2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
25 import java.awt.datatransfer.*;
26 import java.awt.dnd.*;
27 import java.awt.event.*;
28 import java.awt.print.*;
30 import javax.swing.event.MenuEvent;
32 import jalview.analysis.*;
33 import jalview.commands.*;
34 import jalview.datamodel.*;
36 import jalview.jbgui.*;
37 import jalview.schemes.*;
46 public class AlignFrame extends GAlignFrame implements DropTargetListener,
51 public static final int DEFAULT_WIDTH = 700;
54 public static final int DEFAULT_HEIGHT = 500;
56 public AlignmentPanel alignPanel;
58 AlignViewport viewport;
60 Vector alignPanels = new Vector();
63 * Last format used to load or save alignments in this window
65 String currentFileFormat = null;
68 * Current filename for this alignment
70 String fileName = null;
73 * Creates a new AlignFrame object with specific width and height.
79 public AlignFrame(AlignmentI al, int width, int height)
81 this(al, null, width, height);
85 * Creates a new AlignFrame object with specific width, height and
91 * @param sequenceSetId
93 public AlignFrame(AlignmentI al, int width, int height,
96 this(al, null, width, height, sequenceSetId);
100 * Creates a new AlignFrame object with specific width, height and
106 * @param sequenceSetId
109 public AlignFrame(AlignmentI al, int width, int height,
110 String sequenceSetId, String viewId)
112 this(al, null, width, height, sequenceSetId, viewId);
116 * new alignment window with hidden columns
120 * @param hiddenColumns
121 * ColumnSelection or null
123 * Width of alignment frame
127 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
128 int width, int height)
130 this(al, hiddenColumns, width, height, null);
134 * Create alignment frame for al with hiddenColumns, a specific width and
135 * height, and specific sequenceId
138 * @param hiddenColumns
141 * @param sequenceSetId
144 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
145 int width, int height, String sequenceSetId)
147 this(al, hiddenColumns, width, height, sequenceSetId, null);
151 * Create alignment frame for al with hiddenColumns, a specific width and
152 * height, and specific sequenceId
155 * @param hiddenColumns
158 * @param sequenceSetId
163 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
164 int width, int height, String sequenceSetId, String viewId)
166 setSize(width, height);
167 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
169 alignPanel = new AlignmentPanel(this, viewport);
171 if (al.getDataset() == null)
176 addAlignmentPanel(alignPanel, true);
181 * Make a new AlignFrame from exisiting alignmentPanels
188 public AlignFrame(AlignmentPanel ap)
192 addAlignmentPanel(ap, false);
197 * initalise the alignframe from the underlying viewport data and the
202 if (viewport.conservation == null)
204 BLOSUM62Colour.setEnabled(false);
205 conservationMenuItem.setEnabled(false);
206 modifyConservation.setEnabled(false);
207 // PIDColour.setEnabled(false);
208 // abovePIDThreshold.setEnabled(false);
209 // modifyPID.setEnabled(false);
212 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
215 if (sortby.equals("Id"))
217 sortIDMenuItem_actionPerformed(null);
219 else if (sortby.equals("Pairwise Identity"))
221 sortPairwiseMenuItem_actionPerformed(null);
224 if (Desktop.desktop != null)
226 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
227 addServiceListeners();
228 setGUINucleotide(viewport.alignment.isNucleotide());
231 setMenusFromViewport(viewport);
232 buildSortByAnnotationScoresMenu();
233 if (viewport.wrapAlignment)
235 wrapMenuItem_actionPerformed(null);
238 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
240 this.overviewMenuItem_actionPerformed(null);
248 * Change the filename and format for the alignment, and enable the 'reload'
249 * button functionality.
256 public void setFileName(String file, String format)
259 currentFileFormat = format;
260 reload.setEnabled(true);
263 void addKeyListener()
265 addKeyListener(new KeyAdapter()
267 public void keyPressed(KeyEvent evt)
269 if (viewport.cursorMode
270 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
271 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
272 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
273 && Character.isDigit(evt.getKeyChar()))
274 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
276 switch (evt.getKeyCode())
279 case 27: // escape key
280 deselectAllSequenceMenuItem_actionPerformed(null);
284 case KeyEvent.VK_DOWN:
285 if (evt.isAltDown() || !viewport.cursorMode)
286 moveSelectedSequences(false);
287 if (viewport.cursorMode)
288 alignPanel.seqPanel.moveCursor(0, 1);
292 if (evt.isAltDown() || !viewport.cursorMode)
293 moveSelectedSequences(true);
294 if (viewport.cursorMode)
295 alignPanel.seqPanel.moveCursor(0, -1);
299 case KeyEvent.VK_LEFT:
300 if (evt.isAltDown() || !viewport.cursorMode)
301 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
303 alignPanel.seqPanel.moveCursor(-1, 0);
307 case KeyEvent.VK_RIGHT:
308 if (evt.isAltDown() || !viewport.cursorMode)
309 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
311 alignPanel.seqPanel.moveCursor(1, 0);
314 case KeyEvent.VK_SPACE:
315 if (viewport.cursorMode)
317 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
318 || evt.isShiftDown() || evt.isAltDown());
322 case KeyEvent.VK_DELETE:
323 case KeyEvent.VK_BACK_SPACE:
324 if (!viewport.cursorMode)
326 cut_actionPerformed(null);
330 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
331 || evt.isShiftDown() || evt.isAltDown());
337 if (viewport.cursorMode)
339 alignPanel.seqPanel.setCursorRow();
343 if (viewport.cursorMode && !evt.isControlDown())
345 alignPanel.seqPanel.setCursorColumn();
349 if (viewport.cursorMode)
351 alignPanel.seqPanel.setCursorPosition();
355 case KeyEvent.VK_ENTER:
356 case KeyEvent.VK_COMMA:
357 if (viewport.cursorMode)
359 alignPanel.seqPanel.setCursorRowAndColumn();
364 if (viewport.cursorMode)
366 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
370 if (viewport.cursorMode)
372 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
377 viewport.cursorMode = !viewport.cursorMode;
378 statusBar.setText("Keyboard editing mode is "
379 + (viewport.cursorMode ? "on" : "off"));
380 if (viewport.cursorMode)
382 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
383 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
385 alignPanel.seqPanel.seqCanvas.repaint();
391 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
392 java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
394 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
396 javax.help.HelpBroker hb = hs.createHelpBroker();
397 hb.setCurrentID("home");
398 hb.setDisplayed(true);
399 } catch (Exception ex)
401 ex.printStackTrace();
406 boolean toggleSeqs = !evt.isControlDown();
407 boolean toggleCols = !evt.isShiftDown();
408 toggleHiddenRegions(toggleSeqs, toggleCols);
411 case KeyEvent.VK_PAGE_UP:
412 if (viewport.wrapAlignment)
414 alignPanel.scrollUp(true);
418 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
419 - viewport.endSeq + viewport.startSeq);
422 case KeyEvent.VK_PAGE_DOWN:
423 if (viewport.wrapAlignment)
425 alignPanel.scrollUp(false);
429 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
430 + viewport.endSeq - viewport.startSeq);
436 public void keyReleased(KeyEvent evt)
438 switch (evt.getKeyCode())
440 case KeyEvent.VK_LEFT:
441 if (evt.isAltDown() || !viewport.cursorMode)
442 viewport.firePropertyChange("alignment", null, viewport
443 .getAlignment().getSequences());
446 case KeyEvent.VK_RIGHT:
447 if (evt.isAltDown() || !viewport.cursorMode)
448 viewport.firePropertyChange("alignment", null, viewport
449 .getAlignment().getSequences());
456 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
458 ap.alignFrame = this;
460 alignPanels.addElement(ap);
462 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
464 int aSize = alignPanels.size();
466 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
468 if (aSize == 1 && ap.av.viewName == null)
470 this.getContentPane().add(ap, BorderLayout.CENTER);
476 setInitialTabVisible();
479 expandViews.setEnabled(true);
480 gatherViews.setEnabled(true);
481 tabbedPane.addTab(ap.av.viewName, ap);
483 ap.setVisible(false);
490 ap.av.alignment.padGaps();
492 ap.av.updateConservation(ap);
493 ap.av.updateConsensus(ap);
497 public void setInitialTabVisible()
499 expandViews.setEnabled(true);
500 gatherViews.setEnabled(true);
501 tabbedPane.setVisible(true);
502 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
503 tabbedPane.addTab(first.av.viewName, first);
504 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
507 public AlignViewport getViewport()
512 /* Set up intrinsic listeners for dynamically generated GUI bits. */
513 private void addServiceListeners()
515 final java.beans.PropertyChangeListener thisListener;
516 // Do this once to get current state
517 BuildWebServiceMenu();
519 .addPropertyChangeListener(thisListener = new java.beans.PropertyChangeListener()
521 public void propertyChange(PropertyChangeEvent evt)
523 // System.out.println("Discoverer property change.");
524 if (evt.getPropertyName().equals("services"))
526 // System.out.println("Rebuilding web service menu");
527 BuildWebServiceMenu();
532 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
534 public void internalFrameClosed(
535 javax.swing.event.InternalFrameEvent evt)
537 // System.out.println("deregistering discoverer listener");
538 Desktop.discoverer.removePropertyChangeListener(thisListener);
539 closeMenuItem_actionPerformed(true);
544 public void setGUINucleotide(boolean nucleotide)
546 showTranslation.setVisible(nucleotide);
547 conservationMenuItem.setEnabled(!nucleotide);
548 modifyConservation.setEnabled(!nucleotide);
549 showGroupConservation.setEnabled(!nucleotide);
550 // Remember AlignFrame always starts as protein
553 calculateMenu.remove(calculateMenu.getItemCount() - 2);
558 * set up menus for the currently viewport. This may be called after any
559 * operation that affects the data in the current view (selection changed,
560 * etc) to update the menus to reflect the new state.
562 public void setMenusForViewport()
564 setMenusFromViewport(viewport);
568 * Need to call this method when tabs are selected for multiple views, or when
569 * loading from Jalview2XML.java
574 void setMenusFromViewport(AlignViewport av)
576 padGapsMenuitem.setSelected(av.padGaps);
577 colourTextMenuItem.setSelected(av.showColourText);
578 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
579 conservationMenuItem.setSelected(av.getConservationSelected());
580 seqLimits.setSelected(av.getShowJVSuffix());
581 idRightAlign.setSelected(av.rightAlignIds);
582 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
583 renderGapsMenuItem.setSelected(av.renderGaps);
584 wrapMenuItem.setSelected(av.wrapAlignment);
585 scaleAbove.setVisible(av.wrapAlignment);
586 scaleLeft.setVisible(av.wrapAlignment);
587 scaleRight.setVisible(av.wrapAlignment);
588 annotationPanelMenuItem.setState(av.showAnnotation);
589 viewBoxesMenuItem.setSelected(av.showBoxes);
590 viewTextMenuItem.setSelected(av.showText);
591 showNonconservedMenuItem.setSelected(av.showUnconserved);
592 showGroupConsensus.setSelected(av.showGroupConsensus);
593 showGroupConservation.setSelected(av.showGroupConservation);
594 showConsensusHistogram.setSelected(av.showConsensusHistogram);
595 showSequenceLogo.setSelected(av.showSequenceLogo);
596 setColourSelected(ColourSchemeProperty.getColourName(av
597 .getGlobalColourScheme()));
599 showSeqFeatures.setSelected(av.showSequenceFeatures);
600 hiddenMarkers.setState(av.showHiddenMarkers);
601 applyToAllGroups.setState(av.colourAppliesToAllGroups);
602 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
603 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
605 setShowProductsEnabled();
610 Hashtable progressBars, progressBarHandlers;
615 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
617 public void setProgressBar(String message, long id)
619 if (progressBars == null)
621 progressBars = new Hashtable();
622 progressBarHandlers = new Hashtable();
625 JPanel progressPanel;
626 Long lId = new Long(id);
627 GridLayout layout = (GridLayout) statusPanel.getLayout();
628 if (progressBars.get(lId) != null)
630 progressPanel = (JPanel) progressBars.get(new Long(id));
631 statusPanel.remove(progressPanel);
632 progressBars.remove(lId);
633 progressPanel = null;
636 statusBar.setText(message);
638 if (progressBarHandlers.contains(lId))
640 progressBarHandlers.remove(lId);
642 layout.setRows(layout.getRows() - 1);
646 progressPanel = new JPanel(new BorderLayout(10, 5));
648 JProgressBar progressBar = new JProgressBar();
649 progressBar.setIndeterminate(true);
651 progressPanel.add(new JLabel(message), BorderLayout.WEST);
652 progressPanel.add(progressBar, BorderLayout.CENTER);
654 layout.setRows(layout.getRows() + 1);
655 statusPanel.add(progressPanel);
657 progressBars.put(lId, progressPanel);
660 setMenusForViewport();
664 public void registerHandler(final long id,
665 final IProgressIndicatorHandler handler)
667 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
670 "call setProgressBar before registering the progress bar's handler.");
672 progressBarHandlers.put(new Long(id), handler);
673 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
674 if (handler.canCancel())
676 JButton cancel = new JButton("Cancel");
677 final IProgressIndicator us = this;
678 cancel.addActionListener(new ActionListener()
681 public void actionPerformed(ActionEvent e)
683 handler.cancelActivity(id);
684 us.setProgressBar("Cancelled "
685 + ((JLabel) progressPanel.getComponent(0)).getText(), id);
688 progressPanel.add(cancel, BorderLayout.EAST);
694 * @return true if any progress bars are still active
696 public boolean operationInProgress()
698 if (progressBars != null && progressBars.size() > 0)
706 * Added so Castor Mapping file can obtain Jalview Version
708 public String getVersion()
710 return jalview.bin.Cache.getProperty("VERSION");
713 public FeatureRenderer getFeatureRenderer()
715 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
718 public void fetchSequence_actionPerformed(ActionEvent e)
720 new SequenceFetcher(this);
723 public void addFromFile_actionPerformed(ActionEvent e)
725 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
728 public void reload_actionPerformed(ActionEvent e)
730 if (fileName != null)
732 // TODO: work out how to recover feature settings for correct view(s) when
734 if (currentFileFormat.equals("Jalview"))
736 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
737 for (int i = 0; i < frames.length; i++)
739 if (frames[i] instanceof AlignFrame && frames[i] != this
740 && ((AlignFrame) frames[i]).fileName.equals(fileName))
744 frames[i].setSelected(true);
745 Desktop.instance.closeAssociatedWindows();
746 } catch (java.beans.PropertyVetoException ex)
752 Desktop.instance.closeAssociatedWindows();
754 FileLoader loader = new FileLoader();
755 String protocol = fileName.startsWith("http:") ? "URL" : "File";
756 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
760 Rectangle bounds = this.getBounds();
762 FileLoader loader = new FileLoader();
763 String protocol = fileName.startsWith("http:") ? "URL" : "File";
764 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
765 protocol, currentFileFormat);
767 newframe.setBounds(bounds);
768 if (featureSettings != null && featureSettings.isShowing())
770 final Rectangle fspos = featureSettings.frame.getBounds();
771 // TODO: need a 'show feature settings' function that takes bounds -
772 // need to refactor Desktop.addFrame
773 newframe.featureSettings_actionPerformed(null);
774 final FeatureSettings nfs = newframe.featureSettings;
775 SwingUtilities.invokeLater(new Runnable()
779 nfs.frame.setBounds(fspos);
782 this.featureSettings.close();
783 this.featureSettings = null;
785 this.closeMenuItem_actionPerformed(true);
790 public void addFromText_actionPerformed(ActionEvent e)
792 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
795 public void addFromURL_actionPerformed(ActionEvent e)
797 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
800 public void save_actionPerformed(ActionEvent e)
803 || (currentFileFormat == null || !jalview.io.FormatAdapter
804 .isValidIOFormat(currentFileFormat, true))
805 || fileName.startsWith("http"))
807 saveAs_actionPerformed(null);
811 saveAlignment(fileName, currentFileFormat);
821 public void saveAs_actionPerformed(ActionEvent e)
823 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
824 .getProperty("LAST_DIRECTORY"),
825 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
826 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
827 currentFileFormat, false);
829 chooser.setFileView(new JalviewFileView());
830 chooser.setDialogTitle("Save Alignment to file");
831 chooser.setToolTipText("Save");
833 int value = chooser.showSaveDialog(this);
835 if (value == JalviewFileChooser.APPROVE_OPTION)
837 currentFileFormat = chooser.getSelectedFormat();
838 if (currentFileFormat == null)
840 JOptionPane.showInternalMessageDialog(Desktop.desktop,
841 "You must select a file format before saving!",
842 "File format not specified", JOptionPane.WARNING_MESSAGE);
843 value = chooser.showSaveDialog(this);
847 fileName = chooser.getSelectedFile().getPath();
849 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
852 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
853 if (currentFileFormat.indexOf(" ") > -1)
855 currentFileFormat = currentFileFormat.substring(0,
856 currentFileFormat.indexOf(" "));
858 saveAlignment(fileName, currentFileFormat);
862 public boolean saveAlignment(String file, String format)
864 boolean success = true;
866 if (format.equalsIgnoreCase("Jalview"))
868 String shortName = title;
870 if (shortName.indexOf(java.io.File.separatorChar) > -1)
872 shortName = shortName.substring(shortName
873 .lastIndexOf(java.io.File.separatorChar) + 1);
876 success = new Jalview2XML().SaveAlignment(this, file, shortName);
878 statusBar.setText("Successfully saved to file: " + fileName + " in "
879 + format + " format.");
884 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
886 warningMessage("Cannot save file " + fileName + " using format "
887 + format, "Alignment output format not supported");
888 saveAs_actionPerformed(null);
889 // JBPNote need to have a raise_gui flag here
893 String[] omitHidden = null;
895 if (viewport.hasHiddenColumns)
897 int reply = JOptionPane
898 .showInternalConfirmDialog(
900 "The Alignment contains hidden columns."
901 + "\nDo you want to save only the visible alignment?",
902 "Save / Omit Hidden Columns",
903 JOptionPane.YES_NO_OPTION,
904 JOptionPane.QUESTION_MESSAGE);
906 if (reply == JOptionPane.YES_OPTION)
908 omitHidden = viewport.getViewAsString(false);
911 FormatAdapter f = new FormatAdapter();
912 String output = f.formatSequences(format,
913 (Alignment) viewport.alignment, // class cast exceptions will
914 // occur in the distant future
915 omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
925 java.io.PrintWriter out = new java.io.PrintWriter(
926 new java.io.FileWriter(file));
931 statusBar.setText("Successfully saved to file: " + fileName
932 + " in " + format + " format.");
933 } catch (Exception ex)
936 ex.printStackTrace();
943 JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
944 + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
950 private void warningMessage(String warning, String title)
952 if (new jalview.util.Platform().isHeadless())
954 System.err.println("Warning: " + title + "\nWarning: " + warning);
959 JOptionPane.showInternalMessageDialog(this, warning, title,
960 JOptionPane.WARNING_MESSAGE);
971 protected void outputText_actionPerformed(ActionEvent e)
973 String[] omitHidden = null;
975 if (viewport.hasHiddenColumns)
977 int reply = JOptionPane
978 .showInternalConfirmDialog(
980 "The Alignment contains hidden columns."
981 + "\nDo you want to output only the visible alignment?",
982 "Save / Omit Hidden Columns",
983 JOptionPane.YES_NO_OPTION,
984 JOptionPane.QUESTION_MESSAGE);
986 if (reply == JOptionPane.YES_OPTION)
988 omitHidden = viewport.getViewAsString(false);
992 CutAndPasteTransfer cap = new CutAndPasteTransfer();
993 cap.setForInput(null);
994 Desktop.addInternalFrame(cap, "Alignment output - "
995 + e.getActionCommand(), 600, 500);
997 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
998 viewport.alignment, omitHidden, viewport.colSel));
1007 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1009 new HTMLOutput(alignPanel, alignPanel.seqPanel.seqCanvas
1010 .getSequenceRenderer(), alignPanel.seqPanel.seqCanvas
1011 .getFeatureRenderer());
1014 public void createImageMap(File file, String image)
1016 alignPanel.makePNGImageMap(file, image);
1025 public void createPNG(File f)
1027 alignPanel.makePNG(f);
1036 public void createEPS(File f)
1038 alignPanel.makeEPS(f);
1041 public void pageSetup_actionPerformed(ActionEvent e)
1043 PrinterJob printJob = PrinterJob.getPrinterJob();
1044 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1053 public void printMenuItem_actionPerformed(ActionEvent e)
1055 // Putting in a thread avoids Swing painting problems
1056 PrintThread thread = new PrintThread(alignPanel);
1060 public void exportFeatures_actionPerformed(ActionEvent e)
1062 new AnnotationExporter().exportFeatures(alignPanel);
1065 public void exportAnnotations_actionPerformed(ActionEvent e)
1067 new AnnotationExporter().exportAnnotations(alignPanel,
1068 viewport.showAnnotation ? viewport.alignment
1069 .getAlignmentAnnotation() : null, viewport.alignment
1071 ((Alignment) viewport.alignment).alignmentProperties);
1074 public void associatedData_actionPerformed(ActionEvent e)
1076 // Pick the tree file
1077 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
1078 .getProperty("LAST_DIRECTORY"));
1079 chooser.setFileView(new JalviewFileView());
1080 chooser.setDialogTitle("Load Jalview Annotations or Features File");
1081 chooser.setToolTipText("Load Jalview Annotations / Features file");
1083 int value = chooser.showOpenDialog(null);
1085 if (value == JalviewFileChooser.APPROVE_OPTION)
1087 String choice = chooser.getSelectedFile().getPath();
1088 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1089 loadJalviewDataFile(choice);
1095 * Close the current view or all views in the alignment frame. If the frame
1096 * only contains one view then the alignment will be removed from memory.
1098 * @param closeAllTabs
1100 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1102 if (alignPanels != null && alignPanels.size() < 2)
1104 closeAllTabs = true;
1109 if (alignPanels != null)
1113 if (this.isClosed())
1115 // really close all the windows - otherwise wait till
1116 // setClosed(true) is called
1117 for (int i = 0; i < alignPanels.size(); i++)
1119 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1126 closeView(alignPanel);
1132 this.setClosed(true);
1134 } catch (Exception ex)
1136 ex.printStackTrace();
1141 * close alignPanel2 and shuffle tabs appropriately.
1143 * @param alignPanel2
1145 public void closeView(AlignmentPanel alignPanel2)
1147 int index = tabbedPane.getSelectedIndex();
1148 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1149 alignPanels.removeElement(alignPanel2);
1151 // if (viewport == alignPanel2.av)
1155 alignPanel2.closePanel();
1158 tabbedPane.removeTabAt(closedindex);
1159 tabbedPane.validate();
1161 if (index > closedindex || index == tabbedPane.getTabCount())
1163 // modify currently selected tab index if necessary.
1167 this.tabSelectionChanged(index);
1173 void updateEditMenuBar()
1176 if (viewport.historyList.size() > 0)
1178 undoMenuItem.setEnabled(true);
1179 CommandI command = (CommandI) viewport.historyList.peek();
1180 undoMenuItem.setText("Undo " + command.getDescription());
1184 undoMenuItem.setEnabled(false);
1185 undoMenuItem.setText("Undo");
1188 if (viewport.redoList.size() > 0)
1190 redoMenuItem.setEnabled(true);
1192 CommandI command = (CommandI) viewport.redoList.peek();
1193 redoMenuItem.setText("Redo " + command.getDescription());
1197 redoMenuItem.setEnabled(false);
1198 redoMenuItem.setText("Redo");
1202 public void addHistoryItem(CommandI command)
1204 if (command.getSize() > 0)
1206 viewport.historyList.push(command);
1207 viewport.redoList.clear();
1208 updateEditMenuBar();
1209 viewport.hasHiddenColumns = (viewport.colSel != null
1210 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1211 .getHiddenColumns().size() > 0);
1217 * @return alignment objects for all views
1219 AlignmentI[] getViewAlignments()
1221 if (alignPanels != null)
1223 Enumeration e = alignPanels.elements();
1224 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1225 for (int i = 0; e.hasMoreElements(); i++)
1227 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1231 if (viewport != null)
1233 return new AlignmentI[]
1234 { viewport.alignment };
1245 protected void undoMenuItem_actionPerformed(ActionEvent e)
1247 if (viewport.historyList.empty())
1249 CommandI command = (CommandI) viewport.historyList.pop();
1250 viewport.redoList.push(command);
1251 command.undoCommand(getViewAlignments());
1253 AlignViewport originalSource = getOriginatingSource(command);
1254 updateEditMenuBar();
1256 if (originalSource != null)
1258 originalSource.hasHiddenColumns = (viewport.colSel != null
1259 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1260 .getHiddenColumns().size() > 0);
1261 originalSource.firePropertyChange("alignment", null,
1262 originalSource.alignment.getSequences());
1272 protected void redoMenuItem_actionPerformed(ActionEvent e)
1274 if (viewport.redoList.size() < 1)
1279 CommandI command = (CommandI) viewport.redoList.pop();
1280 viewport.historyList.push(command);
1281 command.doCommand(getViewAlignments());
1283 AlignViewport originalSource = getOriginatingSource(command);
1284 updateEditMenuBar();
1286 if (originalSource != null)
1288 originalSource.hasHiddenColumns = (viewport.colSel != null
1289 && viewport.colSel.getHiddenColumns() != null && viewport.colSel
1290 .getHiddenColumns().size() > 0);
1291 originalSource.firePropertyChange("alignment", null,
1292 originalSource.alignment.getSequences());
1296 AlignViewport getOriginatingSource(CommandI command)
1298 AlignViewport originalSource = null;
1299 // For sequence removal and addition, we need to fire
1300 // the property change event FROM the viewport where the
1301 // original alignment was altered
1302 AlignmentI al = null;
1303 if (command instanceof EditCommand)
1305 EditCommand editCommand = (EditCommand) command;
1306 al = editCommand.getAlignment();
1307 Vector comps = (Vector) PaintRefresher.components.get(viewport
1308 .getSequenceSetId());
1310 for (int i = 0; i < comps.size(); i++)
1312 if (comps.elementAt(i) instanceof AlignmentPanel)
1314 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
1316 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1323 if (originalSource == null)
1325 // The original view is closed, we must validate
1326 // the current view against the closed view first
1329 PaintRefresher.validateSequences(al, viewport.alignment);
1332 originalSource = viewport;
1335 return originalSource;
1344 public void moveSelectedSequences(boolean up)
1346 SequenceGroup sg = viewport.getSelectionGroup();
1355 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1357 SequenceI seq = viewport.alignment.getSequenceAt(i);
1359 if (!sg.getSequences(null).contains(seq))
1364 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1366 if (sg.getSequences(null).contains(temp))
1371 viewport.alignment.getSequences().setElementAt(temp, i);
1372 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1377 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1379 SequenceI seq = viewport.alignment.getSequenceAt(i);
1381 if (!sg.getSequences(null).contains(seq))
1386 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1388 if (sg.getSequences(null).contains(temp))
1393 viewport.alignment.getSequences().setElementAt(temp, i);
1394 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1398 alignPanel.paintAlignment(true);
1401 synchronized void slideSequences(boolean right, int size)
1403 Vector sg = new Vector();
1404 if (viewport.cursorMode)
1406 sg.addElement(viewport.alignment
1407 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1409 else if (viewport.getSelectionGroup() != null
1410 && viewport.getSelectionGroup().getSize() != viewport.alignment
1413 sg = viewport.getSelectionGroup().getSequences(
1414 viewport.hiddenRepSequences);
1422 Vector invertGroup = new Vector();
1424 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1426 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
1427 invertGroup.add(viewport.alignment.getSequenceAt(i));
1430 SequenceI[] seqs1 = new SequenceI[sg.size()];
1431 for (int i = 0; i < sg.size(); i++)
1432 seqs1[i] = (SequenceI) sg.elementAt(i);
1434 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1435 for (int i = 0; i < invertGroup.size(); i++)
1436 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1438 SlideSequencesCommand ssc;
1440 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1441 size, viewport.getGapCharacter());
1443 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1444 size, viewport.getGapCharacter());
1446 int groupAdjustment = 0;
1447 if (ssc.getGapsInsertedBegin() && right)
1449 if (viewport.cursorMode)
1450 alignPanel.seqPanel.moveCursor(size, 0);
1452 groupAdjustment = size;
1454 else if (!ssc.getGapsInsertedBegin() && !right)
1456 if (viewport.cursorMode)
1457 alignPanel.seqPanel.moveCursor(-size, 0);
1459 groupAdjustment = -size;
1462 if (groupAdjustment != 0)
1464 viewport.getSelectionGroup().setStartRes(
1465 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1466 viewport.getSelectionGroup().setEndRes(
1467 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1470 boolean appendHistoryItem = false;
1471 if (viewport.historyList != null && viewport.historyList.size() > 0
1472 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1474 appendHistoryItem = ssc
1475 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1479 if (!appendHistoryItem)
1480 addHistoryItem(ssc);
1491 protected void copy_actionPerformed(ActionEvent e)
1494 if (viewport.getSelectionGroup() == null)
1498 // TODO: preserve the ordering of displayed alignment annotation in any
1499 // internal paste (particularly sequence associated annotation)
1500 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1501 String[] omitHidden = null;
1503 if (viewport.hasHiddenColumns)
1505 omitHidden = viewport.getViewAsString(true);
1508 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1511 StringSelection ss = new StringSelection(output);
1515 jalview.gui.Desktop.internalCopy = true;
1516 // Its really worth setting the clipboard contents
1517 // to empty before setting the large StringSelection!!
1518 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
1519 new StringSelection(""), null);
1521 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1523 } catch (OutOfMemoryError er)
1525 new OOMWarning("copying region", er);
1529 Vector hiddenColumns = null;
1530 if (viewport.hasHiddenColumns)
1532 hiddenColumns = new Vector();
1533 int hiddenOffset = viewport.getSelectionGroup().getStartRes(),hiddenCutoff=viewport.getSelectionGroup().getEndRes();
1534 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1537 int[] region = (int[]) viewport.getColumnSelection()
1538 .getHiddenColumns().elementAt(i);
1539 if (region[0]>=hiddenOffset && region[1]<=hiddenCutoff)
1541 hiddenColumns.addElement(new int[]
1542 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1547 Desktop.jalviewClipboard = new Object[]
1548 { seqs, viewport.alignment.getDataset(), hiddenColumns };
1549 statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
1558 protected void pasteNew_actionPerformed(ActionEvent e)
1569 protected void pasteThis_actionPerformed(ActionEvent e)
1575 * Paste contents of Jalview clipboard
1577 * @param newAlignment
1578 * true to paste to a new alignment, otherwise add to this.
1580 void paste(boolean newAlignment)
1582 boolean externalPaste = true;
1585 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1586 Transferable contents = c.getContents(this);
1588 if (contents == null)
1596 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1597 if (str.length() < 1)
1602 format = new IdentifyFile().Identify(str, "Paste");
1604 } catch (OutOfMemoryError er)
1606 new OOMWarning("Out of memory pasting sequences!!", er);
1610 SequenceI[] sequences;
1611 boolean annotationAdded = false;
1612 AlignmentI alignment = null;
1614 if (Desktop.jalviewClipboard != null)
1616 // The clipboard was filled from within Jalview, we must use the
1618 // And dataset from the copied alignment
1619 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1620 // be doubly sure that we create *new* sequence objects.
1621 sequences = new SequenceI[newseq.length];
1622 for (int i = 0; i < newseq.length; i++)
1624 sequences[i] = new Sequence(newseq[i]);
1626 alignment = new Alignment(sequences);
1627 externalPaste = false;
1631 // parse the clipboard as an alignment.
1632 alignment = new FormatAdapter().readFile(str, "Paste", format);
1633 sequences = alignment.getSequencesArray();
1641 if (Desktop.jalviewClipboard != null)
1643 // dataset is inherited
1644 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1648 // new dataset is constructed
1649 alignment.setDataset(null);
1651 alwidth = alignment.getWidth() + 1;
1655 AlignmentI pastedal = alignment; // preserve pasted alignment object
1656 // Add pasted sequences and dataset into existing alignment.
1657 alignment = viewport.getAlignment();
1658 alwidth = alignment.getWidth() + 1;
1659 // decide if we need to import sequences from an existing dataset
1660 boolean importDs = Desktop.jalviewClipboard != null
1661 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1662 // importDs==true instructs us to copy over new dataset sequences from
1663 // an existing alignment
1664 Vector newDs = (importDs) ? new Vector() : null; // used to create
1665 // minimum dataset set
1667 for (int i = 0; i < sequences.length; i++)
1671 newDs.addElement(null);
1673 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1675 if (importDs && ds != null)
1677 if (!newDs.contains(ds))
1679 newDs.setElementAt(ds, i);
1680 ds = new Sequence(ds);
1681 // update with new dataset sequence
1682 sequences[i].setDatasetSequence(ds);
1686 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1691 // copy and derive new dataset sequence
1692 sequences[i] = sequences[i].deriveSequence();
1693 alignment.getDataset().addSequence(
1694 sequences[i].getDatasetSequence());
1695 // TODO: avoid creation of duplicate dataset sequences with a
1696 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1698 alignment.addSequence(sequences[i]); // merges dataset
1702 newDs.clear(); // tidy up
1704 if (pastedal.getAlignmentAnnotation() != null)
1706 // Add any annotation attached to alignment.
1707 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1708 for (int i = 0; i < alann.length; i++)
1710 annotationAdded = true;
1711 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1713 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1714 newann.padAnnotation(alwidth);
1715 alignment.addAnnotation(newann);
1725 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1726 sequences, 0, alignment.getWidth(), alignment));
1728 // Add any annotations attached to sequences
1729 for (int i = 0; i < sequences.length; i++)
1731 if (sequences[i].getAnnotation() != null)
1733 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1735 annotationAdded = true;
1736 sequences[i].getAnnotation()[a].adjustForAlignment();
1737 sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1738 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1743 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1750 // propagate alignment changed.
1751 viewport.setEndSeq(alignment.getHeight());
1752 if (annotationAdded)
1754 // Duplicate sequence annotation in all views.
1755 AlignmentI[] alview = this.getViewAlignments();
1756 for (int i = 0; i < sequences.length; i++)
1758 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1761 for (int avnum = 0; avnum < alview.length; avnum++)
1763 if (alview[avnum] != alignment)
1765 // duplicate in a view other than the one with input focus
1766 int avwidth = alview[avnum].getWidth() + 1;
1767 // this relies on sann being preserved after we
1768 // modify the sequence's annotation array for each duplication
1769 for (int a = 0; a < sann.length; a++)
1771 AlignmentAnnotation newann = new AlignmentAnnotation(
1773 sequences[i].addAlignmentAnnotation(newann);
1774 newann.padAnnotation(avwidth);
1775 alview[avnum].addAnnotation(newann); // annotation was
1776 // duplicated earlier
1777 alview[avnum].setAnnotationIndex(newann, a);
1782 buildSortByAnnotationScoresMenu();
1784 viewport.firePropertyChange("alignment", null, alignment
1790 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
1792 String newtitle = new String("Copied sequences");
1794 if (Desktop.jalviewClipboard != null
1795 && Desktop.jalviewClipboard[2] != null)
1797 Vector hc = (Vector) Desktop.jalviewClipboard[2];
1798 for (int i = 0; i < hc.size(); i++)
1800 int[] region = (int[]) hc.elementAt(i);
1801 af.viewport.hideColumns(region[0], region[1]);
1805 // >>>This is a fix for the moment, until a better solution is
1807 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
1809 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1811 // TODO: maintain provenance of an alignment, rather than just make the
1812 // title a concatenation of operations.
1815 if (title.startsWith("Copied sequences"))
1821 newtitle = newtitle.concat("- from " + title);
1826 newtitle = new String("Pasted sequences");
1829 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1834 } catch (Exception ex)
1836 ex.printStackTrace();
1837 System.out.println("Exception whilst pasting: " + ex);
1838 // could be anything being pasted in here
1849 protected void cut_actionPerformed(ActionEvent e)
1851 copy_actionPerformed(null);
1852 delete_actionPerformed(null);
1861 protected void delete_actionPerformed(ActionEvent evt)
1864 SequenceGroup sg = viewport.getSelectionGroup();
1870 Vector seqs = new Vector();
1872 for (int i = 0; i < sg.getSize(); i++)
1874 seq = sg.getSequenceAt(i);
1875 seqs.addElement(seq);
1878 // If the cut affects all sequences, remove highlighted columns
1879 if (sg.getSize() == viewport.alignment.getHeight())
1881 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1882 sg.getEndRes() + 1);
1885 SequenceI[] cut = new SequenceI[seqs.size()];
1886 for (int i = 0; i < seqs.size(); i++)
1888 cut[i] = (SequenceI) seqs.elementAt(i);
1892 * //ADD HISTORY ITEM
1894 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1895 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1896 viewport.alignment));
1898 viewport.setSelectionGroup(null);
1899 viewport.sendSelection();
1900 viewport.alignment.deleteGroup(sg);
1902 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1904 if (viewport.getAlignment().getHeight() < 1)
1908 this.setClosed(true);
1909 } catch (Exception ex)
1921 protected void deleteGroups_actionPerformed(ActionEvent e)
1923 viewport.alignment.deleteAllGroups();
1924 viewport.sequenceColours = null;
1925 viewport.setSelectionGroup(null);
1926 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1927 alignPanel.updateAnnotation();
1928 alignPanel.paintAlignment(true);
1937 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1939 SequenceGroup sg = new SequenceGroup();
1941 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1943 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1946 sg.setEndRes(viewport.alignment.getWidth() - 1);
1947 viewport.setSelectionGroup(sg);
1948 viewport.sendSelection();
1949 alignPanel.paintAlignment(true);
1950 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1959 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1961 if (viewport.cursorMode)
1963 alignPanel.seqPanel.keyboardNo1 = null;
1964 alignPanel.seqPanel.keyboardNo2 = null;
1966 viewport.setSelectionGroup(null);
1967 viewport.getColumnSelection().clear();
1968 viewport.setSelectionGroup(null);
1969 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1970 alignPanel.idPanel.idCanvas.searchResults = null;
1971 alignPanel.paintAlignment(true);
1972 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1981 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1983 SequenceGroup sg = viewport.getSelectionGroup();
1987 selectAllSequenceMenuItem_actionPerformed(null);
1992 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1994 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1997 alignPanel.paintAlignment(true);
1998 viewport.sendSelection();
1999 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2002 public void invertColSel_actionPerformed(ActionEvent e)
2004 viewport.invertColumnSelection();
2005 alignPanel.paintAlignment(true);
2014 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2016 trimAlignment(true);
2025 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2027 trimAlignment(false);
2030 void trimAlignment(boolean trimLeft)
2032 ColumnSelection colSel = viewport.getColumnSelection();
2035 if (colSel.size() > 0)
2039 column = colSel.getMin();
2043 column = colSel.getMax();
2047 if (viewport.getSelectionGroup() != null)
2049 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2050 viewport.hiddenRepSequences);
2054 seqs = viewport.alignment.getSequencesArray();
2057 TrimRegionCommand trimRegion;
2060 trimRegion = new TrimRegionCommand("Remove Left",
2061 TrimRegionCommand.TRIM_LEFT, seqs, column,
2062 viewport.alignment, viewport.colSel,
2063 viewport.selectionGroup);
2064 viewport.setStartRes(0);
2068 trimRegion = new TrimRegionCommand("Remove Right",
2069 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2070 viewport.alignment, viewport.colSel,
2071 viewport.selectionGroup);
2074 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2076 addHistoryItem(trimRegion);
2078 Vector groups = viewport.alignment.getGroups();
2080 for (int i = 0; i < groups.size(); i++)
2082 SequenceGroup sg = (SequenceGroup) groups.get(i);
2084 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2085 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2087 viewport.alignment.deleteGroup(sg);
2091 viewport.firePropertyChange("alignment", null, viewport
2092 .getAlignment().getSequences());
2102 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2104 int start = 0, end = viewport.alignment.getWidth() - 1;
2107 if (viewport.getSelectionGroup() != null)
2109 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2110 viewport.hiddenRepSequences);
2111 start = viewport.getSelectionGroup().getStartRes();
2112 end = viewport.getSelectionGroup().getEndRes();
2116 seqs = viewport.alignment.getSequencesArray();
2119 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2120 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
2122 addHistoryItem(removeGapCols);
2124 statusBar.setText("Removed " + removeGapCols.getSize()
2125 + " empty columns.");
2127 // This is to maintain viewport position on first residue
2128 // of first sequence
2129 SequenceI seq = viewport.alignment.getSequenceAt(0);
2130 int startRes = seq.findPosition(viewport.startRes);
2131 // ShiftList shifts;
2132 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2133 // edit.alColumnChanges=shifts.getInverse();
2134 // if (viewport.hasHiddenColumns)
2135 // viewport.getColumnSelection().compensateForEdits(shifts);
2136 viewport.setStartRes(seq.findIndex(startRes) - 1);
2137 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2148 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2150 int start = 0, end = viewport.alignment.getWidth() - 1;
2153 if (viewport.getSelectionGroup() != null)
2155 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2156 viewport.hiddenRepSequences);
2157 start = viewport.getSelectionGroup().getStartRes();
2158 end = viewport.getSelectionGroup().getEndRes();
2162 seqs = viewport.alignment.getSequencesArray();
2165 // This is to maintain viewport position on first residue
2166 // of first sequence
2167 SequenceI seq = viewport.alignment.getSequenceAt(0);
2168 int startRes = seq.findPosition(viewport.startRes);
2170 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2171 viewport.alignment));
2173 viewport.setStartRes(seq.findIndex(startRes) - 1);
2175 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2186 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2188 viewport.padGaps = padGapsMenuitem.isSelected();
2189 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2195 // if (justifySeqs>0)
2197 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2209 public void findMenuItem_actionPerformed(ActionEvent e)
2214 public void newView_actionPerformed(ActionEvent e)
2216 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2219 newap.av.gatherViewsHere = false;
2221 if (viewport.viewName == null)
2223 viewport.viewName = "Original";
2226 newap.av.historyList = viewport.historyList;
2227 newap.av.redoList = viewport.redoList;
2229 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2230 String newViewName = "View " + index;
2232 Vector comps = (Vector) PaintRefresher.components.get(viewport
2233 .getSequenceSetId());
2234 Vector existingNames = new Vector();
2235 for (int i = 0; i < comps.size(); i++)
2237 if (comps.elementAt(i) instanceof AlignmentPanel)
2239 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2240 if (!existingNames.contains(ap.av.viewName))
2242 existingNames.addElement(ap.av.viewName);
2247 while (existingNames.contains(newViewName))
2249 newViewName = "View " + (++index);
2252 newap.av.viewName = newViewName;
2254 addAlignmentPanel(newap, true);
2256 if (alignPanels.size() == 2)
2258 viewport.gatherViewsHere = true;
2260 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2263 public void expandViews_actionPerformed(ActionEvent e)
2265 Desktop.instance.explodeViews(this);
2268 public void gatherViews_actionPerformed(ActionEvent e)
2270 Desktop.instance.gatherViews(this);
2279 public void font_actionPerformed(ActionEvent e)
2281 new FontChooser(alignPanel);
2290 protected void seqLimit_actionPerformed(ActionEvent e)
2292 viewport.setShowJVSuffix(seqLimits.isSelected());
2294 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2295 .calculateIdWidth());
2296 alignPanel.paintAlignment(true);
2299 public void idRightAlign_actionPerformed(ActionEvent e)
2301 viewport.rightAlignIds = idRightAlign.isSelected();
2302 alignPanel.paintAlignment(true);
2305 public void centreColumnLabels_actionPerformed(ActionEvent e)
2307 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2308 alignPanel.paintAlignment(true);
2314 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2316 protected void followHighlight_actionPerformed()
2318 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2320 alignPanel.scrollToPosition(
2321 alignPanel.seqPanel.seqCanvas.searchResults, false);
2331 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2333 viewport.setColourText(colourTextMenuItem.isSelected());
2334 alignPanel.paintAlignment(true);
2343 public void wrapMenuItem_actionPerformed(ActionEvent e)
2345 scaleAbove.setVisible(wrapMenuItem.isSelected());
2346 scaleLeft.setVisible(wrapMenuItem.isSelected());
2347 scaleRight.setVisible(wrapMenuItem.isSelected());
2348 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2349 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2352 public void showAllSeqs_actionPerformed(ActionEvent e)
2354 viewport.showAllHiddenSeqs();
2357 public void showAllColumns_actionPerformed(ActionEvent e)
2359 viewport.showAllHiddenColumns();
2363 public void hideSelSequences_actionPerformed(ActionEvent e)
2365 viewport.hideAllSelectedSeqs();
2366 alignPanel.paintAlignment(true);
2370 * called by key handler and the hide all/show all menu items
2375 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2378 boolean hide = false;
2379 SequenceGroup sg = viewport.getSelectionGroup();
2380 if (!toggleSeqs && !toggleCols)
2382 // Hide everything by the current selection - this is a hack - we do the
2383 // invert and then hide
2384 // first check that there will be visible columns after the invert.
2385 if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
2386 .getSelected().size() > 0)
2387 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2390 // now invert the sequence set, if required - empty selection implies
2391 // that no hiding is required.
2394 invertSequenceMenuItem_actionPerformed(null);
2395 sg = viewport.getSelectionGroup();
2399 viewport.expandColSelection(sg, true);
2400 // finally invert the column selection and get the new sequence
2402 invertColSel_actionPerformed(null);
2409 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
2411 hideSelSequences_actionPerformed(null);
2414 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
2416 showAllSeqs_actionPerformed(null);
2422 if (viewport.colSel.getSelected().size() > 0)
2424 hideSelColumns_actionPerformed(null);
2427 viewport.selectionGroup = sg;
2432 showAllColumns_actionPerformed(null);
2441 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2442 * event.ActionEvent)
2444 public void hideAllButSelection_actionPerformed(ActionEvent e)
2446 toggleHiddenRegions(false, false);
2453 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2456 public void hideAllSelection_actionPerformed(ActionEvent e)
2458 SequenceGroup sg = viewport.getSelectionGroup();
2459 viewport.expandColSelection(sg, false);
2460 viewport.hideAllSelectedSeqs();
2461 viewport.hideSelectedColumns();
2462 alignPanel.paintAlignment(true);
2469 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2472 public void showAllhidden_actionPerformed(ActionEvent e)
2474 viewport.showAllHiddenColumns();
2475 viewport.showAllHiddenSeqs();
2476 alignPanel.paintAlignment(true);
2479 public void hideSelColumns_actionPerformed(ActionEvent e)
2481 viewport.hideSelectedColumns();
2482 alignPanel.paintAlignment(true);
2485 public void hiddenMarkers_actionPerformed(ActionEvent e)
2487 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2497 protected void scaleAbove_actionPerformed(ActionEvent e)
2499 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2500 alignPanel.paintAlignment(true);
2509 protected void scaleLeft_actionPerformed(ActionEvent e)
2511 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2512 alignPanel.paintAlignment(true);
2521 protected void scaleRight_actionPerformed(ActionEvent e)
2523 viewport.setScaleRightWrapped(scaleRight.isSelected());
2524 alignPanel.paintAlignment(true);
2533 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2535 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2536 alignPanel.paintAlignment(true);
2545 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2547 viewport.setShowText(viewTextMenuItem.isSelected());
2548 alignPanel.paintAlignment(true);
2557 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2559 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2560 alignPanel.paintAlignment(true);
2563 public FeatureSettings featureSettings;
2565 public void featureSettings_actionPerformed(ActionEvent e)
2567 if (featureSettings != null)
2569 featureSettings.close();
2570 featureSettings = null;
2572 if (!showSeqFeatures.isSelected())
2574 // make sure features are actually displayed
2575 showSeqFeatures.setSelected(true);
2576 showSeqFeatures_actionPerformed(null);
2578 featureSettings = new FeatureSettings(this);
2582 * Set or clear 'Show Sequence Features'
2587 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2589 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2590 alignPanel.paintAlignment(true);
2591 if (alignPanel.getOverviewPanel() != null)
2593 alignPanel.getOverviewPanel().updateOverviewImage();
2598 * Set or clear 'Show Sequence Features'
2603 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2605 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2607 if (viewport.getShowSequenceFeaturesHeight())
2609 // ensure we're actually displaying features
2610 viewport.setShowSequenceFeatures(true);
2611 showSeqFeatures.setSelected(true);
2613 alignPanel.paintAlignment(true);
2614 if (alignPanel.getOverviewPanel() != null)
2616 alignPanel.getOverviewPanel().updateOverviewImage();
2626 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2628 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2629 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2632 public void alignmentProperties()
2634 JEditorPane editPane = new JEditorPane("text/html", "");
2635 editPane.setEditable(false);
2636 StringBuffer contents = new StringBuffer("<html>");
2639 int min = Integer.MAX_VALUE, max = 0;
2640 for (int i = 0; i < viewport.alignment.getHeight(); i++)
2642 int size = viewport.alignment.getSequenceAt(i).getEnd()
2643 - viewport.alignment.getSequenceAt(i).getStart();
2650 avg = avg / (float) viewport.alignment.getHeight();
2652 contents.append("<br>Sequences: " + viewport.alignment.getHeight());
2653 contents.append("<br>Minimum Sequence Length: " + min);
2654 contents.append("<br>Maximum Sequence Length: " + max);
2655 contents.append("<br>Average Length: " + (int) avg);
2657 if (((Alignment) viewport.alignment).getProperties() != null)
2659 Hashtable props = ((Alignment) viewport.alignment).getProperties();
2660 Enumeration en = props.keys();
2661 contents.append("<br><br><table border=\"1\">");
2662 while (en.hasMoreElements())
2664 String key = en.nextElement().toString();
2665 StringBuffer val = new StringBuffer();
2666 String vals = props.get(key).toString();
2670 npos = vals.indexOf("\n", pos);
2673 val.append(vals.substring(pos));
2677 val.append(vals.substring(pos, npos));
2681 } while (npos != -1);
2683 .append("<tr><td>" + key + "</td><td>" + val + "</td></tr>");
2685 contents.append("</table>");
2687 editPane.setText(contents.toString() + "</html>");
2688 JInternalFrame frame = new JInternalFrame();
2689 frame.getContentPane().add(new JScrollPane(editPane));
2691 Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
2692 + getTitle(), 500, 400);
2701 public void overviewMenuItem_actionPerformed(ActionEvent e)
2703 if (alignPanel.overviewPanel != null)
2708 JInternalFrame frame = new JInternalFrame();
2709 OverviewPanel overview = new OverviewPanel(alignPanel);
2710 frame.setContentPane(overview);
2711 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(), frame
2712 .getWidth(), frame.getHeight());
2714 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2716 .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2718 public void internalFrameClosed(
2719 javax.swing.event.InternalFrameEvent evt)
2721 alignPanel.setOverviewPanel(null);
2725 alignPanel.setOverviewPanel(overview);
2728 public void textColour_actionPerformed(ActionEvent e)
2730 new TextColourChooser().chooseColour(alignPanel, null);
2739 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2750 public void clustalColour_actionPerformed(ActionEvent e)
2752 changeColour(new ClustalxColourScheme(
2753 viewport.alignment.getSequences(), viewport.alignment
2763 public void zappoColour_actionPerformed(ActionEvent e)
2765 changeColour(new ZappoColourScheme());
2774 public void taylorColour_actionPerformed(ActionEvent e)
2776 changeColour(new TaylorColourScheme());
2785 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2787 changeColour(new HydrophobicColourScheme());
2796 public void helixColour_actionPerformed(ActionEvent e)
2798 changeColour(new HelixColourScheme());
2807 public void strandColour_actionPerformed(ActionEvent e)
2809 changeColour(new StrandColourScheme());
2818 public void turnColour_actionPerformed(ActionEvent e)
2820 changeColour(new TurnColourScheme());
2829 public void buriedColour_actionPerformed(ActionEvent e)
2831 changeColour(new BuriedColourScheme());
2840 public void nucleotideColour_actionPerformed(ActionEvent e)
2842 changeColour(new NucleotideColourScheme());
2845 public void annotationColour_actionPerformed(ActionEvent e)
2847 new AnnotationColourChooser(viewport, alignPanel);
2856 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2858 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2867 public void changeColour(ColourSchemeI cs)
2873 if (viewport.getAbovePIDThreshold())
2875 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2878 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2880 viewport.setGlobalColourScheme(cs);
2884 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2887 if (viewport.getConservationSelected())
2890 Alignment al = (Alignment) viewport.alignment;
2891 Conservation c = new Conservation("All",
2892 ResidueProperties.propHash, 3, al.getSequences(), 0, al
2896 c.verdict(false, viewport.ConsPercGaps);
2898 cs.setConservation(c);
2900 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
2905 cs.setConservation(null);
2908 cs.setConsensus(viewport.hconsensus);
2911 viewport.setGlobalColourScheme(cs);
2913 if (viewport.getColourAppliesToAllGroups())
2915 Vector groups = viewport.alignment.getGroups();
2917 for (int i = 0; i < groups.size(); i++)
2919 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2927 if (cs instanceof ClustalxColourScheme)
2929 sg.cs = new ClustalxColourScheme(sg
2930 .getSequences(viewport.hiddenRepSequences), sg.getWidth());
2932 else if (cs instanceof UserColourScheme)
2934 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
2940 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2941 } catch (Exception ex)
2946 if (viewport.getAbovePIDThreshold()
2947 || cs instanceof PIDColourScheme
2948 || cs instanceof Blosum62ColourScheme)
2950 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2952 sg.cs.setConsensus(AAFrequency.calculate(sg
2953 .getSequences(viewport.hiddenRepSequences), sg
2954 .getStartRes(), sg.getEndRes() + 1));
2958 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2961 if (viewport.getConservationSelected())
2963 Conservation c = new Conservation("Group",
2964 ResidueProperties.propHash, 3, sg
2965 .getSequences(viewport.hiddenRepSequences), sg
2966 .getStartRes(), sg.getEndRes() + 1);
2968 c.verdict(false, viewport.ConsPercGaps);
2969 sg.cs.setConservation(c);
2973 sg.cs.setConservation(null);
2978 if (alignPanel.getOverviewPanel() != null)
2980 alignPanel.getOverviewPanel().updateOverviewImage();
2983 alignPanel.paintAlignment(true);
2992 protected void modifyPID_actionPerformed(ActionEvent e)
2994 if (viewport.getAbovePIDThreshold()
2995 && viewport.globalColourScheme != null)
2997 SliderPanel.setPIDSliderSource(alignPanel, viewport
2998 .getGlobalColourScheme(), "Background");
2999 SliderPanel.showPIDSlider();
3009 protected void modifyConservation_actionPerformed(ActionEvent e)
3011 if (viewport.getConservationSelected()
3012 && viewport.globalColourScheme != null)
3014 SliderPanel.setConservationSlider(alignPanel,
3015 viewport.globalColourScheme, "Background");
3016 SliderPanel.showConservationSlider();
3026 protected void conservationMenuItem_actionPerformed(ActionEvent e)
3028 viewport.setConservationSelected(conservationMenuItem.isSelected());
3030 viewport.setAbovePIDThreshold(false);
3031 abovePIDThreshold.setSelected(false);
3033 changeColour(viewport.getGlobalColourScheme());
3035 modifyConservation_actionPerformed(null);
3044 public void abovePIDThreshold_actionPerformed(ActionEvent e)
3046 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3048 conservationMenuItem.setSelected(false);
3049 viewport.setConservationSelected(false);
3051 changeColour(viewport.getGlobalColourScheme());
3053 modifyPID_actionPerformed(null);
3062 public void userDefinedColour_actionPerformed(ActionEvent e)
3064 if (e.getActionCommand().equals("User Defined..."))
3066 new UserDefinedColours(alignPanel, null);
3070 UserColourScheme udc = (UserColourScheme) UserDefinedColours
3071 .getUserColourSchemes().get(e.getActionCommand());
3077 public void updateUserColourMenu()
3080 Component[] menuItems = colourMenu.getMenuComponents();
3081 int i, iSize = menuItems.length;
3082 for (i = 0; i < iSize; i++)
3084 if (menuItems[i].getName() != null
3085 && menuItems[i].getName().equals("USER_DEFINED"))
3087 colourMenu.remove(menuItems[i]);
3091 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3093 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3094 .getUserColourSchemes().keys();
3096 while (userColours.hasMoreElements())
3098 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3099 userColours.nextElement().toString());
3100 radioItem.setName("USER_DEFINED");
3101 radioItem.addMouseListener(new MouseAdapter()
3103 public void mousePressed(MouseEvent evt)
3105 if (evt.isControlDown()
3106 || SwingUtilities.isRightMouseButton(evt))
3109 .removeActionListener(radioItem.getActionListeners()[0]);
3111 int option = JOptionPane.showInternalConfirmDialog(
3112 jalview.gui.Desktop.desktop,
3113 "Remove from default list?",
3114 "Remove user defined colour",
3115 JOptionPane.YES_NO_OPTION);
3116 if (option == JOptionPane.YES_OPTION)
3118 jalview.gui.UserDefinedColours
3119 .removeColourFromDefaults(radioItem.getText());
3120 colourMenu.remove(radioItem);
3124 radioItem.addActionListener(new ActionListener()
3126 public void actionPerformed(ActionEvent evt)
3128 userDefinedColour_actionPerformed(evt);
3135 radioItem.addActionListener(new ActionListener()
3137 public void actionPerformed(ActionEvent evt)
3139 userDefinedColour_actionPerformed(evt);
3143 colourMenu.insert(radioItem, 15);
3144 colours.add(radioItem);
3155 public void PIDColour_actionPerformed(ActionEvent e)
3157 changeColour(new PIDColourScheme());
3166 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3168 changeColour(new Blosum62ColourScheme());
3177 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3179 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3180 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3181 .getAlignment().getSequenceAt(0), null);
3182 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3183 viewport.alignment));
3184 alignPanel.paintAlignment(true);
3193 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3195 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3196 AlignmentSorter.sortByID(viewport.getAlignment());
3197 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
3198 alignPanel.paintAlignment(true);
3207 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3209 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3210 AlignmentSorter.sortByLength(viewport.getAlignment());
3211 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3212 viewport.alignment));
3213 alignPanel.paintAlignment(true);
3222 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3224 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3225 AlignmentSorter.sortByGroup(viewport.getAlignment());
3226 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3227 viewport.alignment));
3229 alignPanel.paintAlignment(true);
3238 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3240 new RedundancyPanel(alignPanel, this);
3249 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3251 if ((viewport.getSelectionGroup() == null)
3252 || (viewport.getSelectionGroup().getSize() < 2))
3254 JOptionPane.showInternalMessageDialog(this,
3255 "You must select at least 2 sequences.", "Invalid Selection",
3256 JOptionPane.WARNING_MESSAGE);
3260 JInternalFrame frame = new JInternalFrame();
3261 frame.setContentPane(new PairwiseAlignPanel(viewport));
3262 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
3272 public void PCAMenuItem_actionPerformed(ActionEvent e)
3274 if (((viewport.getSelectionGroup() != null)
3275 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3276 .getSelectionGroup().getSize() > 0))
3277 || (viewport.getAlignment().getHeight() < 4))
3279 JOptionPane.showInternalMessageDialog(this,
3280 "Principal component analysis must take\n"
3281 + "at least 4 input sequences.",
3282 "Sequence selection insufficient",
3283 JOptionPane.WARNING_MESSAGE);
3288 new PCAPanel(alignPanel);
3291 public void autoCalculate_actionPerformed(ActionEvent e)
3293 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3294 if (viewport.autoCalculateConsensus)
3296 viewport.firePropertyChange("alignment", null, viewport
3297 .getAlignment().getSequences());
3307 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3309 NewTreePanel("AV", "PID", "Average distance tree using PID");
3318 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3320 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3329 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3331 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3340 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3342 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3355 void NewTreePanel(String type, String pwType, String title)
3359 if (viewport.getSelectionGroup() != null)
3361 if (viewport.getSelectionGroup().getSize() < 3)
3366 "You need to have more than two sequences selected to build a tree!",
3367 "Not enough sequences", JOptionPane.WARNING_MESSAGE);
3372 SequenceGroup sg = viewport.getSelectionGroup();
3374 /* Decide if the selection is a column region */
3375 while (s < sg.getSize())
3377 if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
3383 "The selected region to create a tree may\nonly contain residues or gaps.\n"
3384 + "Try using the Pad function in the edit menu,\n"
3385 + "or one of the multiple sequence alignment web services.",
3386 "Sequences in selection are not aligned",
3387 JOptionPane.WARNING_MESSAGE);
3393 title = title + " on region";
3394 tp = new TreePanel(alignPanel, type, pwType);
3398 // are the visible sequences aligned?
3399 if (!viewport.alignment.isAligned(false))
3404 "The sequences must be aligned before creating a tree.\n"
3405 + "Try using the Pad function in the edit menu,\n"
3406 + "or one of the multiple sequence alignment web services.",
3407 "Sequences not aligned",
3408 JOptionPane.WARNING_MESSAGE);
3413 if (viewport.alignment.getHeight() < 2)
3418 tp = new TreePanel(alignPanel, type, pwType);
3423 if (viewport.viewName != null)
3425 title += viewport.viewName + " of ";
3428 title += this.title;
3430 Desktop.addInternalFrame(tp, title, 600, 500);
3441 public void addSortByOrderMenuItem(String title,
3442 final AlignmentOrder order)
3444 final JMenuItem item = new JMenuItem("by " + title);
3446 item.addActionListener(new java.awt.event.ActionListener()
3448 public void actionPerformed(ActionEvent e)
3450 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3452 // TODO: JBPNote - have to map order entries to curent SequenceI
3454 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3456 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3457 viewport.alignment));
3459 alignPanel.paintAlignment(true);
3465 * Add a new sort by annotation score menu item
3468 * the menu to add the option to
3470 * the label used to retrieve scores for each sequence on the
3473 public void addSortByAnnotScoreMenuItem(JMenu sort,
3474 final String scoreLabel)
3476 final JMenuItem item = new JMenuItem(scoreLabel);
3478 item.addActionListener(new java.awt.event.ActionListener()
3480 public void actionPerformed(ActionEvent e)
3482 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3483 AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport
3484 .getAlignment());// ,viewport.getSelectionGroup());
3485 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3486 viewport.alignment));
3487 alignPanel.paintAlignment(true);
3493 * last hash for alignment's annotation array - used to minimise cost of
3496 protected int _annotationScoreVectorHash;
3499 * search the alignment and rebuild the sort by annotation score submenu the
3500 * last alignment annotation vector hash is stored to minimize cost of
3501 * rebuilding in subsequence calls.
3504 public void buildSortByAnnotationScoresMenu()
3506 if (viewport.alignment.getAlignmentAnnotation() == null)
3511 if (viewport.alignment.getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3513 sortByAnnotScore.removeAll();
3514 // almost certainly a quicker way to do this - but we keep it simple
3515 Hashtable scoreSorts = new Hashtable();
3516 AlignmentAnnotation aann[];
3517 Enumeration sq = viewport.alignment.getSequences().elements();
3518 while (sq.hasMoreElements())
3520 aann = ((SequenceI) sq.nextElement()).getAnnotation();
3521 for (int i = 0; aann != null && i < aann.length; i++)
3523 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3525 scoreSorts.put(aann[i].label, aann[i].label);
3529 Enumeration labels = scoreSorts.keys();
3530 while (labels.hasMoreElements())
3532 addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels
3535 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3538 _annotationScoreVectorHash = viewport.alignment
3539 .getAlignmentAnnotation().hashCode();
3544 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3545 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3546 * call. Listeners are added to remove the menu item when the treePanel is
3547 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3551 * Displayed tree window.
3553 * SortBy menu item title.
3555 public void buildTreeMenu()
3557 sortByTreeMenu.removeAll();
3559 Vector comps = (Vector) PaintRefresher.components.get(viewport
3560 .getSequenceSetId());
3561 Vector treePanels = new Vector();
3562 int i, iSize = comps.size();
3563 for (i = 0; i < iSize; i++)
3565 if (comps.elementAt(i) instanceof TreePanel)
3567 treePanels.add(comps.elementAt(i));
3571 iSize = treePanels.size();
3575 sortByTreeMenu.setVisible(false);
3579 sortByTreeMenu.setVisible(true);
3581 for (i = 0; i < treePanels.size(); i++)
3583 TreePanel tp = (TreePanel) treePanels.elementAt(i);
3584 final JMenuItem item = new JMenuItem(tp.getTitle());
3585 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3586 item.addActionListener(new java.awt.event.ActionListener()
3588 public void actionPerformed(ActionEvent e)
3590 SequenceI[] oldOrder = viewport.getAlignment()
3591 .getSequencesArray();
3592 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
3594 addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
3595 viewport.alignment));
3597 alignPanel.paintAlignment(true);
3601 sortByTreeMenu.add(item);
3606 * Work out whether the whole set of sequences or just the selected set will
3607 * be submitted for multiple alignment.
3610 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3612 // Now, check we have enough sequences
3613 AlignmentView msa = null;
3615 if ((viewport.getSelectionGroup() != null)
3616 && (viewport.getSelectionGroup().getSize() > 1))
3618 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3619 // some common interface!
3621 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3622 * SequenceI[sz = seqs.getSize(false)];
3624 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3625 * seqs.getSequenceAt(i); }
3627 msa = viewport.getAlignmentView(true);
3632 * Vector seqs = viewport.getAlignment().getSequences();
3634 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3636 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3637 * seqs.elementAt(i); } }
3639 msa = viewport.getAlignmentView(false);
3645 * Decides what is submitted to a secondary structure prediction service: the
3646 * first sequence in the alignment, or in the current selection, or, if the
3647 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3648 * region or the whole alignment. (where the first sequence in the set is the
3649 * one that the prediction will be for).
3651 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3653 AlignmentView seqs = null;
3655 if ((viewport.getSelectionGroup() != null)
3656 && (viewport.getSelectionGroup().getSize() > 0))
3658 seqs = viewport.getAlignmentView(true);
3662 seqs = viewport.getAlignmentView(false);
3664 // limit sequences - JBPNote in future - could spawn multiple prediction
3666 // TODO: viewport.alignment.isAligned is a global state - the local
3667 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3668 if (!viewport.alignment.isAligned(false))
3670 seqs.setSequences(new SeqCigar[]
3671 { seqs.getSequences()[0] });
3672 // TODO: if seqs.getSequences().length>1 then should really have warned
3685 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3687 // Pick the tree file
3688 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
3689 .getProperty("LAST_DIRECTORY"));
3690 chooser.setFileView(new JalviewFileView());
3691 chooser.setDialogTitle("Select a newick-like tree file");
3692 chooser.setToolTipText("Load a tree file");
3694 int value = chooser.showOpenDialog(null);
3696 if (value == JalviewFileChooser.APPROVE_OPTION)
3698 String choice = chooser.getSelectedFile().getPath();
3699 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3700 jalview.io.NewickFile fin = null;
3703 fin = new jalview.io.NewickFile(choice, "File");
3704 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3705 } catch (Exception ex)
3707 JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3708 "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
3709 ex.printStackTrace();
3711 if (fin != null && fin.hasWarningMessage())
3713 JOptionPane.showMessageDialog(Desktop.desktop, fin
3714 .getWarningMessage(), "Possible problem with tree file",
3715 JOptionPane.WARNING_MESSAGE);
3720 public TreePanel ShowNewickTree(NewickFile nf, String title)
3722 return ShowNewickTree(nf, title, 600, 500, 4, 5);
3725 public TreePanel ShowNewickTree(NewickFile nf, String title,
3726 AlignmentView input)
3728 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
3731 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
3732 int h, int x, int y)
3734 return ShowNewickTree(nf, title, null, w, h, x, y);
3738 * Add a treeviewer for the tree extracted from a newick file object to the
3739 * current alignment view
3746 * Associated alignment input data (or null)
3755 * @return TreePanel handle
3757 public TreePanel ShowNewickTree(NewickFile nf, String title,
3758 AlignmentView input, int w, int h, int x, int y)
3760 TreePanel tp = null;
3766 if (nf.getTree() != null)
3768 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
3774 tp.setLocation(x, y);
3777 Desktop.addInternalFrame(tp, title, w, h);
3779 } catch (Exception ex)
3781 ex.printStackTrace();
3788 * Generates menu items and listener event actions for web service clients
3791 public void BuildWebServiceMenu()
3793 // TODO: add support for context dependent disabling of services based on
3794 // alignment and current selection
3795 // TODO: add additional serviceHandle parameter to specify abstract handler
3796 // class independently of AbstractName
3797 // TODO: add in rediscovery GUI function to restart discoverer
3798 // TODO: group services by location as well as function and/or introduce
3799 // object broker mechanism.
3800 if ((Discoverer.services != null) && (Discoverer.services.size() > 0))
3802 // TODO: refactor to allow list of AbstractName/Handler bindings to be
3803 // stored or retrieved from elsewhere
3804 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
3805 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
3806 Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
3807 // TODO: move GUI generation code onto service implementation - so a
3808 // client instance attaches itself to the GUI with method call like
3809 // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
3811 Vector wsmenu = new Vector();
3812 final IProgressIndicator af = this;
3815 // Add any Multiple Sequence Alignment Services
3816 final JMenu msawsmenu = new JMenu("Alignment");
3817 for (int i = 0, j = msaws.size(); i < j; i++)
3819 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
3821 jalview.ws.WSClient impl = jalview.ws.Discoverer
3822 .getServiceClient(sh);
3823 impl.attachWSMenuEntry(msawsmenu, this);
3826 wsmenu.add(msawsmenu);
3828 if (secstrpr != null)
3830 // Add any secondary structure prediction services
3831 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
3832 for (int i = 0, j = secstrpr.size(); i < j; i++)
3834 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
3836 jalview.ws.WSClient impl = jalview.ws.Discoverer
3837 .getServiceClient(sh);
3838 impl.attachWSMenuEntry(secstrmenu, this);
3840 wsmenu.add(secstrmenu);
3842 if (seqsrch != null)
3844 // Add any sequence search services
3845 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
3846 for (int i = 0, j = seqsrch.size(); i < j; i++)
3848 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
3850 jalview.ws.WSClient impl = jalview.ws.Discoverer
3851 .getServiceClient(sh);
3852 impl.attachWSMenuEntry(seqsrchmenu, this);
3854 wsmenu.add(seqsrchmenu);
3856 // finally, add the whole shebang onto the webservices menu
3857 resetWebServiceMenu();
3858 for (int i = 0, j = wsmenu.size(); i < j; i++)
3860 webService.add((JMenu) wsmenu.get(i));
3865 resetWebServiceMenu();
3866 this.webService.add(this.webServiceNoServices);
3871 * empty the web service menu and add any ad-hoc functions not dynamically
3875 private void resetWebServiceMenu()
3877 webService.removeAll();
3878 build_fetchdbmenu(webService);
3879 build_urlServiceMenu(webService);
3883 * construct any groupURL type service menu entries.
3887 private void build_urlServiceMenu(JMenu webService)
3889 jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
3894 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
3895 * chooser = new JalviewFileChooser(jalview.bin.Cache.
3896 * getProperty("LAST_DIRECTORY"));
3898 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
3899 * to Vamsas file"); chooser.setToolTipText("Export");
3901 * int value = chooser.showSaveDialog(this);
3903 * if (value == JalviewFileChooser.APPROVE_OPTION) {
3904 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
3905 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
3906 * chooser.getSelectedFile().getAbsolutePath(), this); } }
3909 * prototype of an automatically enabled/disabled analysis function
3912 protected void setShowProductsEnabled()
3914 SequenceI[] selection = viewport.getSequenceSelection();
3915 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
3916 viewport.getAlignment().getDataset()))
3918 showProducts.setEnabled(true);
3923 showProducts.setEnabled(false);
3928 * search selection for sequence xRef products and build the show products
3933 * @return true if showProducts menu should be enabled.
3935 public boolean canShowProducts(SequenceI[] selection,
3936 boolean isRegionSelection, Alignment dataset)
3938 boolean showp = false;
3941 showProducts.removeAll();
3942 final boolean dna = viewport.getAlignment().isNucleotide();
3943 final Alignment ds = dataset;
3944 String[] ptypes = (selection == null || selection.length == 0) ? null
3945 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
3947 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
3948 // selection, dataset, true);
3949 final SequenceI[] sel = selection;
3950 for (int t = 0; ptypes != null && t < ptypes.length; t++)
3953 final boolean isRegSel = isRegionSelection;
3954 final AlignFrame af = this;
3955 final String source = ptypes[t];
3956 JMenuItem xtype = new JMenuItem(ptypes[t]);
3957 xtype.addActionListener(new ActionListener()
3960 public void actionPerformed(ActionEvent e)
3962 // TODO: new thread for this call with vis-delay
3963 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
3964 isRegSel, dna, source);
3968 showProducts.add(xtype);
3970 showProducts.setVisible(showp);
3971 showProducts.setEnabled(showp);
3972 } catch (Exception e)
3974 jalview.bin.Cache.log
3976 "canTranslate threw an exception - please report to help@jalview.org",
3983 protected void showProductsFor(SequenceI[] sel, Alignment ds,
3984 boolean isRegSel, boolean dna, String source)
3986 final boolean fisRegSel = isRegSel;
3987 final boolean fdna = dna;
3988 final String fsrc = source;
3989 final AlignFrame ths = this;
3990 final SequenceI[] fsel = sel;
3991 Runnable foo = new Runnable()
3996 final long sttime = System.currentTimeMillis();
3997 ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4000 Alignment ds = ths.getViewport().alignment.getDataset(); // update
4004 Alignment prods = CrossRef
4005 .findXrefSequences(fsel, fdna, fsrc, ds);
4008 SequenceI[] sprods = new SequenceI[prods.getHeight()];
4009 for (int s = 0; s < sprods.length; s++)
4011 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4012 if (ds.getSequences() == null
4013 || !ds.getSequences().contains(
4014 sprods[s].getDatasetSequence()))
4015 ds.addSequence(sprods[s].getDatasetSequence());
4016 sprods[s].updatePDBIds();
4018 Alignment al = new Alignment(sprods);
4019 AlignedCodonFrame[] cf = prods.getCodonFrames();
4021 for (int s = 0; cf != null && s < cf.length; s++)
4023 al.addCodonFrame(cf[s]);
4026 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4028 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4029 + " for " + ((fisRegSel) ? "selected region of " : "")
4031 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4036 System.err.println("No Sequences generated for xRef type "
4039 } catch (Exception e)
4041 jalview.bin.Cache.log.error(
4042 "Exception when finding crossreferences", e);
4043 } catch (OutOfMemoryError e)
4045 new OOMWarning("whilst fetching crossreferences", e);
4048 jalview.bin.Cache.log.error("Error when finding crossreferences",
4051 ths.setProgressBar("Finished searching for sequences from " + fsrc,
4056 Thread frunner = new Thread(foo);
4060 public boolean canShowTranslationProducts(SequenceI[] selection,
4061 AlignmentI alignment)
4066 return (jalview.analysis.Dna.canTranslate(selection, viewport
4067 .getViewAsVisibleContigs(true)));
4068 } catch (Exception e)
4070 jalview.bin.Cache.log
4072 "canTranslate threw an exception - please report to help@jalview.org",
4078 public void showProducts_actionPerformed(ActionEvent e)
4080 // /////////////////////////////
4081 // Collect Data to be translated/transferred
4083 SequenceI[] selection = viewport.getSequenceSelection();
4084 AlignmentI al = null;
4087 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4088 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4089 viewport.getAlignment().getDataset());
4090 } catch (Exception ex)
4093 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4100 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4101 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4105 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4106 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4107 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4111 public void showTranslation_actionPerformed(ActionEvent e)
4113 // /////////////////////////////
4114 // Collect Data to be translated/transferred
4116 SequenceI[] selection = viewport.getSequenceSelection();
4117 String[] seqstring = viewport.getViewAsString(true);
4118 AlignmentI al = null;
4121 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4122 viewport.getViewAsVisibleContigs(true), viewport
4123 .getGapCharacter(), viewport.alignment
4124 .getAlignmentAnnotation(), viewport.alignment
4125 .getWidth(), viewport.getAlignment().getDataset());
4126 } catch (Exception ex)
4129 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4136 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4137 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4141 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4142 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4143 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4148 * Try to load a features file onto the alignment.
4151 * contents or path to retrieve file
4153 * access mode of file (see jalview.io.AlignFile)
4154 * @return true if features file was parsed corectly.
4156 public boolean parseFeaturesFile(String file, String type)
4158 boolean featuresFile = false;
4161 featuresFile = new FeaturesFile(file, type).parse(viewport.alignment
4162 .getDataset(), alignPanel.seqPanel.seqCanvas
4163 .getFeatureRenderer().featureColours, false);
4164 } catch (Exception ex)
4166 ex.printStackTrace();
4171 viewport.showSequenceFeatures = true;
4172 showSeqFeatures.setSelected(true);
4173 if (alignPanel.seqPanel.seqCanvas.fr != null)
4175 // update the min/max ranges where necessary
4176 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4178 if (featureSettings != null)
4180 featureSettings.setTableData();
4182 alignPanel.paintAlignment(true);
4185 return featuresFile;
4188 public void dragEnter(DropTargetDragEvent evt)
4192 public void dragExit(DropTargetEvent evt)
4196 public void dragOver(DropTargetDragEvent evt)
4200 public void dropActionChanged(DropTargetDragEvent evt)
4204 public void drop(DropTargetDropEvent evt)
4206 Transferable t = evt.getTransferable();
4207 java.util.List files = null;
4211 DataFlavor uriListFlavor = new DataFlavor(
4212 "text/uri-list;class=java.lang.String");
4213 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4215 // Works on Windows and MacOSX
4216 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4217 files = (java.util.List) t
4218 .getTransferData(DataFlavor.javaFileListFlavor);
4220 else if (t.isDataFlavorSupported(uriListFlavor))
4222 // This is used by Unix drag system
4223 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4224 String data = (String) t.getTransferData(uriListFlavor);
4225 files = new java.util.ArrayList(1);
4226 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4227 data, "\r\n"); st.hasMoreTokens();)
4229 String s = st.nextToken();
4230 if (s.startsWith("#"))
4232 // the line is a comment (as per the RFC 2483)
4236 java.net.URI uri = new java.net.URI(s);
4237 // check to see if we can handle this kind of URI
4238 if (uri.getScheme().toLowerCase().startsWith("http"))
4240 files.add(uri.toString());
4244 // otherwise preserve old behaviour: catch all for file objects
4245 java.io.File file = new java.io.File(uri);
4246 files.add(file.toString());
4250 } catch (Exception e)
4252 e.printStackTrace();
4259 for (int i = 0; i < files.size(); i++)
4261 loadJalviewDataFile(files.get(i).toString());
4263 } catch (Exception ex)
4265 ex.printStackTrace();
4271 * Attempt to load a "dropped" file or URL string: First by testing whether
4272 * it's and Annotation file, then a JNet file, and finally a features file. If
4273 * all are false then the user may have dropped an alignment file onto this
4277 * either a filename or a URL string.
4279 public void loadJalviewDataFile(String file)
4283 String protocol = jalview.io.FormatAdapter.FILE;
4284 String f = file.toLowerCase();
4285 if (f.indexOf("http:") == 0 || f.indexOf("https:") == 0
4286 || f.indexOf("file:") == 0)
4288 protocol = jalview.io.FormatAdapter.URL;
4291 boolean isAnnotation = new AnnotationFile().readAnnotationFile(
4292 viewport.alignment, file, protocol);
4296 // try to see if its a JNet 'concise' style annotation file *before* we
4297 // try to parse it as a features file
4298 String format = new IdentifyFile().Identify(file, protocol);
4299 if (format.equalsIgnoreCase("JnetFile"))
4301 jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
4303 new JnetAnnotationMaker().add_annotation(predictions, viewport
4304 .getAlignment(), 0, false);
4305 isAnnotation = true;
4309 // try to parse it as a features file
4310 boolean isGroupsFile = parseFeaturesFile(file, protocol);
4311 // if it wasn't a features file then we just treat it as a general
4312 // alignment file to load into the current view.
4315 new FileLoader().LoadFile(viewport, file, protocol, format);
4319 alignPanel.paintAlignment(true);
4326 alignPanel.adjustAnnotationHeight();
4327 viewport.updateSequenceIdColours();
4328 buildSortByAnnotationScoresMenu();
4329 alignPanel.paintAlignment(true);
4331 } catch (Exception ex)
4333 ex.printStackTrace();
4337 public void tabSelectionChanged(int index)
4341 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
4342 viewport = alignPanel.av;
4343 setMenusFromViewport(viewport);
4347 public void tabbedPane_mousePressed(MouseEvent e)
4349 if (SwingUtilities.isRightMouseButton(e))
4351 String reply = JOptionPane.showInternalInputDialog(this,
4352 "Enter View Name", "Edit View Name",
4353 JOptionPane.QUESTION_MESSAGE);
4357 viewport.viewName = reply;
4358 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4363 public AlignViewport getCurrentView()
4369 * Open the dialog for regex description parsing.
4371 protected void extractScores_actionPerformed(ActionEvent e)
4373 ParseProperties pp = new jalview.analysis.ParseProperties(
4374 viewport.alignment);
4375 // TODO: verify regex and introduce GUI dialog for version 2.5
4376 // if (pp.getScoresFromDescription("col", "score column ",
4377 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4379 if (pp.getScoresFromDescription("description column",
4380 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4382 buildSortByAnnotationScoresMenu();
4390 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4393 protected void showDbRefs_actionPerformed(ActionEvent e)
4395 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
4401 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4404 protected void showNpFeats_actionPerformed(ActionEvent e)
4406 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
4410 * find the viewport amongst the tabs in this alignment frame and close that
4415 public boolean closeView(AlignViewport av)
4419 this.closeMenuItem_actionPerformed(false);
4422 Component[] comp = tabbedPane.getComponents();
4423 for (int i = 0; comp != null && i < comp.length; i++)
4425 if (comp[i] instanceof AlignmentPanel)
4427 if (((AlignmentPanel) comp[i]).av == av)
4430 closeView((AlignmentPanel) comp[i]);
4438 protected void build_fetchdbmenu(JMenu webService)
4440 // Temporary hack - DBRef Fetcher always top level ws entry.
4441 // TODO We probably want to store a sequence database checklist in
4442 // preferences and have checkboxes.. rather than individual sources selected
4444 JMenu rfetch = new JMenu("Fetch DB References");
4446 .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
4447 webService.add(rfetch);
4449 JMenuItem fetchr = new JMenuItem("Standard Databases");
4451 .setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
4452 fetchr.addActionListener(new ActionListener()
4455 public void actionPerformed(ActionEvent e)
4457 new Thread(new Runnable()
4462 new jalview.ws.DBRefFetcher(alignPanel.av
4463 .getSequenceSelection(), alignPanel.alignFrame)
4464 .fetchDBRefs(false);
4472 JMenu dfetch = new JMenu();
4474 jalview.ws.SequenceFetcher sf = SequenceFetcher
4475 .getSequenceFetcherSingleton(this);
4476 String[] otherdb = sf.getOrderedSupportedSources();
4477 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4478 // jalview.util.QuickSort.sort(otherdb, otherdb);
4479 int comp = 0, mcomp = 15;
4480 String mname = null;
4481 if (otherdb != null && otherdb.length > 0)
4483 for (int i = 0; i < otherdb.length; i++)
4485 String dbname = sf.getSourceProxy(otherdb[i]).getDbName();
4488 mname = "from '" + dbname + "'";
4490 fetchr = new JMenuItem(otherdb[i]);
4491 final String[] dassource = new String[]
4493 fetchr.addActionListener(new ActionListener()
4496 public void actionPerformed(ActionEvent e)
4498 new Thread(new Runnable()
4503 new jalview.ws.DBRefFetcher(alignPanel.av
4504 .getSequenceSelection(), alignPanel.alignFrame,
4505 dassource).fetchDBRefs(false);
4511 fetchr.setToolTipText("Retrieve from " + dbname);
4513 if (comp++ == mcomp || i == (otherdb.length - 1))
4515 dfetch.setText(mname + " to '" + dbname + "'");
4517 dfetch = new JMenu();
4526 * Left justify the whole alignment.
4528 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
4530 AlignmentI al = viewport.getAlignment();
4532 viewport.firePropertyChange("alignment", null, al);
4536 * Right justify the whole alignment.
4538 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
4540 AlignmentI al = viewport.getAlignment();
4542 viewport.firePropertyChange("alignment", null, al);
4545 public void setShowSeqFeatures(boolean b)
4547 showSeqFeatures.setSelected(true);
4548 viewport.setShowSequenceFeatures(true);
4555 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
4556 * awt.event.ActionEvent)
4558 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
4560 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
4561 alignPanel.paintAlignment(true);
4568 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
4571 protected void showGroupConsensus_actionPerformed(ActionEvent e)
4573 viewport.setShowGroupConsensus(showGroupConsensus.getState());
4574 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4582 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
4583 * .event.ActionEvent)
4585 protected void showGroupConservation_actionPerformed(ActionEvent e)
4587 viewport.setShowGroupConservation(showGroupConservation.getState());
4588 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4595 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
4596 * .event.ActionEvent)
4598 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
4600 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
4601 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4608 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
4609 * .event.ActionEvent)
4611 protected void showSequenceLogo_actionPerformed(ActionEvent e)
4613 viewport.setShowSequenceLogo(showSequenceLogo.getState());
4614 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4617 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
4619 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
4626 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
4627 * .event.ActionEvent)
4629 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
4631 if (viewport.getSelectionGroup() != null)
4633 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
4634 viewport.getSequenceSelection(), viewport.getAlignmentView(
4635 true).getSequenceStrings(viewport.getGapCharacter()),
4636 viewport.alignment.getGroups());
4637 viewport.alignment.deleteAllGroups();
4638 viewport.sequenceColours = null;
4639 viewport.setSelectionGroup(null);
4640 // set view properties for each group
4641 for (int g = 0; g < gps.length; g++)
4643 gps[g].setShowNonconserved(viewport.getShowUnconserved());
4644 gps[g].setIncludeAllConsSymbols(viewport
4645 .isIncludeAllConsensusSymbols());
4646 viewport.alignment.addGroup(gps[g]);
4647 Color col = new Color((int) (Math.random() * 255), (int) (Math
4648 .random() * 255), (int) (Math.random() * 255));
4649 col = col.brighter();
4650 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
4651 .hasMoreElements(); viewport.setSequenceColour(
4652 (SequenceI) sq.nextElement(), col))
4655 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
4656 alignPanel.updateAnnotation();
4657 alignPanel.paintAlignment(true);
4662 class PrintThread extends Thread
4666 public PrintThread(AlignmentPanel ap)
4671 static PageFormat pf;
4675 PrinterJob printJob = PrinterJob.getPrinterJob();
4679 printJob.setPrintable(ap, pf);
4683 printJob.setPrintable(ap);
4686 if (printJob.printDialog())
4691 } catch (Exception PrintException)
4693 PrintException.printStackTrace();