colSel.getHiddenColumns().size()>0);
1328 originalSource.firePropertyChange("alignment", null,
1329 originalSource.alignment.getSequences());
1333 AlignViewport getOriginatingSource(CommandI command)
1335 AlignViewport originalSource = null;
1336 // For sequence removal and addition, we need to fire
1337 // the property change event FROM the viewport where the
1338 // original alignment was altered
1339 AlignmentI al = null;
1340 if (command instanceof EditCommand)
1342 EditCommand editCommand = (EditCommand) command;
1343 al = editCommand.getAlignment();
1344 Vector comps = (Vector) PaintRefresher.components.get(viewport
1345 .getSequenceSetId());
1347 for (int i = 0; i < comps.size(); i++)
1349 if (comps.elementAt(i) instanceof AlignmentPanel)
1351 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
1353 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1360 if (originalSource == null)
1362 // The original view is closed, we must validate
1363 // the current view against the closed view first
1366 PaintRefresher.validateSequences(al, viewport.alignment);
1369 originalSource = viewport;
1372 return originalSource;
1381 public void moveSelectedSequences(boolean up)
1383 SequenceGroup sg = viewport.getSelectionGroup();
1392 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1394 SequenceI seq = viewport.alignment.getSequenceAt(i);
1396 if (!sg.getSequences(null).contains(seq))
1401 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1403 if (sg.getSequences(null).contains(temp))
1408 viewport.alignment.getSequences().setElementAt(temp, i);
1409 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1414 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1416 SequenceI seq = viewport.alignment.getSequenceAt(i);
1418 if (!sg.getSequences(null).contains(seq))
1423 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1425 if (sg.getSequences(null).contains(temp))
1430 viewport.alignment.getSequences().setElementAt(temp, i);
1431 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1435 alignPanel.paintAlignment(true);
1438 synchronized void slideSequences(boolean right, int size)
1440 Vector sg = new Vector();
1441 if (viewport.cursorMode)
1443 sg.addElement(viewport.alignment
1444 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1446 else if (viewport.getSelectionGroup() != null
1447 && viewport.getSelectionGroup().getSize() != viewport.alignment
1450 sg = viewport.getSelectionGroup().getSequences(
1451 viewport.hiddenRepSequences);
1459 Vector invertGroup = new Vector();
1461 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1463 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
1464 invertGroup.add(viewport.alignment.getSequenceAt(i));
1467 SequenceI[] seqs1 = new SequenceI[sg.size()];
1468 for (int i = 0; i < sg.size(); i++)
1469 seqs1[i] = (SequenceI) sg.elementAt(i);
1471 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1472 for (int i = 0; i < invertGroup.size(); i++)
1473 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1475 SlideSequencesCommand ssc;
1477 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1478 size, viewport.getGapCharacter());
1480 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1481 size, viewport.getGapCharacter());
1483 int groupAdjustment = 0;
1484 if (ssc.getGapsInsertedBegin() && right)
1486 if (viewport.cursorMode)
1487 alignPanel.seqPanel.moveCursor(size, 0);
1489 groupAdjustment = size;
1491 else if (!ssc.getGapsInsertedBegin() && !right)
1493 if (viewport.cursorMode)
1494 alignPanel.seqPanel.moveCursor(-size, 0);
1496 groupAdjustment = -size;
1499 if (groupAdjustment != 0)
1501 viewport.getSelectionGroup().setStartRes(
1502 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1503 viewport.getSelectionGroup().setEndRes(
1504 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1507 boolean appendHistoryItem = false;
1508 if (viewport.historyList != null && viewport.historyList.size() > 0
1509 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1511 appendHistoryItem = ssc
1512 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1516 if (!appendHistoryItem)
1517 addHistoryItem(ssc);
1528 protected void copy_actionPerformed(ActionEvent e)
1531 if (viewport.getSelectionGroup() == null)
1535 // TODO: preserve the ordering of displayed alignment annotation in any
1536 // internal paste (particularly sequence associated annotation)
1537 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1538 String[] omitHidden = null;
1540 if (viewport.hasHiddenColumns)
1542 omitHidden = viewport.getViewAsString(true);
1545 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1548 StringSelection ss = new StringSelection(output);
1552 jalview.gui.Desktop.internalCopy = true;
1553 // Its really worth setting the clipboard contents
1554 // to empty before setting the large StringSelection!!
1555 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
1556 new StringSelection(""), null);
1558 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1560 } catch (OutOfMemoryError er)
1562 new OOMWarning("copying region", er);
1566 Vector hiddenColumns = null;
1567 if (viewport.hasHiddenColumns)
1569 hiddenColumns = new Vector();
1570 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1571 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1574 int[] region = (int[]) viewport.getColumnSelection()
1575 .getHiddenColumns().elementAt(i);
1577 hiddenColumns.addElement(new int[]
1578 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1582 Desktop.jalviewClipboard = new Object[]
1583 { seqs, viewport.alignment.getDataset(), hiddenColumns };
1584 statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
1593 protected void pasteNew_actionPerformed(ActionEvent e)
1604 protected void pasteThis_actionPerformed(ActionEvent e)
1610 * Paste contents of Jalview clipboard
1612 * @param newAlignment
1613 * true to paste to a new alignment, otherwise add to this.
1615 void paste(boolean newAlignment)
1617 boolean externalPaste = true;
1620 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1621 Transferable contents = c.getContents(this);
1623 if (contents == null)
1631 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1632 if (str.length() < 1)
1637 format = new IdentifyFile().Identify(str, "Paste");
1639 } catch (OutOfMemoryError er)
1641 new OOMWarning("Out of memory pasting sequences!!", er);
1645 SequenceI[] sequences;
1646 boolean annotationAdded = false;
1647 AlignmentI alignment = null;
1649 if (Desktop.jalviewClipboard != null)
1651 // The clipboard was filled from within Jalview, we must use the
1653 // And dataset from the copied alignment
1654 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1655 // be doubly sure that we create *new* sequence objects.
1656 sequences = new SequenceI[newseq.length];
1657 for (int i = 0; i < newseq.length; i++)
1659 sequences[i] = new Sequence(newseq[i]);
1661 alignment = new Alignment(sequences);
1662 externalPaste = false;
1666 // parse the clipboard as an alignment.
1667 alignment = new FormatAdapter().readFile(str, "Paste", format);
1668 sequences = alignment.getSequencesArray();
1676 if (Desktop.jalviewClipboard != null)
1678 // dataset is inherited
1679 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1683 // new dataset is constructed
1684 alignment.setDataset(null);
1686 alwidth = alignment.getWidth() + 1;
1690 AlignmentI pastedal = alignment; // preserve pasted alignment object
1691 // Add pasted sequences and dataset into existing alignment.
1692 alignment = viewport.getAlignment();
1693 alwidth = alignment.getWidth() + 1;
1694 // decide if we need to import sequences from an existing dataset
1695 boolean importDs = Desktop.jalviewClipboard != null
1696 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1697 // importDs==true instructs us to copy over new dataset sequences from
1698 // an existing alignment
1699 Vector newDs = (importDs) ? new Vector() : null; // used to create
1700 // minimum dataset set
1702 for (int i = 0; i < sequences.length; i++)
1706 newDs.addElement(null);
1708 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1710 if (importDs && ds != null)
1712 if (!newDs.contains(ds))
1714 newDs.setElementAt(ds, i);
1715 ds = new Sequence(ds);
1716 // update with new dataset sequence
1717 sequences[i].setDatasetSequence(ds);
1721 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1726 // copy and derive new dataset sequence
1727 sequences[i] = sequences[i].deriveSequence();
1728 alignment.getDataset().addSequence(
1729 sequences[i].getDatasetSequence());
1730 // TODO: avoid creation of duplicate dataset sequences with a
1731 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1733 alignment.addSequence(sequences[i]); // merges dataset
1737 newDs.clear(); // tidy up
1739 if (pastedal.getAlignmentAnnotation() != null)
1741 // Add any annotation attached to alignment.
1742 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1743 for (int i = 0; i < alann.length; i++)
1745 annotationAdded = true;
1746 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1748 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1749 newann.padAnnotation(alwidth);
1750 alignment.addAnnotation(newann);
1760 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1761 sequences, 0, alignment.getWidth(), alignment));
1763 // Add any annotations attached to sequences
1764 for (int i = 0; i < sequences.length; i++)
1766 if (sequences[i].getAnnotation() != null)
1768 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1770 annotationAdded = true;
1771 sequences[i].getAnnotation()[a].adjustForAlignment();
1772 sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1773 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1778 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1785 // propagate alignment changed.
1786 viewport.setEndSeq(alignment.getHeight());
1787 if (annotationAdded)
1789 // Duplicate sequence annotation in all views.
1790 AlignmentI[] alview = this.getViewAlignments();
1791 for (int i = 0; i < sequences.length; i++)
1793 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1796 for (int avnum = 0; avnum < alview.length; avnum++)
1798 if (alview[avnum] != alignment)
1800 // duplicate in a view other than the one with input focus
1801 int avwidth = alview[avnum].getWidth() + 1;
1802 // this relies on sann being preserved after we
1803 // modify the sequence's annotation array for each duplication
1804 for (int a = 0; a < sann.length; a++)
1806 AlignmentAnnotation newann = new AlignmentAnnotation(
1808 sequences[i].addAlignmentAnnotation(newann);
1809 newann.padAnnotation(avwidth);
1810 alview[avnum].addAnnotation(newann); // annotation was
1811 // duplicated earlier
1812 alview[avnum].setAnnotationIndex(newann, a);
1817 buildSortByAnnotationScoresMenu();
1819 viewport.firePropertyChange("alignment", null, alignment
1825 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
1827 String newtitle = new String("Copied sequences");
1829 if (Desktop.jalviewClipboard != null
1830 && Desktop.jalviewClipboard[2] != null)
1832 Vector hc = (Vector) Desktop.jalviewClipboard[2];
1833 for (int i = 0; i < hc.size(); i++)
1835 int[] region = (int[]) hc.elementAt(i);
1836 af.viewport.hideColumns(region[0], region[1]);
1840 // >>>This is a fix for the moment, until a better solution is
1842 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
1844 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1846 // TODO: maintain provenance of an alignment, rather than just make the
1847 // title a concatenation of operations.
1850 if (title.startsWith("Copied sequences"))
1856 newtitle = newtitle.concat("- from " + title);
1861 newtitle = new String("Pasted sequences");
1864 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1869 } catch (Exception ex)
1871 ex.printStackTrace();
1872 System.out.println("Exception whilst pasting: " + ex);
1873 // could be anything being pasted in here
1884 protected void cut_actionPerformed(ActionEvent e)
1886 copy_actionPerformed(null);
1887 delete_actionPerformed(null);
1896 protected void delete_actionPerformed(ActionEvent evt)
1899 SequenceGroup sg = viewport.getSelectionGroup();
1905 Vector seqs = new Vector();
1907 for (int i = 0; i < sg.getSize(); i++)
1909 seq = sg.getSequenceAt(i);
1910 seqs.addElement(seq);
1913 // If the cut affects all sequences, remove highlighted columns
1914 if (sg.getSize() == viewport.alignment.getHeight())
1916 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1917 sg.getEndRes() + 1);
1920 SequenceI[] cut = new SequenceI[seqs.size()];
1921 for (int i = 0; i < seqs.size(); i++)
1923 cut[i] = (SequenceI) seqs.elementAt(i);
1927 * //ADD HISTORY ITEM
1929 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1930 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1931 viewport.alignment));
1933 viewport.setSelectionGroup(null);
1934 viewport.sendSelection();
1935 viewport.alignment.deleteGroup(sg);
1937 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1939 if (viewport.getAlignment().getHeight() < 1)
1943 this.setClosed(true);
1944 } catch (Exception ex)
1956 protected void deleteGroups_actionPerformed(ActionEvent e)
1958 viewport.alignment.deleteAllGroups();
1959 viewport.sequenceColours = null;
1960 viewport.setSelectionGroup(null);
1961 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1962 alignPanel.updateAnnotation();
1963 alignPanel.paintAlignment(true);
1972 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1974 SequenceGroup sg = new SequenceGroup();
1976 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1978 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1981 sg.setEndRes(viewport.alignment.getWidth() - 1);
1982 viewport.setSelectionGroup(sg);
1983 viewport.sendSelection();
1984 alignPanel.paintAlignment(true);
1985 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1994 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1996 if (viewport.cursorMode)
1998 alignPanel.seqPanel.keyboardNo1 = null;
1999 alignPanel.seqPanel.keyboardNo2 = null;
2001 viewport.setSelectionGroup(null);
2002 viewport.getColumnSelection().clear();
2003 viewport.setSelectionGroup(null);
2004 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2005 alignPanel.idPanel.idCanvas.searchResults = null;
2006 alignPanel.paintAlignment(true);
2007 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2016 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2018 SequenceGroup sg = viewport.getSelectionGroup();
2022 selectAllSequenceMenuItem_actionPerformed(null);
2027 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2029 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2032 alignPanel.paintAlignment(true);
2033 viewport.sendSelection();
2034 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2037 public void invertColSel_actionPerformed(ActionEvent e)
2039 viewport.invertColumnSelection();
2040 alignPanel.paintAlignment(true);
2049 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2051 trimAlignment(true);
2060 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2062 trimAlignment(false);
2065 void trimAlignment(boolean trimLeft)
2067 ColumnSelection colSel = viewport.getColumnSelection();
2070 if (colSel.size() > 0)
2074 column = colSel.getMin();
2078 column = colSel.getMax();
2082 if (viewport.getSelectionGroup() != null)
2084 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2085 viewport.hiddenRepSequences);
2089 seqs = viewport.alignment.getSequencesArray();
2092 TrimRegionCommand trimRegion;
2095 trimRegion = new TrimRegionCommand("Remove Left",
2096 TrimRegionCommand.TRIM_LEFT, seqs, column,
2097 viewport.alignment, viewport.colSel,
2098 viewport.selectionGroup);
2099 viewport.setStartRes(0);
2103 trimRegion = new TrimRegionCommand("Remove Right",
2104 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2105 viewport.alignment, viewport.colSel,
2106 viewport.selectionGroup);
2109 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2111 addHistoryItem(trimRegion);
2113 Vector groups = viewport.alignment.getGroups();
2115 for (int i = 0; i < groups.size(); i++)
2117 SequenceGroup sg = (SequenceGroup) groups.get(i);
2119 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2120 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2122 viewport.alignment.deleteGroup(sg);
2126 viewport.firePropertyChange("alignment", null, viewport
2127 .getAlignment().getSequences());
2137 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2139 int start = 0, end = viewport.alignment.getWidth() - 1;
2142 if (viewport.getSelectionGroup() != null)
2144 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2145 viewport.hiddenRepSequences);
2146 start = viewport.getSelectionGroup().getStartRes();
2147 end = viewport.getSelectionGroup().getEndRes();
2151 seqs = viewport.alignment.getSequencesArray();
2154 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2155 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
2157 addHistoryItem(removeGapCols);
2159 statusBar.setText("Removed " + removeGapCols.getSize()
2160 + " empty columns.");
2162 // This is to maintain viewport position on first residue
2163 // of first sequence
2164 SequenceI seq = viewport.alignment.getSequenceAt(0);
2165 int startRes = seq.findPosition(viewport.startRes);
2166 // ShiftList shifts;
2167 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2168 // edit.alColumnChanges=shifts.getInverse();
2169 // if (viewport.hasHiddenColumns)
2170 // viewport.getColumnSelection().compensateForEdits(shifts);
2171 viewport.setStartRes(seq.findIndex(startRes) - 1);
2172 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2183 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2185 int start = 0, end = viewport.alignment.getWidth() - 1;
2188 if (viewport.getSelectionGroup() != null)
2190 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2191 viewport.hiddenRepSequences);
2192 start = viewport.getSelectionGroup().getStartRes();
2193 end = viewport.getSelectionGroup().getEndRes();
2197 seqs = viewport.alignment.getSequencesArray();
2200 // This is to maintain viewport position on first residue
2201 // of first sequence
2202 SequenceI seq = viewport.alignment.getSequenceAt(0);
2203 int startRes = seq.findPosition(viewport.startRes);
2205 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2206 viewport.alignment));
2208 viewport.setStartRes(seq.findIndex(startRes) - 1);
2210 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2221 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2223 viewport.padGaps = padGapsMenuitem.isSelected();
2224 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2230 // if (justifySeqs>0)
2232 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2244 public void findMenuItem_actionPerformed(ActionEvent e)
2249 public void newView_actionPerformed(ActionEvent e)
2251 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2254 newap.av.gatherViewsHere = false;
2256 if (viewport.viewName == null)
2258 viewport.viewName = "Original";
2261 newap.av.historyList = viewport.historyList;
2262 newap.av.redoList = viewport.redoList;
2264 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2265 String newViewName = "View " + index;
2267 Vector comps = (Vector) PaintRefresher.components.get(viewport
2268 .getSequenceSetId());
2269 Vector existingNames = new Vector();
2270 for (int i = 0; i < comps.size(); i++)
2272 if (comps.elementAt(i) instanceof AlignmentPanel)
2274 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2275 if (!existingNames.contains(ap.av.viewName))
2277 existingNames.addElement(ap.av.viewName);
2282 while (existingNames.contains(newViewName))
2284 newViewName = "View " + (++index);
2287 newap.av.viewName = newViewName;
2289 addAlignmentPanel(newap, true);
2291 if (alignPanels.size() == 2)
2293 viewport.gatherViewsHere = true;
2295 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2298 public void expandViews_actionPerformed(ActionEvent e)
2300 Desktop.instance.explodeViews(this);
2303 public void gatherViews_actionPerformed(ActionEvent e)
2305 Desktop.instance.gatherViews(this);
2314 public void font_actionPerformed(ActionEvent e)
2316 new FontChooser(alignPanel);
2325 protected void seqLimit_actionPerformed(ActionEvent e)
2327 viewport.setShowJVSuffix(seqLimits.isSelected());
2329 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2330 .calculateIdWidth());
2331 alignPanel.paintAlignment(true);
2334 public void idRightAlign_actionPerformed(ActionEvent e)
2336 viewport.rightAlignIds = idRightAlign.isSelected();
2337 alignPanel.paintAlignment(true);
2340 public void centreColumnLabels_actionPerformed(ActionEvent e)
2342 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2343 alignPanel.paintAlignment(true);
2349 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2351 protected void followHighlight_actionPerformed()
2353 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2355 alignPanel.scrollToPosition(
2356 alignPanel.seqPanel.seqCanvas.searchResults, false);
2366 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2368 viewport.setColourText(colourTextMenuItem.isSelected());
2369 alignPanel.paintAlignment(true);
2378 public void wrapMenuItem_actionPerformed(ActionEvent e)
2380 scaleAbove.setVisible(wrapMenuItem.isSelected());
2381 scaleLeft.setVisible(wrapMenuItem.isSelected());
2382 scaleRight.setVisible(wrapMenuItem.isSelected());
2383 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2384 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2387 public void showAllSeqs_actionPerformed(ActionEvent e)
2389 viewport.showAllHiddenSeqs();
2392 public void showAllColumns_actionPerformed(ActionEvent e)
2394 viewport.showAllHiddenColumns();
2398 public void hideSelSequences_actionPerformed(ActionEvent e)
2400 viewport.hideAllSelectedSeqs();
2401 alignPanel.paintAlignment(true);
2404 public void hideSelColumns_actionPerformed(ActionEvent e)
2406 viewport.hideSelectedColumns();
2407 alignPanel.paintAlignment(true);
2410 public void hiddenMarkers_actionPerformed(ActionEvent e)
2412 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2422 protected void scaleAbove_actionPerformed(ActionEvent e)
2424 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2425 alignPanel.paintAlignment(true);
2434 protected void scaleLeft_actionPerformed(ActionEvent e)
2436 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2437 alignPanel.paintAlignment(true);
2446 protected void scaleRight_actionPerformed(ActionEvent e)
2448 viewport.setScaleRightWrapped(scaleRight.isSelected());
2449 alignPanel.paintAlignment(true);
2458 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2460 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2461 alignPanel.paintAlignment(true);
2470 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2472 viewport.setShowText(viewTextMenuItem.isSelected());
2473 alignPanel.paintAlignment(true);
2482 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2484 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2485 alignPanel.paintAlignment(true);
2488 public FeatureSettings featureSettings;
2490 public void featureSettings_actionPerformed(ActionEvent e)
2492 if (featureSettings != null)
2494 featureSettings.close();
2495 featureSettings = null;
2497 featureSettings = new FeatureSettings(this);
2501 * Set or clear 'Show Sequence Features'
2506 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2508 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2509 alignPanel.paintAlignment(true);
2510 if (alignPanel.getOverviewPanel() != null)
2512 alignPanel.getOverviewPanel().updateOverviewImage();
2517 * Set or clear 'Show Sequence Features'
2522 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2524 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2526 if (viewport.getShowSequenceFeaturesHeight())
2528 // ensure we're actually displaying features
2529 viewport.setShowSequenceFeatures(true);
2530 showSeqFeatures.setSelected(true);
2532 alignPanel.paintAlignment(true);
2533 if (alignPanel.getOverviewPanel() != null)
2535 alignPanel.getOverviewPanel().updateOverviewImage();
2545 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2547 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2548 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2551 public void alignmentProperties()
2553 JEditorPane editPane = new JEditorPane("text/html", "");
2554 editPane.setEditable(false);
2555 StringBuffer contents = new StringBuffer("<html>");
2558 int min = Integer.MAX_VALUE, max = 0;
2559 for (int i = 0; i < viewport.alignment.getHeight(); i++)
2561 int size = viewport.alignment.getSequenceAt(i).getEnd()
2562 - viewport.alignment.getSequenceAt(i).getStart();
2569 avg = avg / (float) viewport.alignment.getHeight();
2571 contents.append("<br>Sequences: " + viewport.alignment.getHeight());
2572 contents.append("<br>Minimum Sequence Length: " + min);
2573 contents.append("<br>Maximum Sequence Length: " + max);
2574 contents.append("<br>Average Length: " + (int) avg);
2576 if (((Alignment) viewport.alignment).getProperties() != null)
2578 Hashtable props = ((Alignment) viewport.alignment).getProperties();
2579 Enumeration en = props.keys();
2580 contents.append("<br><br><table border=\"1\">");
2581 while (en.hasMoreElements())
2583 String key = en.nextElement().toString();
2584 StringBuffer val = new StringBuffer();
2585 String vals = props.get(key).toString();
2589 npos = vals.indexOf("\n", pos);
2592 val.append(vals.substring(pos));
2596 val.append(vals.substring(pos, npos));
2600 } while (npos != -1);
2602 .append("<tr><td>" + key + "</td><td>" + val + "</td></tr>");
2604 contents.append("</table>");
2606 editPane.setText(contents.toString() + "</html>");
2607 JInternalFrame frame = new JInternalFrame();
2608 frame.getContentPane().add(new JScrollPane(editPane));
2610 Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
2611 + getTitle(), 500, 400);
2620 public void overviewMenuItem_actionPerformed(ActionEvent e)
2622 if (alignPanel.overviewPanel != null)
2627 JInternalFrame frame = new JInternalFrame();
2628 OverviewPanel overview = new OverviewPanel(alignPanel);
2629 frame.setContentPane(overview);
2630 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(), frame
2631 .getWidth(), frame.getHeight());
2633 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2635 .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2637 public void internalFrameClosed(
2638 javax.swing.event.InternalFrameEvent evt)
2640 alignPanel.setOverviewPanel(null);
2644 alignPanel.setOverviewPanel(overview);
2647 public void textColour_actionPerformed(ActionEvent e)
2649 new TextColourChooser().chooseColour(alignPanel, null);
2658 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2669 public void clustalColour_actionPerformed(ActionEvent e)
2671 changeColour(new ClustalxColourScheme(
2672 viewport.alignment.getSequences(), viewport.alignment
2682 public void zappoColour_actionPerformed(ActionEvent e)
2684 changeColour(new ZappoColourScheme());
2693 public void taylorColour_actionPerformed(ActionEvent e)
2695 changeColour(new TaylorColourScheme());
2704 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2706 changeColour(new HydrophobicColourScheme());
2715 public void helixColour_actionPerformed(ActionEvent e)
2717 changeColour(new HelixColourScheme());
2726 public void strandColour_actionPerformed(ActionEvent e)
2728 changeColour(new StrandColourScheme());
2737 public void turnColour_actionPerformed(ActionEvent e)
2739 changeColour(new TurnColourScheme());
2748 public void buriedColour_actionPerformed(ActionEvent e)
2750 changeColour(new BuriedColourScheme());
2759 public void nucleotideColour_actionPerformed(ActionEvent e)
2761 changeColour(new NucleotideColourScheme());
2764 public void annotationColour_actionPerformed(ActionEvent e)
2766 new AnnotationColourChooser(viewport, alignPanel);
2775 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2777 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2786 public void changeColour(ColourSchemeI cs)
2792 if (viewport.getAbovePIDThreshold())
2794 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2797 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2799 viewport.setGlobalColourScheme(cs);
2803 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2806 if (viewport.getConservationSelected())
2809 Alignment al = (Alignment) viewport.alignment;
2810 Conservation c = new Conservation("All",
2811 ResidueProperties.propHash, 3, al.getSequences(), 0, al
2815 c.verdict(false, viewport.ConsPercGaps);
2817 cs.setConservation(c);
2819 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
2824 cs.setConservation(null);
2827 cs.setConsensus(viewport.hconsensus);
2830 viewport.setGlobalColourScheme(cs);
2832 if (viewport.getColourAppliesToAllGroups())
2834 Vector groups = viewport.alignment.getGroups();
2836 for (int i = 0; i < groups.size(); i++)
2838 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2846 if (cs instanceof ClustalxColourScheme)
2848 sg.cs = new ClustalxColourScheme(sg
2849 .getSequences(viewport.hiddenRepSequences), sg.getWidth());
2851 else if (cs instanceof UserColourScheme)
2853 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
2859 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2860 } catch (Exception ex)
2865 if (viewport.getAbovePIDThreshold()
2866 || cs instanceof PIDColourScheme
2867 || cs instanceof Blosum62ColourScheme)
2869 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2871 sg.cs.setConsensus(AAFrequency.calculate(sg
2872 .getSequences(viewport.hiddenRepSequences), sg
2873 .getStartRes(), sg.getEndRes() + 1));
2877 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2880 if (viewport.getConservationSelected())
2882 Conservation c = new Conservation("Group",
2883 ResidueProperties.propHash, 3, sg
2884 .getSequences(viewport.hiddenRepSequences), sg
2885 .getStartRes(), sg.getEndRes() + 1);
2887 c.verdict(false, viewport.ConsPercGaps);
2888 sg.cs.setConservation(c);
2892 sg.cs.setConservation(null);
2897 if (alignPanel.getOverviewPanel() != null)
2899 alignPanel.getOverviewPanel().updateOverviewImage();
2902 alignPanel.paintAlignment(true);
2911 protected void modifyPID_actionPerformed(ActionEvent e)
2913 if (viewport.getAbovePIDThreshold()
2914 && viewport.globalColourScheme != null)
2916 SliderPanel.setPIDSliderSource(alignPanel, viewport
2917 .getGlobalColourScheme(), "Background");
2918 SliderPanel.showPIDSlider();
2928 protected void modifyConservation_actionPerformed(ActionEvent e)
2930 if (viewport.getConservationSelected()
2931 && viewport.globalColourScheme != null)
2933 SliderPanel.setConservationSlider(alignPanel,
2934 viewport.globalColourScheme, "Background");
2935 SliderPanel.showConservationSlider();
2945 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2947 viewport.setConservationSelected(conservationMenuItem.isSelected());
2949 viewport.setAbovePIDThreshold(false);
2950 abovePIDThreshold.setSelected(false);
2952 changeColour(viewport.getGlobalColourScheme());
2954 modifyConservation_actionPerformed(null);
2963 public void abovePIDThreshold_actionPerformed(ActionEvent e)
2965 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
2967 conservationMenuItem.setSelected(false);
2968 viewport.setConservationSelected(false);
2970 changeColour(viewport.getGlobalColourScheme());
2972 modifyPID_actionPerformed(null);
2981 public void userDefinedColour_actionPerformed(ActionEvent e)
2983 if (e.getActionCommand().equals("User Defined..."))
2985 new UserDefinedColours(alignPanel, null);
2989 UserColourScheme udc = (UserColourScheme) UserDefinedColours
2990 .getUserColourSchemes().get(e.getActionCommand());
2996 public void updateUserColourMenu()
2999 Component[] menuItems = colourMenu.getMenuComponents();
3000 int i, iSize = menuItems.length;
3001 for (i = 0; i < iSize; i++)
3003 if (menuItems[i].getName() != null
3004 && menuItems[i].getName().equals("USER_DEFINED"))
3006 colourMenu.remove(menuItems[i]);
3010 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3012 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3013 .getUserColourSchemes().keys();
3015 while (userColours.hasMoreElements())
3017 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3018 userColours.nextElement().toString());
3019 radioItem.setName("USER_DEFINED");
3020 radioItem.addMouseListener(new MouseAdapter()
3022 public void mousePressed(MouseEvent evt)
3024 if (evt.isControlDown()
3025 || SwingUtilities.isRightMouseButton(evt))
3028 .removeActionListener(radioItem.getActionListeners()[0]);
3030 int option = JOptionPane.showInternalConfirmDialog(
3031 jalview.gui.Desktop.desktop,
3032 "Remove from default list?",
3033 "Remove user defined colour",
3034 JOptionPane.YES_NO_OPTION);
3035 if (option == JOptionPane.YES_OPTION)
3037 jalview.gui.UserDefinedColours
3038 .removeColourFromDefaults(radioItem.getText());
3039 colourMenu.remove(radioItem);
3043 radioItem.addActionListener(new ActionListener()
3045 public void actionPerformed(ActionEvent evt)
3047 userDefinedColour_actionPerformed(evt);
3054 radioItem.addActionListener(new ActionListener()
3056 public void actionPerformed(ActionEvent evt)
3058 userDefinedColour_actionPerformed(evt);
3062 colourMenu.insert(radioItem, 15);
3063 colours.add(radioItem);
3074 public void PIDColour_actionPerformed(ActionEvent e)
3076 changeColour(new PIDColourScheme());
3085 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3087 changeColour(new Blosum62ColourScheme());
3096 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3098 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3099 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3100 .getAlignment().getSequenceAt(0), null);
3101 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3102 viewport.alignment));
3103 alignPanel.paintAlignment(true);
3112 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3114 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3115 AlignmentSorter.sortByID(viewport.getAlignment());
3116 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
3117 alignPanel.paintAlignment(true);
3126 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3128 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3129 AlignmentSorter.sortByLength(viewport.getAlignment());
3130 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3131 viewport.alignment));
3132 alignPanel.paintAlignment(true);
3141 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3143 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3144 AlignmentSorter.sortByGroup(viewport.getAlignment());
3145 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3146 viewport.alignment));
3148 alignPanel.paintAlignment(true);
3157 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3159 new RedundancyPanel(alignPanel, this);
3168 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3170 if ((viewport.getSelectionGroup() == null)
3171 || (viewport.getSelectionGroup().getSize() < 2))
3173 JOptionPane.showInternalMessageDialog(this,
3174 "You must select at least 2 sequences.", "Invalid Selection",
3175 JOptionPane.WARNING_MESSAGE);
3179 JInternalFrame frame = new JInternalFrame();
3180 frame.setContentPane(new PairwiseAlignPanel(viewport));
3181 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
3191 public void PCAMenuItem_actionPerformed(ActionEvent e)
3193 if (((viewport.getSelectionGroup() != null)
3194 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3195 .getSelectionGroup().getSize() > 0))
3196 || (viewport.getAlignment().getHeight() < 4))
3198 JOptionPane.showInternalMessageDialog(this,
3199 "Principal component analysis must take\n"
3200 + "at least 4 input sequences.",
3201 "Sequence selection insufficient",
3202 JOptionPane.WARNING_MESSAGE);
3207 new PCAPanel(alignPanel);
3210 public void autoCalculate_actionPerformed(ActionEvent e)
3212 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3213 if (viewport.autoCalculateConsensus)
3215 viewport.firePropertyChange("alignment", null, viewport
3216 .getAlignment().getSequences());
3226 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3228 NewTreePanel("AV", "PID", "Average distance tree using PID");
3237 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3239 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3248 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3250 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3259 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3261 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3274 void NewTreePanel(String type, String pwType, String title)
3278 if (viewport.getSelectionGroup() != null)
3280 if (viewport.getSelectionGroup().getSize() < 3)
3285 "You need to have more than two sequences selected to build a tree!",
3286 "Not enough sequences", JOptionPane.WARNING_MESSAGE);
3291 SequenceGroup sg = viewport.getSelectionGroup();
3293 /* Decide if the selection is a column region */
3294 while (s < sg.getSize())
3296 if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
3302 "The selected region to create a tree may\nonly contain residues or gaps.\n"
3303 + "Try using the Pad function in the edit menu,\n"
3304 + "or one of the multiple sequence alignment web services.",
3305 "Sequences in selection are not aligned",
3306 JOptionPane.WARNING_MESSAGE);
3312 title = title + " on region";
3313 tp = new TreePanel(alignPanel, type, pwType);
3317 // are the sequences aligned?
3318 if (!viewport.alignment.isAligned())
3323 "The sequences must be aligned before creating a tree.\n"
3324 + "Try using the Pad function in the edit menu,\n"
3325 + "or one of the multiple sequence alignment web services.",
3326 "Sequences not aligned",
3327 JOptionPane.WARNING_MESSAGE);
3332 if (viewport.alignment.getHeight() < 2)
3337 tp = new TreePanel(alignPanel, type, pwType);
3342 if (viewport.viewName != null)
3344 title += viewport.viewName + " of ";
3347 title += this.title;
3349 Desktop.addInternalFrame(tp, title, 600, 500);
3360 public void addSortByOrderMenuItem(String title,
3361 final AlignmentOrder order)
3363 final JMenuItem item = new JMenuItem("by " + title);
3365 item.addActionListener(new java.awt.event.ActionListener()
3367 public void actionPerformed(ActionEvent e)
3369 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3371 // TODO: JBPNote - have to map order entries to curent SequenceI
3373 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3375 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3376 viewport.alignment));
3378 alignPanel.paintAlignment(true);
3384 * Add a new sort by annotation score menu item
3387 * the menu to add the option to
3389 * the label used to retrieve scores for each sequence on the
3392 public void addSortByAnnotScoreMenuItem(JMenu sort,
3393 final String scoreLabel)
3395 final JMenuItem item = new JMenuItem(scoreLabel);
3397 item.addActionListener(new java.awt.event.ActionListener()
3399 public void actionPerformed(ActionEvent e)
3401 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3402 AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport
3403 .getAlignment());// ,viewport.getSelectionGroup());
3404 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3405 viewport.alignment));
3406 alignPanel.paintAlignment(true);
3412 * last hash for alignment's annotation array - used to minimise cost of
3415 protected int _annotationScoreVectorHash;
3418 * search the alignment and rebuild the sort by annotation score submenu the
3419 * last alignment annotation vector hash is stored to minimize cost of
3420 * rebuilding in subsequence calls.
3423 public void buildSortByAnnotationScoresMenu()
3425 if (viewport.alignment.getAlignmentAnnotation() == null)
3430 if (viewport.alignment.getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3432 sortByAnnotScore.removeAll();
3433 // almost certainly a quicker way to do this - but we keep it simple
3434 Hashtable scoreSorts = new Hashtable();
3435 AlignmentAnnotation aann[];
3436 Enumeration sq = viewport.alignment.getSequences().elements();
3437 while (sq.hasMoreElements())
3439 aann = ((SequenceI) sq.nextElement()).getAnnotation();
3440 for (int i = 0; aann != null && i < aann.length; i++)
3442 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3444 scoreSorts.put(aann[i].label, aann[i].label);
3448 Enumeration labels = scoreSorts.keys();
3449 while (labels.hasMoreElements())
3451 addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels
3454 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3457 _annotationScoreVectorHash = viewport.alignment
3458 .getAlignmentAnnotation().hashCode();
3463 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3464 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3465 * call. Listeners are added to remove the menu item when the treePanel is
3466 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3470 * Displayed tree window.
3472 * SortBy menu item title.
3474 public void buildTreeMenu()
3476 sortByTreeMenu.removeAll();
3478 Vector comps = (Vector) PaintRefresher.components.get(viewport
3479 .getSequenceSetId());
3480 Vector treePanels = new Vector();
3481 int i, iSize = comps.size();
3482 for (i = 0; i < iSize; i++)
3484 if (comps.elementAt(i) instanceof TreePanel)
3486 treePanels.add(comps.elementAt(i));
3490 iSize = treePanels.size();
3494 sortByTreeMenu.setVisible(false);
3498 sortByTreeMenu.setVisible(true);
3500 for (i = 0; i < treePanels.size(); i++)
3502 TreePanel tp = (TreePanel) treePanels.elementAt(i);
3503 final JMenuItem item = new JMenuItem(tp.getTitle());
3504 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3505 item.addActionListener(new java.awt.event.ActionListener()
3507 public void actionPerformed(ActionEvent e)
3509 SequenceI[] oldOrder = viewport.getAlignment()
3510 .getSequencesArray();
3511 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
3513 addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
3514 viewport.alignment));
3516 alignPanel.paintAlignment(true);
3520 sortByTreeMenu.add(item);
3525 * Work out whether the whole set of sequences or just the selected set will
3526 * be submitted for multiple alignment.
3529 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3531 // Now, check we have enough sequences
3532 AlignmentView msa = null;
3534 if ((viewport.getSelectionGroup() != null)
3535 && (viewport.getSelectionGroup().getSize() > 1))
3537 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3538 // some common interface!
3540 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3541 * SequenceI[sz = seqs.getSize(false)];
3543 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3544 * seqs.getSequenceAt(i); }
3546 msa = viewport.getAlignmentView(true);
3551 * Vector seqs = viewport.getAlignment().getSequences();
3553 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3555 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3556 * seqs.elementAt(i); } }
3558 msa = viewport.getAlignmentView(false);
3564 * Decides what is submitted to a secondary structure prediction service: the
3565 * first sequence in the alignment, or in the current selection, or, if the
3566 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3567 * region or the whole alignment. (where the first sequence in the set is the
3568 * one that the prediction will be for).
3570 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3572 AlignmentView seqs = null;
3574 if ((viewport.getSelectionGroup() != null)
3575 && (viewport.getSelectionGroup().getSize() > 0))
3577 seqs = viewport.getAlignmentView(true);
3581 seqs = viewport.getAlignmentView(false);
3583 // limit sequences - JBPNote in future - could spawn multiple prediction
3585 // TODO: viewport.alignment.isAligned is a global state - the local
3586 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3587 if (!viewport.alignment.isAligned())
3589 seqs.setSequences(new SeqCigar[]
3590 { seqs.getSequences()[0] });
3591 // TODO: if seqs.getSequences().length>1 then should really have warned user!
3603 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3605 // Pick the tree file
3606 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
3607 .getProperty("LAST_DIRECTORY"));
3608 chooser.setFileView(new JalviewFileView());
3609 chooser.setDialogTitle("Select a newick-like tree file");
3610 chooser.setToolTipText("Load a tree file");
3612 int value = chooser.showOpenDialog(null);
3614 if (value == JalviewFileChooser.APPROVE_OPTION)
3616 String choice = chooser.getSelectedFile().getPath();
3617 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3618 jalview.io.NewickFile fin = null;
3621 fin = new jalview.io.NewickFile(choice, "File");
3622 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3623 } catch (Exception ex)
3625 JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3626 "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
3627 ex.printStackTrace();
3629 if (fin != null && fin.hasWarningMessage())
3631 JOptionPane.showMessageDialog(Desktop.desktop, fin
3632 .getWarningMessage(), "Possible problem with tree file",
3633 JOptionPane.WARNING_MESSAGE);
3638 public TreePanel ShowNewickTree(NewickFile nf, String title)
3640 return ShowNewickTree(nf, title, 600, 500, 4, 5);
3643 public TreePanel ShowNewickTree(NewickFile nf, String title,
3644 AlignmentView input)
3646 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
3649 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
3650 int h, int x, int y)
3652 return ShowNewickTree(nf, title, null, w, h, x, y);
3656 * Add a treeviewer for the tree extracted from a newick file object to the
3657 * current alignment view
3664 * Associated alignment input data (or null)
3673 * @return TreePanel handle
3675 public TreePanel ShowNewickTree(NewickFile nf, String title,
3676 AlignmentView input, int w, int h, int x, int y)
3678 TreePanel tp = null;
3684 if (nf.getTree() != null)
3686 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
3692 tp.setLocation(x, y);
3695 Desktop.addInternalFrame(tp, title, w, h);
3697 } catch (Exception ex)
3699 ex.printStackTrace();
3706 * Generates menu items and listener event actions for web service clients
3709 public void BuildWebServiceMenu()
3711 // TODO: add support for context dependent disabling of services based on
3712 // alignment and current selection
3713 // TODO: add additional serviceHandle parameter to specify abstract handler
3714 // class independently of AbstractName
3715 // TODO: add in rediscovery GUI function to restart discoverer
3716 // TODO: group services by location as well as function and/or introduce
3717 // object broker mechanism.
3718 if ((Discoverer.services != null) && (Discoverer.services.size() > 0))
3720 // TODO: refactor to allow list of AbstractName/Handler bindings to be
3721 // stored or retrieved from elsewhere
3722 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
3723 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
3724 Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
3725 // TODO: move GUI generation code onto service implementation - so a
3726 // client instance attaches itself to the GUI with method call like
3727 // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
3729 Vector wsmenu = new Vector();
3730 final IProgressIndicator af = this;
3733 // Add any Multiple Sequence Alignment Services
3734 final JMenu msawsmenu = new JMenu("Alignment");
3735 for (int i = 0, j = msaws.size(); i < j; i++)
3737 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
3739 jalview.ws.WSClient impl = jalview.ws.Discoverer
3740 .getServiceClient(sh);
3741 impl.attachWSMenuEntry(msawsmenu, this);
3744 wsmenu.add(msawsmenu);
3746 if (secstrpr != null)
3748 // Add any secondary structure prediction services
3749 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
3750 for (int i = 0, j = secstrpr.size(); i < j; i++)
3752 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
3754 jalview.ws.WSClient impl = jalview.ws.Discoverer
3755 .getServiceClient(sh);
3756 impl.attachWSMenuEntry(secstrmenu, this);
3758 wsmenu.add(secstrmenu);
3760 if (seqsrch != null)
3762 // Add any sequence search services
3763 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
3764 for (int i = 0, j = seqsrch.size(); i < j; i++)
3766 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
3768 jalview.ws.WSClient impl = jalview.ws.Discoverer
3769 .getServiceClient(sh);
3770 impl.attachWSMenuEntry(seqsrchmenu, this);
3772 // finally, add the whole shebang onto the webservices menu
3773 wsmenu.add(seqsrchmenu);
3775 resetWebServiceMenu();
3776 for (int i = 0, j = wsmenu.size(); i < j; i++)
3778 webService.add((JMenu) wsmenu.get(i));
3783 resetWebServiceMenu();
3784 this.webService.add(this.webServiceNoServices);
3789 * empty the web service menu and add any ad-hoc functions not dynamically
3793 private void resetWebServiceMenu()
3795 webService.removeAll();
3796 build_fetchdbmenu(webService);
3800 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
3801 * chooser = new JalviewFileChooser(jalview.bin.Cache.
3802 * getProperty("LAST_DIRECTORY"));
3804 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
3805 * to Vamsas file"); chooser.setToolTipText("Export");
3807 * int value = chooser.showSaveDialog(this);
3809 * if (value == JalviewFileChooser.APPROVE_OPTION) {
3810 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
3811 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
3812 * chooser.getSelectedFile().getAbsolutePath(), this); } }
3815 * prototype of an automatically enabled/disabled analysis function
3818 protected void setShowProductsEnabled()
3820 SequenceI[] selection = viewport.getSequenceSelection();
3821 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
3822 viewport.getAlignment().getDataset()))
3824 showProducts.setEnabled(true);
3829 showProducts.setEnabled(false);
3834 * search selection for sequence xRef products and build the show products
3839 * @return true if showProducts menu should be enabled.
3841 public boolean canShowProducts(SequenceI[] selection,
3842 boolean isRegionSelection, Alignment dataset)
3844 boolean showp = false;
3847 showProducts.removeAll();
3848 final boolean dna = viewport.getAlignment().isNucleotide();
3849 final Alignment ds = dataset;
3850 String[] ptypes = (selection == null || selection.length == 0) ? null
3851 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
3853 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
3854 // selection, dataset, true);
3855 final SequenceI[] sel = selection;
3856 for (int t = 0; ptypes != null && t < ptypes.length; t++)
3859 final boolean isRegSel = isRegionSelection;
3860 final AlignFrame af = this;
3861 final String source = ptypes[t];
3862 JMenuItem xtype = new JMenuItem(ptypes[t]);
3863 xtype.addActionListener(new ActionListener()
3866 public void actionPerformed(ActionEvent e)
3868 // TODO: new thread for this call with vis-delay
3869 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
3870 isRegSel, dna, source);
3874 showProducts.add(xtype);
3876 showProducts.setVisible(showp);
3877 showProducts.setEnabled(showp);
3878 } catch (Exception e)
3880 jalview.bin.Cache.log
3882 "canTranslate threw an exception - please report to help@jalview.org",
3889 protected void showProductsFor(SequenceI[] sel, Alignment ds,
3890 boolean isRegSel, boolean dna, String source)
3892 final boolean fisRegSel = isRegSel;
3893 final boolean fdna = dna;
3894 final String fsrc = source;
3895 final AlignFrame ths = this;
3896 final SequenceI[] fsel = sel;
3897 Runnable foo = new Runnable()
3902 final long sttime = System.currentTimeMillis();
3903 ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
3906 Alignment ds = ths.getViewport().alignment.getDataset(); // update
3910 Alignment prods = CrossRef
3911 .findXrefSequences(fsel, fdna, fsrc, ds);
3914 SequenceI[] sprods = new SequenceI[prods.getHeight()];
3915 for (int s = 0; s < sprods.length; s++)
3917 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
3918 if (ds.getSequences() == null
3919 || !ds.getSequences().contains(
3920 sprods[s].getDatasetSequence()))
3921 ds.addSequence(sprods[s].getDatasetSequence());
3922 sprods[s].updatePDBIds();
3924 Alignment al = new Alignment(sprods);
3925 AlignedCodonFrame[] cf = prods.getCodonFrames();
3927 for (int s = 0; cf != null && s < cf.length; s++)
3929 al.addCodonFrame(cf[s]);
3932 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
3934 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
3935 + " for " + ((fisRegSel) ? "selected region of " : "")
3937 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
3942 System.err.println("No Sequences generated for xRef type "
3945 } catch (Exception e)
3947 jalview.bin.Cache.log.error(
3948 "Exception when finding crossreferences", e);
3949 } catch (OutOfMemoryError e)
3951 new OOMWarning("whilst fetching crossreferences", e);
3954 jalview.bin.Cache.log.error("Error when finding crossreferences",
3957 ths.setProgressBar("Finished searching for sequences from " + fsrc,
3962 Thread frunner = new Thread(foo);
3966 public boolean canShowTranslationProducts(SequenceI[] selection,
3967 AlignmentI alignment)
3972 return (jalview.analysis.Dna.canTranslate(selection, viewport
3973 .getViewAsVisibleContigs(true)));
3974 } catch (Exception e)
3976 jalview.bin.Cache.log
3978 "canTranslate threw an exception - please report to help@jalview.org",
3984 public void showProducts_actionPerformed(ActionEvent e)
3986 // /////////////////////////////
3987 // Collect Data to be translated/transferred
3989 SequenceI[] selection = viewport.getSequenceSelection();
3990 AlignmentI al = null;
3993 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
3994 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
3995 viewport.getAlignment().getDataset());
3996 } catch (Exception ex)
3999 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4006 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4007 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4011 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4012 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4013 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4017 public void showTranslation_actionPerformed(ActionEvent e)
4019 // /////////////////////////////
4020 // Collect Data to be translated/transferred
4022 SequenceI[] selection = viewport.getSequenceSelection();
4023 String[] seqstring = viewport.getViewAsString(true);
4024 AlignmentI al = null;
4027 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4028 viewport.getViewAsVisibleContigs(true), viewport
4029 .getGapCharacter(), viewport.alignment
4030 .getAlignmentAnnotation(), viewport.alignment
4031 .getWidth(), viewport.getAlignment().getDataset());
4032 } catch (Exception ex)
4035 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4042 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4043 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4047 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4048 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4049 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4054 * Try to load a features file onto the alignment.
4057 * contents or path to retrieve file
4059 * access mode of file (see jalview.io.AlignFile)
4060 * @return true if features file was parsed corectly.
4062 public boolean parseFeaturesFile(String file, String type)
4064 boolean featuresFile = false;
4067 featuresFile = new FeaturesFile(file, type).parse(viewport.alignment
4068 .getDataset(), alignPanel.seqPanel.seqCanvas
4069 .getFeatureRenderer().featureColours, false);
4070 } catch (Exception ex)
4072 ex.printStackTrace();
4077 viewport.showSequenceFeatures = true;
4078 showSeqFeatures.setSelected(true);
4079 if (alignPanel.seqPanel.seqCanvas.fr != null)
4081 // update the min/max ranges where necessary
4082 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4084 alignPanel.paintAlignment(true);
4087 return featuresFile;
4090 public void dragEnter(DropTargetDragEvent evt)
4094 public void dragExit(DropTargetEvent evt)
4098 public void dragOver(DropTargetDragEvent evt)
4102 public void dropActionChanged(DropTargetDragEvent evt)
4106 public void drop(DropTargetDropEvent evt)
4108 Transferable t = evt.getTransferable();
4109 java.util.List files = null;
4113 DataFlavor uriListFlavor = new DataFlavor(
4114 "text/uri-list;class=java.lang.String");
4115 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4117 // Works on Windows and MacOSX
4118 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4119 files = (java.util.List) t
4120 .getTransferData(DataFlavor.javaFileListFlavor);
4122 else if (t.isDataFlavorSupported(uriListFlavor))
4124 // This is used by Unix drag system
4125 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4126 String data = (String) t.getTransferData(uriListFlavor);
4127 files = new java.util.ArrayList(1);
4128 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4129 data, "\r\n"); st.hasMoreTokens();)
4131 String s = st.nextToken();
4132 if (s.startsWith("#"))
4134 // the line is a comment (as per the RFC 2483)
4138 java.net.URI uri = new java.net.URI(s);
4139 // check to see if we can handle this kind of URI
4140 if (uri.getScheme().toLowerCase().startsWith("http"))
4142 files.add(uri.toString());
4146 // otherwise preserve old behaviour: catch all for file objects
4147 java.io.File file = new java.io.File(uri);
4148 files.add(file.toString());
4152 } catch (Exception e)
4154 e.printStackTrace();
4161 for (int i = 0; i < files.size(); i++)
4163 loadJalviewDataFile(files.get(i).toString());
4165 } catch (Exception ex)
4167 ex.printStackTrace();
4173 * Attempt to load a "dropped" file or URL string: First by testing whether
4174 * it's and Annotation file, then a JNet file, and finally a features file. If
4175 * all are false then the user may have dropped an alignment file onto this
4179 * either a filename or a URL string.
4181 public void loadJalviewDataFile(String file)
4185 String protocol = jalview.io.FormatAdapter.FILE;
4186 String f = file.toLowerCase();
4187 if (f.indexOf("http:") == 0 || f.indexOf("https:") == 0
4188 || f.indexOf("file:") == 0)
4190 protocol = jalview.io.FormatAdapter.URL;
4193 boolean isAnnotation = new AnnotationFile().readAnnotationFile(
4194 viewport.alignment, file, protocol);
4198 // try to see if its a JNet 'concise' style annotation file *before* we
4199 // try to parse it as a features file
4200 String format = new IdentifyFile().Identify(file, protocol);
4201 if (format.equalsIgnoreCase("JnetFile"))
4203 jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
4205 new JnetAnnotationMaker().add_annotation(predictions, viewport
4206 .getAlignment(), 0, false);
4207 isAnnotation = true;
4211 // try to parse it as a features file
4212 boolean isGroupsFile = parseFeaturesFile(file, protocol);
4213 // if it wasn't a features file then we just treat it as a general
4214 // alignment file to load into the current view.
4217 new FileLoader().LoadFile(viewport, file, protocol, format);
4221 alignPanel.paintAlignment(true);
4228 alignPanel.adjustAnnotationHeight();
4229 viewport.updateSequenceIdColours();
4230 buildSortByAnnotationScoresMenu();
4231 alignPanel.paintAlignment(true);
4233 } catch (Exception ex)
4235 ex.printStackTrace();
4239 public void tabSelectionChanged(int index)
4243 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
4244 viewport = alignPanel.av;
4245 setMenusFromViewport(viewport);
4249 public void tabbedPane_mousePressed(MouseEvent e)
4251 if (SwingUtilities.isRightMouseButton(e))
4253 String reply = JOptionPane.showInternalInputDialog(this,
4254 "Enter View Name", "Edit View Name",
4255 JOptionPane.QUESTION_MESSAGE);
4259 viewport.viewName = reply;
4260 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4265 public AlignViewport getCurrentView()
4271 * Open the dialog for regex description parsing.
4273 protected void extractScores_actionPerformed(ActionEvent e)
4275 ParseProperties pp = new jalview.analysis.ParseProperties(
4276 viewport.alignment);
4277 // TODO: verify regex and introduce GUI dialog for version 2.5
4278 // if (pp.getScoresFromDescription("col", "score column ",
4279 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4281 if (pp.getScoresFromDescription("description column",
4282 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4284 buildSortByAnnotationScoresMenu();
4292 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4295 protected void showDbRefs_actionPerformed(ActionEvent e)
4297 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
4303 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4306 protected void showNpFeats_actionPerformed(ActionEvent e)
4308 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
4312 * find the viewport amongst the tabs in this alignment frame and close that
4317 public boolean closeView(AlignViewport av)
4321 this.closeMenuItem_actionPerformed(false);
4324 Component[] comp = tabbedPane.getComponents();
4325 for (int i = 0; comp != null && i < comp.length; i++)
4327 if (comp[i] instanceof AlignmentPanel)
4329 if (((AlignmentPanel) comp[i]).av == av)
4332 closeView((AlignmentPanel) comp[i]);
4340 protected void build_fetchdbmenu(JMenu webService)
4342 // Temporary hack - DBRef Fetcher always top level ws entry.
4343 // TODO We probably want to store a sequence database checklist in
4344 // preferences and have checkboxes.. rather than individual sources selected
4346 JMenu rfetch = new JMenu("Fetch DB References");
4348 .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
4349 webService.add(rfetch);
4351 JMenuItem fetchr = new JMenuItem("Standard Databases");
4353 .setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
4354 fetchr.addActionListener(new ActionListener()
4357 public void actionPerformed(ActionEvent e)
4359 new Thread(new Runnable()
4364 new jalview.ws.DBRefFetcher(alignPanel.av
4365 .getSequenceSelection(), alignPanel.alignFrame)
4366 .fetchDBRefs(false);
4374 JMenu dfetch = new JMenu();
4376 jalview.ws.SequenceFetcher sf = SequenceFetcher
4377 .getSequenceFetcherSingleton(this);
4378 String[] otherdb = sf.getOrderedSupportedSources();
4379 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4380 // jalview.util.QuickSort.sort(otherdb, otherdb);
4381 int comp = 0, mcomp = 15;
4382 String mname = null;
4383 if (otherdb != null && otherdb.length > 0)
4385 for (int i = 0; i < otherdb.length; i++)
4387 String dbname = sf.getSourceProxy(otherdb[i]).getDbName();
4390 mname = "from '" + dbname + "'";
4392 fetchr = new JMenuItem(otherdb[i]);
4393 final String[] dassource = new String[]
4395 fetchr.addActionListener(new ActionListener()
4398 public void actionPerformed(ActionEvent e)
4400 new Thread(new Runnable()
4405 new jalview.ws.DBRefFetcher(alignPanel.av
4406 .getSequenceSelection(), alignPanel.alignFrame,
4407 dassource).fetchDBRefs(false);
4413 fetchr.setToolTipText("Retrieve from " + dbname);
4415 if (comp++ == mcomp || i == (otherdb.length - 1))
4417 dfetch.setText(mname + " to '" + dbname + "'");
4419 dfetch = new JMenu();
4428 * Left justify the whole alignment.
4430 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
4432 AlignmentI al = viewport.getAlignment();
4434 viewport.firePropertyChange("alignment", null, al);
4438 * Right justify the whole alignment.
4440 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
4442 AlignmentI al = viewport.getAlignment();
4444 viewport.firePropertyChange("alignment", null, al);
4447 public void setShowSeqFeatures(boolean b)
4449 showSeqFeatures.setSelected(true);
4450 viewport.setShowSequenceFeatures(true);
4457 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
4458 * awt.event.ActionEvent)
4460 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
4462 viewport.setShowUnconserved(showUnconservedMenuItem.getState());
4463 alignPanel.paintAlignment(true);
4470 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
4473 protected void showGroupConsensus_actionPerformed(ActionEvent e)
4475 viewport.setShowGroupConsensus(showGroupConsensus.getState());
4476 alignPanel.updateAnnotation();
4484 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
4485 * .event.ActionEvent)
4487 protected void showGroupConservation_actionPerformed(ActionEvent e)
4489 viewport.setShowGroupConservation(showGroupConservation.getState());
4490 alignPanel.updateAnnotation();
4497 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
4498 * .event.ActionEvent)
4500 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
4502 if (viewport.getSelectionGroup() != null)
4504 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
4505 viewport.getSequenceSelection(), viewport.getAlignmentView(
4506 true).getSequenceStrings(viewport.getGapCharacter()),
4507 viewport.alignment.getGroups());
4508 viewport.alignment.deleteAllGroups();
4509 viewport.sequenceColours = null;
4510 viewport.setSelectionGroup(null);
4511 // set view properties for each group
4512 for (int g = 0; g < gps.length; g++)
4514 gps[g].setShowunconserved(viewport.getShowUnconserved());
4515 gps[g].setIncludeAllConsSymbols(viewport.isIncludeAllConsensusSymbols());
4516 viewport.alignment.addGroup(gps[g]);
4517 Color col = new Color((int) (Math.random() * 255), (int) (Math
4518 .random() * 255), (int) (Math.random() * 255));
4519 col = col.brighter();
4520 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
4521 .hasMoreElements(); viewport.setSequenceColour(
4522 (SequenceI) sq.nextElement(), col))
4525 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
4526 alignPanel.updateAnnotation();
4527 alignPanel.paintAlignment(true);
4532 class PrintThread extends Thread
4536 public PrintThread(AlignmentPanel ap)
4541 static PageFormat pf;
4545 PrinterJob printJob = PrinterJob.getPrinterJob();
4549 printJob.setPrintable(ap, pf);
4553 printJob.setPrintable(ap);
4556 if (printJob.printDialog())
4561 } catch (Exception PrintException)
4563 PrintException.printStackTrace();