2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
3 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
26 import java.awt.datatransfer.*;
27 import java.awt.dnd.*;
28 import java.awt.event.*;
29 import java.awt.print.*;
31 import javax.swing.event.MenuEvent;
33 import jalview.analysis.*;
34 import jalview.commands.*;
35 import jalview.datamodel.*;
37 import jalview.jbgui.*;
38 import jalview.schemes.*;
47 public class AlignFrame extends GAlignFrame implements DropTargetListener,
52 public static final int DEFAULT_WIDTH = 700;
55 public static final int DEFAULT_HEIGHT = 500;
57 public AlignmentPanel alignPanel;
59 AlignViewport viewport;
61 Vector alignPanels = new Vector();
64 * Last format used to load or save alignments in this window
66 String currentFileFormat = null;
69 * Current filename for this alignment
71 String fileName = null;
74 * Creates a new AlignFrame object with specific width and height.
80 public AlignFrame(AlignmentI al, int width, int height)
82 this(al, null, width, height);
86 * Creates a new AlignFrame object with specific width, height and
92 * @param sequenceSetId
94 public AlignFrame(AlignmentI al, int width, int height,
97 this(al, null, width, height, sequenceSetId);
101 * Creates a new AlignFrame object with specific width, height and
107 * @param sequenceSetId
110 public AlignFrame(AlignmentI al, int width, int height,
111 String sequenceSetId, String viewId)
113 this(al, null, width, height, sequenceSetId, viewId);
117 * new alignment window with hidden columns
121 * @param hiddenColumns
122 * ColumnSelection or null
124 * Width of alignment frame
128 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
129 int width, int height)
131 this(al, hiddenColumns, width, height, null);
135 * Create alignment frame for al with hiddenColumns, a specific width and
136 * height, and specific sequenceId
139 * @param hiddenColumns
142 * @param sequenceSetId
145 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
146 int width, int height, String sequenceSetId)
148 this(al, hiddenColumns, width, height, sequenceSetId, null);
152 * Create alignment frame for al with hiddenColumns, a specific width and
153 * height, and specific sequenceId
156 * @param hiddenColumns
159 * @param sequenceSetId
164 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
165 int width, int height, String sequenceSetId, String viewId)
167 setSize(width, height);
168 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
170 alignPanel = new AlignmentPanel(this, viewport);
172 if (al.getDataset() == null)
177 addAlignmentPanel(alignPanel, true);
182 * Make a new AlignFrame from exisiting alignmentPanels
189 public AlignFrame(AlignmentPanel ap)
193 addAlignmentPanel(ap, false);
198 * initalise the alignframe from the underlying viewport data and the
203 if (viewport.conservation == null)
205 BLOSUM62Colour.setEnabled(false);
206 conservationMenuItem.setEnabled(false);
207 modifyConservation.setEnabled(false);
208 // PIDColour.setEnabled(false);
209 // abovePIDThreshold.setEnabled(false);
210 // modifyPID.setEnabled(false);
213 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
216 if (sortby.equals("Id"))
218 sortIDMenuItem_actionPerformed(null);
220 else if (sortby.equals("Pairwise Identity"))
222 sortPairwiseMenuItem_actionPerformed(null);
225 if (Desktop.desktop != null)
227 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
228 addServiceListeners();
229 setGUINucleotide(viewport.alignment.isNucleotide());
232 setMenusFromViewport(viewport);
233 buildSortByAnnotationScoresMenu();
234 if (viewport.wrapAlignment)
236 wrapMenuItem_actionPerformed(null);
239 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
241 this.overviewMenuItem_actionPerformed(null);
249 * Change the filename and format for the alignment, and enable the 'reload'
250 * button functionality.
257 public void setFileName(String file, String format)
260 currentFileFormat = format;
261 reload.setEnabled(true);
264 void addKeyListener()
266 addKeyListener(new KeyAdapter()
268 public void keyPressed(KeyEvent evt)
270 if (viewport.cursorMode
271 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
272 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
273 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
274 && Character.isDigit(evt.getKeyChar()))
275 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
277 switch (evt.getKeyCode())
280 case 27: // escape key
281 deselectAllSequenceMenuItem_actionPerformed(null);
285 case KeyEvent.VK_DOWN:
286 if (evt.isAltDown() || !viewport.cursorMode)
287 moveSelectedSequences(false);
288 if (viewport.cursorMode)
289 alignPanel.seqPanel.moveCursor(0, 1);
293 if (evt.isAltDown() || !viewport.cursorMode)
294 moveSelectedSequences(true);
295 if (viewport.cursorMode)
296 alignPanel.seqPanel.moveCursor(0, -1);
300 case KeyEvent.VK_LEFT:
301 if (evt.isAltDown() || !viewport.cursorMode)
302 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
304 alignPanel.seqPanel.moveCursor(-1, 0);
308 case KeyEvent.VK_RIGHT:
309 if (evt.isAltDown() || !viewport.cursorMode)
310 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
312 alignPanel.seqPanel.moveCursor(1, 0);
315 case KeyEvent.VK_SPACE:
316 if (viewport.cursorMode)
318 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
319 || evt.isShiftDown() || evt.isAltDown());
323 case KeyEvent.VK_DELETE:
324 case KeyEvent.VK_BACK_SPACE:
325 if (!viewport.cursorMode)
327 cut_actionPerformed(null);
331 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
332 || evt.isShiftDown() || evt.isAltDown());
338 if (viewport.cursorMode)
340 alignPanel.seqPanel.setCursorRow();
344 if (viewport.cursorMode && !evt.isControlDown())
346 alignPanel.seqPanel.setCursorColumn();
350 if (viewport.cursorMode)
352 alignPanel.seqPanel.setCursorPosition();
356 case KeyEvent.VK_ENTER:
357 case KeyEvent.VK_COMMA:
358 if (viewport.cursorMode)
360 alignPanel.seqPanel.setCursorRowAndColumn();
365 if (viewport.cursorMode)
367 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
371 if (viewport.cursorMode)
373 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
378 viewport.cursorMode = !viewport.cursorMode;
379 statusBar.setText("Keyboard editing mode is "
380 + (viewport.cursorMode ? "on" : "off"));
381 if (viewport.cursorMode)
383 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
384 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
386 alignPanel.seqPanel.seqCanvas.repaint();
392 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
393 java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
395 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
397 javax.help.HelpBroker hb = hs.createHelpBroker();
398 hb.setCurrentID("home");
399 hb.setDisplayed(true);
400 } catch (Exception ex)
402 ex.printStackTrace();
407 boolean toggleSeqs = !evt.isControlDown();
408 boolean toggleCols = !evt.isShiftDown();
410 boolean hide = false;
412 SequenceGroup sg = viewport.getSelectionGroup();
416 && sg.getSize() != viewport.alignment.getHeight())
418 hideSelSequences_actionPerformed(null);
421 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
423 showAllSeqs_actionPerformed(null);
429 if (viewport.colSel.getSelected().size() > 0)
431 hideSelColumns_actionPerformed(null);
434 viewport.selectionGroup = sg;
439 showAllColumns_actionPerformed(null);
444 case KeyEvent.VK_PAGE_UP:
445 if (viewport.wrapAlignment)
447 alignPanel.scrollUp(true);
451 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
452 - viewport.endSeq + viewport.startSeq);
455 case KeyEvent.VK_PAGE_DOWN:
456 if (viewport.wrapAlignment)
458 alignPanel.scrollUp(false);
462 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
463 + viewport.endSeq - viewport.startSeq);
469 public void keyReleased(KeyEvent evt)
471 switch (evt.getKeyCode())
473 case KeyEvent.VK_LEFT:
474 if (evt.isAltDown() || !viewport.cursorMode)
475 viewport.firePropertyChange("alignment", null, viewport
476 .getAlignment().getSequences());
479 case KeyEvent.VK_RIGHT:
480 if (evt.isAltDown() || !viewport.cursorMode)
481 viewport.firePropertyChange("alignment", null, viewport
482 .getAlignment().getSequences());
489 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
491 ap.alignFrame = this;
493 alignPanels.addElement(ap);
495 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
497 int aSize = alignPanels.size();
499 tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
501 if (aSize == 1 && ap.av.viewName == null)
503 this.getContentPane().add(ap, BorderLayout.CENTER);
509 setInitialTabVisible();
512 expandViews.setEnabled(true);
513 gatherViews.setEnabled(true);
514 tabbedPane.addTab(ap.av.viewName, ap);
516 ap.setVisible(false);
523 ap.av.alignment.padGaps();
525 ap.av.updateConservation(ap);
526 ap.av.updateConsensus(ap);
530 public void setInitialTabVisible()
532 expandViews.setEnabled(true);
533 gatherViews.setEnabled(true);
534 tabbedPane.setVisible(true);
535 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
536 tabbedPane.addTab(first.av.viewName, first);
537 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
540 public AlignViewport getViewport()
545 /* Set up intrinsic listeners for dynamically generated GUI bits. */
546 private void addServiceListeners()
548 final java.beans.PropertyChangeListener thisListener;
549 // Do this once to get current state
550 BuildWebServiceMenu();
552 .addPropertyChangeListener(thisListener = new java.beans.PropertyChangeListener()
554 public void propertyChange(PropertyChangeEvent evt)
556 // System.out.println("Discoverer property change.");
557 if (evt.getPropertyName().equals("services"))
559 // System.out.println("Rebuilding web service menu");
560 BuildWebServiceMenu();
565 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
567 public void internalFrameClosed(
568 javax.swing.event.InternalFrameEvent evt)
570 // System.out.println("deregistering discoverer listener");
571 Desktop.discoverer.removePropertyChangeListener(thisListener);
572 closeMenuItem_actionPerformed(true);
577 public void setGUINucleotide(boolean nucleotide)
579 showTranslation.setVisible(nucleotide);
580 conservationMenuItem.setEnabled(!nucleotide);
581 modifyConservation.setEnabled(!nucleotide);
583 // Remember AlignFrame always starts as protein
586 calculateMenu.remove(calculateMenu.getItemCount() - 2);
591 * set up menus for the currently viewport. This may be called after any
592 * operation that affects the data in the current view (selection changed,
593 * etc) to update the menus to reflect the new state.
595 public void setMenusForViewport()
597 setMenusFromViewport(viewport);
601 * Need to call this method when tabs are selected for multiple views, or when
602 * loading from Jalview2XML.java
607 void setMenusFromViewport(AlignViewport av)
609 padGapsMenuitem.setSelected(av.padGaps);
610 colourTextMenuItem.setSelected(av.showColourText);
611 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
612 conservationMenuItem.setSelected(av.getConservationSelected());
613 seqLimits.setSelected(av.getShowJVSuffix());
614 idRightAlign.setSelected(av.rightAlignIds);
615 centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
616 renderGapsMenuItem.setSelected(av.renderGaps);
617 wrapMenuItem.setSelected(av.wrapAlignment);
618 scaleAbove.setVisible(av.wrapAlignment);
619 scaleLeft.setVisible(av.wrapAlignment);
620 scaleRight.setVisible(av.wrapAlignment);
621 annotationPanelMenuItem.setState(av.showAnnotation);
622 viewBoxesMenuItem.setSelected(av.showBoxes);
623 viewTextMenuItem.setSelected(av.showText);
624 showUnconservedMenuItem.setSelected(av.showUnconserved);
625 showGroupConsensus.setSelected(av.showGroupConsensus);
626 showGroupConservation.setSelected(av.showGroupConservation);
627 setColourSelected(ColourSchemeProperty.getColourName(av
628 .getGlobalColourScheme()));
630 showSeqFeatures.setSelected(av.showSequenceFeatures);
631 hiddenMarkers.setState(av.showHiddenMarkers);
632 applyToAllGroups.setState(av.colourAppliesToAllGroups);
633 showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
634 showDbRefsMenuitem.setSelected(av.isShowDbRefs());
636 setShowProductsEnabled();
641 Hashtable progressBars, progressBarHandlers;
646 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
648 public void setProgressBar(String message, long id)
650 if (progressBars == null)
652 progressBars = new Hashtable();
653 progressBarHandlers = new Hashtable();
656 JPanel progressPanel;
657 GridLayout layout = (GridLayout) statusPanel.getLayout();
658 if (progressBars.get(new Long(id)) != null)
660 progressPanel = (JPanel) progressBars.get(new Long(id));
661 statusPanel.remove(progressPanel);
662 progressBars.remove(progressPanel);
663 progressPanel = null;
666 statusBar.setText(message);
668 if (progressBarHandlers.contains(new Long(id)))
670 progressBarHandlers.remove(new Long(id));
672 layout.setRows(layout.getRows() - 1);
676 progressPanel = new JPanel(new BorderLayout(10, 5));
678 JProgressBar progressBar = new JProgressBar();
679 progressBar.setIndeterminate(true);
681 progressPanel.add(new JLabel(message), BorderLayout.WEST);
682 progressPanel.add(progressBar, BorderLayout.CENTER);
684 layout.setRows(layout.getRows() + 1);
685 statusPanel.add(progressPanel);
687 progressBars.put(new Long(id), progressPanel);
690 setMenusForViewport();
694 public void registerHandler(final long id,
695 final IProgressIndicatorHandler handler)
697 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
700 "call setProgressBar before registering the progress bar's handler.");
702 progressBarHandlers.put(new Long(id), handler);
703 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
704 if (handler.canCancel())
706 JButton cancel = new JButton("Cancel");
707 final IProgressIndicator us = this;
708 cancel.addActionListener(new ActionListener()
711 public void actionPerformed(ActionEvent e)
713 handler.cancelActivity(id);
714 us.setProgressBar("Cancelled "
715 + ((JLabel) progressPanel.getComponent(0)).getText(), id);
718 progressPanel.add(cancel, BorderLayout.EAST);
724 * @return true if any progress bars are still active
726 public boolean operationInProgress()
728 if (progressBars != null && progressBars.size() > 0)
736 * Added so Castor Mapping file can obtain Jalview Version
738 public String getVersion()
740 return jalview.bin.Cache.getProperty("VERSION");
743 public FeatureRenderer getFeatureRenderer()
745 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
748 public void fetchSequence_actionPerformed(ActionEvent e)
750 new SequenceFetcher(this);
753 public void addFromFile_actionPerformed(ActionEvent e)
755 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
758 public void reload_actionPerformed(ActionEvent e)
760 if (fileName != null)
762 if (currentFileFormat.equals("Jalview"))
764 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
765 for (int i = 0; i < frames.length; i++)
767 if (frames[i] instanceof AlignFrame && frames[i] != this
768 && ((AlignFrame) frames[i]).fileName.equals(fileName))
772 frames[i].setSelected(true);
773 Desktop.instance.closeAssociatedWindows();
774 } catch (java.beans.PropertyVetoException ex)
780 Desktop.instance.closeAssociatedWindows();
782 FileLoader loader = new FileLoader();
783 String protocol = fileName.startsWith("http:") ? "URL" : "File";
784 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
788 Rectangle bounds = this.getBounds();
790 FileLoader loader = new FileLoader();
791 String protocol = fileName.startsWith("http:") ? "URL" : "File";
792 AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
793 protocol, currentFileFormat);
795 newframe.setBounds(bounds);
797 this.closeMenuItem_actionPerformed(true);
802 public void addFromText_actionPerformed(ActionEvent e)
804 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
807 public void addFromURL_actionPerformed(ActionEvent e)
809 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
812 public void save_actionPerformed(ActionEvent e)
815 || (currentFileFormat == null || !jalview.io.FormatAdapter
816 .isValidIOFormat(currentFileFormat, true))
817 || fileName.startsWith("http"))
819 saveAs_actionPerformed(null);
823 saveAlignment(fileName, currentFileFormat);
833 public void saveAs_actionPerformed(ActionEvent e)
835 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
836 .getProperty("LAST_DIRECTORY"),
837 jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
838 jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
839 currentFileFormat, false);
841 chooser.setFileView(new JalviewFileView());
842 chooser.setDialogTitle("Save Alignment to file");
843 chooser.setToolTipText("Save");
845 int value = chooser.showSaveDialog(this);
847 if (value == JalviewFileChooser.APPROVE_OPTION)
849 currentFileFormat = chooser.getSelectedFormat();
850 if (currentFileFormat == null)
852 JOptionPane.showInternalMessageDialog(Desktop.desktop,
853 "You must select a file format before saving!",
854 "File format not specified", JOptionPane.WARNING_MESSAGE);
855 value = chooser.showSaveDialog(this);
859 fileName = chooser.getSelectedFile().getPath();
861 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
864 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
865 if (currentFileFormat.indexOf(" ") > -1)
867 currentFileFormat = currentFileFormat.substring(0,
868 currentFileFormat.indexOf(" "));
870 saveAlignment(fileName, currentFileFormat);
874 public boolean saveAlignment(String file, String format)
876 boolean success = true;
878 if (format.equalsIgnoreCase("Jalview"))
880 String shortName = title;
882 if (shortName.indexOf(java.io.File.separatorChar) > -1)
884 shortName = shortName.substring(shortName
885 .lastIndexOf(java.io.File.separatorChar) + 1);
888 success = new Jalview2XML().SaveAlignment(this, file, shortName);
890 statusBar.setText("Successfully saved to file: " + fileName + " in "
891 + format + " format.");
896 if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
898 warningMessage("Cannot save file "
899 + fileName + " using format " + format,
900 "Alignment output format not supported");
901 saveAs_actionPerformed(null);
902 // JBPNote need to have a raise_gui flag here
906 String[] omitHidden = null;
908 if (viewport.hasHiddenColumns)
910 int reply = JOptionPane
911 .showInternalConfirmDialog(
913 "The Alignment contains hidden columns."
914 + "\nDo you want to save only the visible alignment?",
915 "Save / Omit Hidden Columns",
916 JOptionPane.YES_NO_OPTION,
917 JOptionPane.QUESTION_MESSAGE);
919 if (reply == JOptionPane.YES_OPTION)
921 omitHidden = viewport.getViewAsString(false);
924 FormatAdapter f = new FormatAdapter();
925 String output = f.formatSequences(format,
926 (Alignment) viewport.alignment, // class cast exceptions will
927 // occur in the distant future
928 omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
938 java.io.PrintWriter out = new java.io.PrintWriter(
939 new java.io.FileWriter(file));
944 statusBar.setText("Successfully saved to file: " + fileName
945 + " in " + format + " format.");
946 } catch (Exception ex)
949 ex.printStackTrace();
956 JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
957 + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
963 private void warningMessage(String warning, String title)
965 if (new jalview.util.Platform().isHeadless())
967 System.err.println("Warning: "+title+"\nWarning: "+warning);
970 JOptionPane.showInternalMessageDialog(this,warning,title,JOptionPane.WARNING_MESSAGE);
981 protected void outputText_actionPerformed(ActionEvent e)
983 String[] omitHidden = null;
985 if (viewport.hasHiddenColumns)
987 int reply = JOptionPane
988 .showInternalConfirmDialog(
990 "The Alignment contains hidden columns."
991 + "\nDo you want to output only the visible alignment?",
992 "Save / Omit Hidden Columns",
993 JOptionPane.YES_NO_OPTION,
994 JOptionPane.QUESTION_MESSAGE);
996 if (reply == JOptionPane.YES_OPTION)
998 omitHidden = viewport.getViewAsString(false);
1002 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1003 cap.setForInput(null);
1004 Desktop.addInternalFrame(cap, "Alignment output - "
1005 + e.getActionCommand(), 600, 500);
1007 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1008 viewport.alignment, omitHidden, viewport.colSel));
1017 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1019 new HTMLOutput(alignPanel, alignPanel.seqPanel.seqCanvas
1020 .getSequenceRenderer(), alignPanel.seqPanel.seqCanvas
1021 .getFeatureRenderer());
1024 public void createImageMap(File file, String image)
1026 alignPanel.makePNGImageMap(file, image);
1035 public void createPNG(File f)
1037 alignPanel.makePNG(f);
1046 public void createEPS(File f)
1048 alignPanel.makeEPS(f);
1051 public void pageSetup_actionPerformed(ActionEvent e)
1053 PrinterJob printJob = PrinterJob.getPrinterJob();
1054 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1063 public void printMenuItem_actionPerformed(ActionEvent e)
1065 // Putting in a thread avoids Swing painting problems
1066 PrintThread thread = new PrintThread(alignPanel);
1070 public void exportFeatures_actionPerformed(ActionEvent e)
1072 new AnnotationExporter().exportFeatures(alignPanel);
1075 public void exportAnnotations_actionPerformed(ActionEvent e)
1077 new AnnotationExporter().exportAnnotations(alignPanel,
1078 viewport.showAnnotation ? viewport.alignment
1079 .getAlignmentAnnotation() : null, viewport.alignment
1081 ((Alignment) viewport.alignment).alignmentProperties);
1084 public void associatedData_actionPerformed(ActionEvent e)
1086 // Pick the tree file
1087 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
1088 .getProperty("LAST_DIRECTORY"));
1089 chooser.setFileView(new JalviewFileView());
1090 chooser.setDialogTitle("Load Jalview Annotations or Features File");
1091 chooser.setToolTipText("Load Jalview Annotations / Features file");
1093 int value = chooser.showOpenDialog(null);
1095 if (value == JalviewFileChooser.APPROVE_OPTION)
1097 String choice = chooser.getSelectedFile().getPath();
1098 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1099 loadJalviewDataFile(choice);
1105 * Close the current view or all views in the alignment frame. If the frame
1106 * only contains one view then the alignment will be removed from memory.
1108 * @param closeAllTabs
1110 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1112 if (alignPanels != null && alignPanels.size() < 2)
1114 closeAllTabs = true;
1119 if (alignPanels != null)
1123 if (this.isClosed())
1125 // really close all the windows - otherwise wait till
1126 // setClosed(true) is called
1127 for (int i = 0; i < alignPanels.size(); i++)
1129 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1136 closeView(alignPanel);
1142 this.setClosed(true);
1144 } catch (Exception ex)
1146 ex.printStackTrace();
1151 * close alignPanel2 and shuffle tabs appropriately.
1153 * @param alignPanel2
1155 public void closeView(AlignmentPanel alignPanel2)
1157 int index = tabbedPane.getSelectedIndex();
1158 int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1159 alignPanels.removeElement(alignPanel2);
1161 // if (viewport == alignPanel2.av)
1165 alignPanel2.closePanel();
1168 tabbedPane.removeTabAt(closedindex);
1169 tabbedPane.validate();
1171 if (index > closedindex || index == tabbedPane.getTabCount())
1173 // modify currently selected tab index if necessary.
1177 this.tabSelectionChanged(index);
1183 void updateEditMenuBar()
1186 if (viewport.historyList.size() > 0)
1188 undoMenuItem.setEnabled(true);
1189 CommandI command = (CommandI) viewport.historyList.peek();
1190 undoMenuItem.setText("Undo " + command.getDescription());
1194 undoMenuItem.setEnabled(false);
1195 undoMenuItem.setText("Undo");
1198 if (viewport.redoList.size() > 0)
1200 redoMenuItem.setEnabled(true);
1202 CommandI command = (CommandI) viewport.redoList.peek();
1203 redoMenuItem.setText("Redo " + command.getDescription());
1207 redoMenuItem.setEnabled(false);
1208 redoMenuItem.setText("Redo");
1212 public void addHistoryItem(CommandI command)
1214 if (command.getSize() > 0)
1216 viewport.historyList.push(command);
1217 viewport.redoList.clear();
1218 updateEditMenuBar();
1219 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1225 * @return alignment objects for all views
1227 AlignmentI[] getViewAlignments()
1229 if (alignPanels != null)
1231 Enumeration e = alignPanels.elements();
1232 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1233 for (int i = 0; e.hasMoreElements(); i++)
1235 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1239 if (viewport != null)
1241 return new AlignmentI[]
1242 { viewport.alignment };
1253 protected void undoMenuItem_actionPerformed(ActionEvent e)
1255 if (viewport.historyList.empty())
1257 CommandI command = (CommandI) viewport.historyList.pop();
1258 viewport.redoList.push(command);
1259 command.undoCommand(getViewAlignments());
1261 AlignViewport originalSource = getOriginatingSource(command);
1262 updateEditMenuBar();
1264 if (originalSource != null)
1266 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1267 originalSource.firePropertyChange("alignment", null,
1268 originalSource.alignment.getSequences());
1278 protected void redoMenuItem_actionPerformed(ActionEvent e)
1280 if (viewport.redoList.size() < 1)
1285 CommandI command = (CommandI) viewport.redoList.pop();
1286 viewport.historyList.push(command);
1287 command.doCommand(getViewAlignments());
1289 AlignViewport originalSource = getOriginatingSource(command);
1290 updateEditMenuBar();
1292 if (originalSource != null)
1294 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1295 originalSource.firePropertyChange("alignment", null,
1296 originalSource.alignment.getSequences());
1300 AlignViewport getOriginatingSource(CommandI command)
1302 AlignViewport originalSource = null;
1303 // For sequence removal and addition, we need to fire
1304 // the property change event FROM the viewport where the
1305 // original alignment was altered
1306 AlignmentI al = null;
1307 if (command instanceof EditCommand)
1309 EditCommand editCommand = (EditCommand) command;
1310 al = editCommand.getAlignment();
1311 Vector comps = (Vector) PaintRefresher.components.get(viewport
1312 .getSequenceSetId());
1314 for (int i = 0; i < comps.size(); i++)
1316 if (comps.elementAt(i) instanceof AlignmentPanel)
1318 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
1320 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1327 if (originalSource == null)
1329 // The original view is closed, we must validate
1330 // the current view against the closed view first
1333 PaintRefresher.validateSequences(al, viewport.alignment);
1336 originalSource = viewport;
1339 return originalSource;
1348 public void moveSelectedSequences(boolean up)
1350 SequenceGroup sg = viewport.getSelectionGroup();
1359 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1361 SequenceI seq = viewport.alignment.getSequenceAt(i);
1363 if (!sg.getSequences(null).contains(seq))
1368 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1370 if (sg.getSequences(null).contains(temp))
1375 viewport.alignment.getSequences().setElementAt(temp, i);
1376 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1381 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1383 SequenceI seq = viewport.alignment.getSequenceAt(i);
1385 if (!sg.getSequences(null).contains(seq))
1390 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1392 if (sg.getSequences(null).contains(temp))
1397 viewport.alignment.getSequences().setElementAt(temp, i);
1398 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1402 alignPanel.paintAlignment(true);
1405 synchronized void slideSequences(boolean right, int size)
1407 Vector sg = new Vector();
1408 if (viewport.cursorMode)
1410 sg.addElement(viewport.alignment
1411 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1413 else if (viewport.getSelectionGroup() != null
1414 && viewport.getSelectionGroup().getSize() != viewport.alignment
1417 sg = viewport.getSelectionGroup().getSequences(
1418 viewport.hiddenRepSequences);
1426 Vector invertGroup = new Vector();
1428 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1430 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
1431 invertGroup.add(viewport.alignment.getSequenceAt(i));
1434 SequenceI[] seqs1 = new SequenceI[sg.size()];
1435 for (int i = 0; i < sg.size(); i++)
1436 seqs1[i] = (SequenceI) sg.elementAt(i);
1438 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1439 for (int i = 0; i < invertGroup.size(); i++)
1440 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1442 SlideSequencesCommand ssc;
1444 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1445 size, viewport.getGapCharacter());
1447 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1448 size, viewport.getGapCharacter());
1450 int groupAdjustment = 0;
1451 if (ssc.getGapsInsertedBegin() && right)
1453 if (viewport.cursorMode)
1454 alignPanel.seqPanel.moveCursor(size, 0);
1456 groupAdjustment = size;
1458 else if (!ssc.getGapsInsertedBegin() && !right)
1460 if (viewport.cursorMode)
1461 alignPanel.seqPanel.moveCursor(-size, 0);
1463 groupAdjustment = -size;
1466 if (groupAdjustment != 0)
1468 viewport.getSelectionGroup().setStartRes(
1469 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1470 viewport.getSelectionGroup().setEndRes(
1471 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1474 boolean appendHistoryItem = false;
1475 if (viewport.historyList != null && viewport.historyList.size() > 0
1476 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1478 appendHistoryItem = ssc
1479 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1483 if (!appendHistoryItem)
1484 addHistoryItem(ssc);
1495 protected void copy_actionPerformed(ActionEvent e)
1498 if (viewport.getSelectionGroup() == null)
1502 // TODO: preserve the ordering of displayed alignment annotation in any
1503 // internal paste (particularly sequence associated annotation)
1504 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1505 String[] omitHidden = null;
1507 if (viewport.hasHiddenColumns)
1509 omitHidden = viewport.getViewAsString(true);
1512 String output = new FormatAdapter().formatSequences("Fasta", seqs,
1515 StringSelection ss = new StringSelection(output);
1519 jalview.gui.Desktop.internalCopy = true;
1520 // Its really worth setting the clipboard contents
1521 // to empty before setting the large StringSelection!!
1522 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
1523 new StringSelection(""), null);
1525 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1527 } catch (OutOfMemoryError er)
1529 new OOMWarning("copying region", er);
1533 Vector hiddenColumns = null;
1534 if (viewport.hasHiddenColumns)
1536 hiddenColumns = new Vector();
1537 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1538 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1541 int[] region = (int[]) viewport.getColumnSelection()
1542 .getHiddenColumns().elementAt(i);
1544 hiddenColumns.addElement(new int[]
1545 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1549 Desktop.jalviewClipboard = new Object[]
1550 { seqs, viewport.alignment.getDataset(), hiddenColumns };
1551 statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
1560 protected void pasteNew_actionPerformed(ActionEvent e)
1571 protected void pasteThis_actionPerformed(ActionEvent e)
1577 * Paste contents of Jalview clipboard
1579 * @param newAlignment
1580 * true to paste to a new alignment, otherwise add to this.
1582 void paste(boolean newAlignment)
1584 boolean externalPaste = true;
1587 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1588 Transferable contents = c.getContents(this);
1590 if (contents == null)
1598 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1599 if (str.length() < 1)
1604 format = new IdentifyFile().Identify(str, "Paste");
1606 } catch (OutOfMemoryError er)
1608 new OOMWarning("Out of memory pasting sequences!!", er);
1612 SequenceI[] sequences;
1613 boolean annotationAdded = false;
1614 AlignmentI alignment = null;
1616 if (Desktop.jalviewClipboard != null)
1618 // The clipboard was filled from within Jalview, we must use the
1620 // And dataset from the copied alignment
1621 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1622 // be doubly sure that we create *new* sequence objects.
1623 sequences = new SequenceI[newseq.length];
1624 for (int i = 0; i < newseq.length; i++)
1626 sequences[i] = new Sequence(newseq[i]);
1628 alignment = new Alignment(sequences);
1629 externalPaste = false;
1633 // parse the clipboard as an alignment.
1634 alignment = new FormatAdapter().readFile(str, "Paste", format);
1635 sequences = alignment.getSequencesArray();
1643 if (Desktop.jalviewClipboard != null)
1645 // dataset is inherited
1646 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1650 // new dataset is constructed
1651 alignment.setDataset(null);
1653 alwidth = alignment.getWidth() + 1;
1657 AlignmentI pastedal = alignment; // preserve pasted alignment object
1658 // Add pasted sequences and dataset into existing alignment.
1659 alignment = viewport.getAlignment();
1660 alwidth = alignment.getWidth() + 1;
1661 // decide if we need to import sequences from an existing dataset
1662 boolean importDs = Desktop.jalviewClipboard != null
1663 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1664 // importDs==true instructs us to copy over new dataset sequences from
1665 // an existing alignment
1666 Vector newDs = (importDs) ? new Vector() : null; // used to create
1667 // minimum dataset set
1669 for (int i = 0; i < sequences.length; i++)
1673 newDs.addElement(null);
1675 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1677 if (importDs && ds != null)
1679 if (!newDs.contains(ds))
1681 newDs.setElementAt(ds, i);
1682 ds = new Sequence(ds);
1683 // update with new dataset sequence
1684 sequences[i].setDatasetSequence(ds);
1688 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1693 // copy and derive new dataset sequence
1694 sequences[i] = sequences[i].deriveSequence();
1695 alignment.getDataset().addSequence(
1696 sequences[i].getDatasetSequence());
1697 // TODO: avoid creation of duplicate dataset sequences with a
1698 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1700 alignment.addSequence(sequences[i]); // merges dataset
1704 newDs.clear(); // tidy up
1706 if (pastedal.getAlignmentAnnotation() != null)
1708 // Add any annotation attached to alignment.
1709 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1710 for (int i = 0; i < alann.length; i++)
1712 annotationAdded = true;
1713 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1715 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1716 newann.padAnnotation(alwidth);
1717 alignment.addAnnotation(newann);
1727 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1728 sequences, 0, alignment.getWidth(), alignment));
1730 // Add any annotations attached to sequences
1731 for (int i = 0; i < sequences.length; i++)
1733 if (sequences[i].getAnnotation() != null)
1735 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1737 annotationAdded = true;
1738 sequences[i].getAnnotation()[a].adjustForAlignment();
1739 sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1740 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1745 .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1752 // propagate alignment changed.
1753 viewport.setEndSeq(alignment.getHeight());
1754 if (annotationAdded)
1756 // Duplicate sequence annotation in all views.
1757 AlignmentI[] alview = this.getViewAlignments();
1758 for (int i = 0; i < sequences.length; i++)
1760 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1763 for (int avnum = 0; avnum < alview.length; avnum++)
1765 if (alview[avnum] != alignment)
1767 // duplicate in a view other than the one with input focus
1768 int avwidth = alview[avnum].getWidth() + 1;
1769 // this relies on sann being preserved after we
1770 // modify the sequence's annotation array for each duplication
1771 for (int a = 0; a < sann.length; a++)
1773 AlignmentAnnotation newann = new AlignmentAnnotation(
1775 sequences[i].addAlignmentAnnotation(newann);
1776 newann.padAnnotation(avwidth);
1777 alview[avnum].addAnnotation(newann); // annotation was
1778 // duplicated earlier
1779 alview[avnum].setAnnotationIndex(newann, a);
1784 buildSortByAnnotationScoresMenu();
1786 viewport.firePropertyChange("alignment", null, alignment
1792 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
1794 String newtitle = new String("Copied sequences");
1796 if (Desktop.jalviewClipboard != null
1797 && Desktop.jalviewClipboard[2] != null)
1799 Vector hc = (Vector) Desktop.jalviewClipboard[2];
1800 for (int i = 0; i < hc.size(); i++)
1802 int[] region = (int[]) hc.elementAt(i);
1803 af.viewport.hideColumns(region[0], region[1]);
1807 // >>>This is a fix for the moment, until a better solution is
1809 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
1811 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1813 // TODO: maintain provenance of an alignment, rather than just make the
1814 // title a concatenation of operations.
1817 if (title.startsWith("Copied sequences"))
1823 newtitle = newtitle.concat("- from " + title);
1828 newtitle = new String("Pasted sequences");
1831 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1836 } catch (Exception ex)
1838 ex.printStackTrace();
1839 System.out.println("Exception whilst pasting: " + ex);
1840 // could be anything being pasted in here
1851 protected void cut_actionPerformed(ActionEvent e)
1853 copy_actionPerformed(null);
1854 delete_actionPerformed(null);
1863 protected void delete_actionPerformed(ActionEvent evt)
1866 SequenceGroup sg = viewport.getSelectionGroup();
1872 Vector seqs = new Vector();
1874 for (int i = 0; i < sg.getSize(); i++)
1876 seq = sg.getSequenceAt(i);
1877 seqs.addElement(seq);
1880 // If the cut affects all sequences, remove highlighted columns
1881 if (sg.getSize() == viewport.alignment.getHeight())
1883 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1884 sg.getEndRes() + 1);
1887 SequenceI[] cut = new SequenceI[seqs.size()];
1888 for (int i = 0; i < seqs.size(); i++)
1890 cut[i] = (SequenceI) seqs.elementAt(i);
1894 * //ADD HISTORY ITEM
1896 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1897 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1898 viewport.alignment));
1900 viewport.setSelectionGroup(null);
1901 viewport.sendSelection();
1902 viewport.alignment.deleteGroup(sg);
1904 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1906 if (viewport.getAlignment().getHeight() < 1)
1910 this.setClosed(true);
1911 } catch (Exception ex)
1923 protected void deleteGroups_actionPerformed(ActionEvent e)
1925 viewport.alignment.deleteAllGroups();
1926 viewport.sequenceColours = null;
1927 viewport.setSelectionGroup(null);
1928 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1929 alignPanel.updateAnnotation();
1930 alignPanel.paintAlignment(true);
1939 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1941 SequenceGroup sg = new SequenceGroup();
1943 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1945 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1948 sg.setEndRes(viewport.alignment.getWidth() - 1);
1949 viewport.setSelectionGroup(sg);
1950 viewport.sendSelection();
1951 alignPanel.paintAlignment(true);
1952 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1961 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1963 if (viewport.cursorMode)
1965 alignPanel.seqPanel.keyboardNo1 = null;
1966 alignPanel.seqPanel.keyboardNo2 = null;
1968 viewport.setSelectionGroup(null);
1969 viewport.getColumnSelection().clear();
1970 viewport.setSelectionGroup(null);
1971 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1972 alignPanel.idPanel.idCanvas.searchResults = null;
1973 alignPanel.paintAlignment(true);
1974 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1983 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1985 SequenceGroup sg = viewport.getSelectionGroup();
1989 selectAllSequenceMenuItem_actionPerformed(null);
1994 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1996 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1999 alignPanel.paintAlignment(true);
2000 viewport.sendSelection();
2001 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2004 public void invertColSel_actionPerformed(ActionEvent e)
2006 viewport.invertColumnSelection();
2007 alignPanel.paintAlignment(true);
2016 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2018 trimAlignment(true);
2027 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2029 trimAlignment(false);
2032 void trimAlignment(boolean trimLeft)
2034 ColumnSelection colSel = viewport.getColumnSelection();
2037 if (colSel.size() > 0)
2041 column = colSel.getMin();
2045 column = colSel.getMax();
2049 if (viewport.getSelectionGroup() != null)
2051 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2052 viewport.hiddenRepSequences);
2056 seqs = viewport.alignment.getSequencesArray();
2059 TrimRegionCommand trimRegion;
2062 trimRegion = new TrimRegionCommand("Remove Left",
2063 TrimRegionCommand.TRIM_LEFT, seqs, column,
2064 viewport.alignment, viewport.colSel,
2065 viewport.selectionGroup);
2066 viewport.setStartRes(0);
2070 trimRegion = new TrimRegionCommand("Remove Right",
2071 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2072 viewport.alignment, viewport.colSel,
2073 viewport.selectionGroup);
2076 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2078 addHistoryItem(trimRegion);
2080 Vector groups = viewport.alignment.getGroups();
2082 for (int i = 0; i < groups.size(); i++)
2084 SequenceGroup sg = (SequenceGroup) groups.get(i);
2086 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2087 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2089 viewport.alignment.deleteGroup(sg);
2093 viewport.firePropertyChange("alignment", null, viewport
2094 .getAlignment().getSequences());
2104 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2106 int start = 0, end = viewport.alignment.getWidth() - 1;
2109 if (viewport.getSelectionGroup() != null)
2111 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2112 viewport.hiddenRepSequences);
2113 start = viewport.getSelectionGroup().getStartRes();
2114 end = viewport.getSelectionGroup().getEndRes();
2118 seqs = viewport.alignment.getSequencesArray();
2121 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2122 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
2124 addHistoryItem(removeGapCols);
2126 statusBar.setText("Removed " + removeGapCols.getSize()
2127 + " empty columns.");
2129 // This is to maintain viewport position on first residue
2130 // of first sequence
2131 SequenceI seq = viewport.alignment.getSequenceAt(0);
2132 int startRes = seq.findPosition(viewport.startRes);
2133 // ShiftList shifts;
2134 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2135 // edit.alColumnChanges=shifts.getInverse();
2136 // if (viewport.hasHiddenColumns)
2137 // viewport.getColumnSelection().compensateForEdits(shifts);
2138 viewport.setStartRes(seq.findIndex(startRes) - 1);
2139 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2150 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2152 int start = 0, end = viewport.alignment.getWidth() - 1;
2155 if (viewport.getSelectionGroup() != null)
2157 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2158 viewport.hiddenRepSequences);
2159 start = viewport.getSelectionGroup().getStartRes();
2160 end = viewport.getSelectionGroup().getEndRes();
2164 seqs = viewport.alignment.getSequencesArray();
2167 // This is to maintain viewport position on first residue
2168 // of first sequence
2169 SequenceI seq = viewport.alignment.getSequenceAt(0);
2170 int startRes = seq.findPosition(viewport.startRes);
2172 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2173 viewport.alignment));
2175 viewport.setStartRes(seq.findIndex(startRes) - 1);
2177 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2188 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2190 viewport.padGaps = padGapsMenuitem.isSelected();
2191 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2197 // if (justifySeqs>0)
2199 // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2211 public void findMenuItem_actionPerformed(ActionEvent e)
2216 public void newView_actionPerformed(ActionEvent e)
2218 AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2221 newap.av.gatherViewsHere = false;
2223 if (viewport.viewName == null)
2225 viewport.viewName = "Original";
2228 newap.av.historyList = viewport.historyList;
2229 newap.av.redoList = viewport.redoList;
2231 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2232 String newViewName = "View " + index;
2234 Vector comps = (Vector) PaintRefresher.components.get(viewport
2235 .getSequenceSetId());
2236 Vector existingNames = new Vector();
2237 for (int i = 0; i < comps.size(); i++)
2239 if (comps.elementAt(i) instanceof AlignmentPanel)
2241 AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2242 if (!existingNames.contains(ap.av.viewName))
2244 existingNames.addElement(ap.av.viewName);
2249 while (existingNames.contains(newViewName))
2251 newViewName = "View " + (++index);
2254 newap.av.viewName = newViewName;
2256 addAlignmentPanel(newap, true);
2258 if (alignPanels.size() == 2)
2260 viewport.gatherViewsHere = true;
2262 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2265 public void expandViews_actionPerformed(ActionEvent e)
2267 Desktop.instance.explodeViews(this);
2270 public void gatherViews_actionPerformed(ActionEvent e)
2272 Desktop.instance.gatherViews(this);
2281 public void font_actionPerformed(ActionEvent e)
2283 new FontChooser(alignPanel);
2292 protected void seqLimit_actionPerformed(ActionEvent e)
2294 viewport.setShowJVSuffix(seqLimits.isSelected());
2296 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2297 .calculateIdWidth());
2298 alignPanel.paintAlignment(true);
2301 public void idRightAlign_actionPerformed(ActionEvent e)
2303 viewport.rightAlignIds = idRightAlign.isSelected();
2304 alignPanel.paintAlignment(true);
2307 public void centreColumnLabels_actionPerformed(ActionEvent e)
2309 viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2310 alignPanel.paintAlignment(true);
2316 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2318 protected void followHighlight_actionPerformed()
2320 if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2322 alignPanel.scrollToPosition(
2323 alignPanel.seqPanel.seqCanvas.searchResults, false);
2333 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2335 viewport.setColourText(colourTextMenuItem.isSelected());
2336 alignPanel.paintAlignment(true);
2345 public void wrapMenuItem_actionPerformed(ActionEvent e)
2347 scaleAbove.setVisible(wrapMenuItem.isSelected());
2348 scaleLeft.setVisible(wrapMenuItem.isSelected());
2349 scaleRight.setVisible(wrapMenuItem.isSelected());
2350 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2351 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2354 public void showAllSeqs_actionPerformed(ActionEvent e)
2356 viewport.showAllHiddenSeqs();
2359 public void showAllColumns_actionPerformed(ActionEvent e)
2361 viewport.showAllHiddenColumns();
2365 public void hideSelSequences_actionPerformed(ActionEvent e)
2367 viewport.hideAllSelectedSeqs();
2368 alignPanel.paintAlignment(true);
2371 public void hideSelColumns_actionPerformed(ActionEvent e)
2373 viewport.hideSelectedColumns();
2374 alignPanel.paintAlignment(true);
2377 public void hiddenMarkers_actionPerformed(ActionEvent e)
2379 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2389 protected void scaleAbove_actionPerformed(ActionEvent e)
2391 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2392 alignPanel.paintAlignment(true);
2401 protected void scaleLeft_actionPerformed(ActionEvent e)
2403 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2404 alignPanel.paintAlignment(true);
2413 protected void scaleRight_actionPerformed(ActionEvent e)
2415 viewport.setScaleRightWrapped(scaleRight.isSelected());
2416 alignPanel.paintAlignment(true);
2425 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2427 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2428 alignPanel.paintAlignment(true);
2437 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2439 viewport.setShowText(viewTextMenuItem.isSelected());
2440 alignPanel.paintAlignment(true);
2449 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2451 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2452 alignPanel.paintAlignment(true);
2455 public FeatureSettings featureSettings;
2457 public void featureSettings_actionPerformed(ActionEvent e)
2459 if (featureSettings != null)
2461 featureSettings.close();
2462 featureSettings = null;
2464 featureSettings = new FeatureSettings(this);
2468 * Set or clear 'Show Sequence Features'
2473 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2475 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2476 alignPanel.paintAlignment(true);
2477 if (alignPanel.getOverviewPanel() != null)
2479 alignPanel.getOverviewPanel().updateOverviewImage();
2484 * Set or clear 'Show Sequence Features'
2489 public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2491 viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2493 if (viewport.getShowSequenceFeaturesHeight())
2495 // ensure we're actually displaying features
2496 viewport.setShowSequenceFeatures(true);
2497 showSeqFeatures.setSelected(true);
2499 alignPanel.paintAlignment(true);
2500 if (alignPanel.getOverviewPanel() != null)
2502 alignPanel.getOverviewPanel().updateOverviewImage();
2512 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2514 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2515 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2518 public void alignmentProperties()
2520 JEditorPane editPane = new JEditorPane("text/html", "");
2521 editPane.setEditable(false);
2522 StringBuffer contents = new StringBuffer("<html>");
2525 int min = Integer.MAX_VALUE, max = 0;
2526 for (int i = 0; i < viewport.alignment.getHeight(); i++)
2528 int size = viewport.alignment.getSequenceAt(i).getEnd()
2529 - viewport.alignment.getSequenceAt(i).getStart();
2536 avg = avg / (float) viewport.alignment.getHeight();
2538 contents.append("<br>Sequences: " + viewport.alignment.getHeight());
2539 contents.append("<br>Minimum Sequence Length: " + min);
2540 contents.append("<br>Maximum Sequence Length: " + max);
2541 contents.append("<br>Average Length: " + (int) avg);
2543 if (((Alignment) viewport.alignment).getProperties() != null)
2545 Hashtable props = ((Alignment) viewport.alignment).getProperties();
2546 Enumeration en = props.keys();
2547 contents.append("<br><br><table border=\"1\">");
2548 while (en.hasMoreElements())
2550 String key = en.nextElement().toString();
2551 StringBuffer val = new StringBuffer();
2552 String vals = props.get(key).toString();
2556 npos = vals.indexOf("\n", pos);
2559 val.append(vals.substring(pos));
2563 val.append(vals.substring(pos, npos));
2567 } while (npos != -1);
2569 .append("<tr><td>" + key + "</td><td>" + val + "</td></tr>");
2571 contents.append("</table>");
2573 editPane.setText(contents.toString() + "</html>");
2574 JInternalFrame frame = new JInternalFrame();
2575 frame.getContentPane().add(new JScrollPane(editPane));
2577 Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
2578 + getTitle(), 500, 400);
2587 public void overviewMenuItem_actionPerformed(ActionEvent e)
2589 if (alignPanel.overviewPanel != null)
2594 JInternalFrame frame = new JInternalFrame();
2595 OverviewPanel overview = new OverviewPanel(alignPanel);
2596 frame.setContentPane(overview);
2597 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(), frame
2598 .getWidth(), frame.getHeight());
2600 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2602 .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2604 public void internalFrameClosed(
2605 javax.swing.event.InternalFrameEvent evt)
2607 alignPanel.setOverviewPanel(null);
2611 alignPanel.setOverviewPanel(overview);
2614 public void textColour_actionPerformed(ActionEvent e)
2616 new TextColourChooser().chooseColour(alignPanel, null);
2625 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2636 public void clustalColour_actionPerformed(ActionEvent e)
2638 changeColour(new ClustalxColourScheme(
2639 viewport.alignment.getSequences(), viewport.alignment
2649 public void zappoColour_actionPerformed(ActionEvent e)
2651 changeColour(new ZappoColourScheme());
2660 public void taylorColour_actionPerformed(ActionEvent e)
2662 changeColour(new TaylorColourScheme());
2671 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2673 changeColour(new HydrophobicColourScheme());
2682 public void helixColour_actionPerformed(ActionEvent e)
2684 changeColour(new HelixColourScheme());
2693 public void strandColour_actionPerformed(ActionEvent e)
2695 changeColour(new StrandColourScheme());
2704 public void turnColour_actionPerformed(ActionEvent e)
2706 changeColour(new TurnColourScheme());
2715 public void buriedColour_actionPerformed(ActionEvent e)
2717 changeColour(new BuriedColourScheme());
2726 public void nucleotideColour_actionPerformed(ActionEvent e)
2728 changeColour(new NucleotideColourScheme());
2731 public void annotationColour_actionPerformed(ActionEvent e)
2733 new AnnotationColourChooser(viewport, alignPanel);
2742 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2744 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2753 public void changeColour(ColourSchemeI cs)
2759 if (viewport.getAbovePIDThreshold())
2761 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2764 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2766 viewport.setGlobalColourScheme(cs);
2770 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2773 if (viewport.getConservationSelected())
2776 Alignment al = (Alignment) viewport.alignment;
2777 Conservation c = new Conservation("All",
2778 ResidueProperties.propHash, 3, al.getSequences(), 0, al
2782 c.verdict(false, viewport.ConsPercGaps);
2784 cs.setConservation(c);
2786 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
2791 cs.setConservation(null);
2794 cs.setConsensus(viewport.hconsensus);
2797 viewport.setGlobalColourScheme(cs);
2799 if (viewport.getColourAppliesToAllGroups())
2801 Vector groups = viewport.alignment.getGroups();
2803 for (int i = 0; i < groups.size(); i++)
2805 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2813 if (cs instanceof ClustalxColourScheme)
2815 sg.cs = new ClustalxColourScheme(sg
2816 .getSequences(viewport.hiddenRepSequences), sg.getWidth());
2818 else if (cs instanceof UserColourScheme)
2820 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
2826 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2827 } catch (Exception ex)
2832 if (viewport.getAbovePIDThreshold()
2833 || cs instanceof PIDColourScheme
2834 || cs instanceof Blosum62ColourScheme)
2836 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2838 sg.cs.setConsensus(AAFrequency.calculate(sg
2839 .getSequences(viewport.hiddenRepSequences), sg
2840 .getStartRes(), sg.getEndRes() + 1));
2844 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2847 if (viewport.getConservationSelected())
2849 Conservation c = new Conservation("Group",
2850 ResidueProperties.propHash, 3, sg
2851 .getSequences(viewport.hiddenRepSequences), sg
2852 .getStartRes(), sg.getEndRes() + 1);
2854 c.verdict(false, viewport.ConsPercGaps);
2855 sg.cs.setConservation(c);
2859 sg.cs.setConservation(null);
2864 if (alignPanel.getOverviewPanel() != null)
2866 alignPanel.getOverviewPanel().updateOverviewImage();
2869 alignPanel.paintAlignment(true);
2878 protected void modifyPID_actionPerformed(ActionEvent e)
2880 if (viewport.getAbovePIDThreshold()
2881 && viewport.globalColourScheme != null)
2883 SliderPanel.setPIDSliderSource(alignPanel, viewport
2884 .getGlobalColourScheme(), "Background");
2885 SliderPanel.showPIDSlider();
2895 protected void modifyConservation_actionPerformed(ActionEvent e)
2897 if (viewport.getConservationSelected()
2898 && viewport.globalColourScheme != null)
2900 SliderPanel.setConservationSlider(alignPanel,
2901 viewport.globalColourScheme, "Background");
2902 SliderPanel.showConservationSlider();
2912 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2914 viewport.setConservationSelected(conservationMenuItem.isSelected());
2916 viewport.setAbovePIDThreshold(false);
2917 abovePIDThreshold.setSelected(false);
2919 changeColour(viewport.getGlobalColourScheme());
2921 modifyConservation_actionPerformed(null);
2930 public void abovePIDThreshold_actionPerformed(ActionEvent e)
2932 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
2934 conservationMenuItem.setSelected(false);
2935 viewport.setConservationSelected(false);
2937 changeColour(viewport.getGlobalColourScheme());
2939 modifyPID_actionPerformed(null);
2948 public void userDefinedColour_actionPerformed(ActionEvent e)
2950 if (e.getActionCommand().equals("User Defined..."))
2952 new UserDefinedColours(alignPanel, null);
2956 UserColourScheme udc = (UserColourScheme) UserDefinedColours
2957 .getUserColourSchemes().get(e.getActionCommand());
2963 public void updateUserColourMenu()
2966 Component[] menuItems = colourMenu.getMenuComponents();
2967 int i, iSize = menuItems.length;
2968 for (i = 0; i < iSize; i++)
2970 if (menuItems[i].getName() != null
2971 && menuItems[i].getName().equals("USER_DEFINED"))
2973 colourMenu.remove(menuItems[i]);
2977 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
2979 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
2980 .getUserColourSchemes().keys();
2982 while (userColours.hasMoreElements())
2984 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
2985 userColours.nextElement().toString());
2986 radioItem.setName("USER_DEFINED");
2987 radioItem.addMouseListener(new MouseAdapter()
2989 public void mousePressed(MouseEvent evt)
2991 if (evt.isControlDown()
2992 || SwingUtilities.isRightMouseButton(evt))
2995 .removeActionListener(radioItem.getActionListeners()[0]);
2997 int option = JOptionPane.showInternalConfirmDialog(
2998 jalview.gui.Desktop.desktop,
2999 "Remove from default list?",
3000 "Remove user defined colour",
3001 JOptionPane.YES_NO_OPTION);
3002 if (option == JOptionPane.YES_OPTION)
3004 jalview.gui.UserDefinedColours
3005 .removeColourFromDefaults(radioItem.getText());
3006 colourMenu.remove(radioItem);
3010 radioItem.addActionListener(new ActionListener()
3012 public void actionPerformed(ActionEvent evt)
3014 userDefinedColour_actionPerformed(evt);
3021 radioItem.addActionListener(new ActionListener()
3023 public void actionPerformed(ActionEvent evt)
3025 userDefinedColour_actionPerformed(evt);
3029 colourMenu.insert(radioItem, 15);
3030 colours.add(radioItem);
3041 public void PIDColour_actionPerformed(ActionEvent e)
3043 changeColour(new PIDColourScheme());
3052 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3054 changeColour(new Blosum62ColourScheme());
3063 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3065 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3066 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3067 .getAlignment().getSequenceAt(0), null);
3068 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3069 viewport.alignment));
3070 alignPanel.paintAlignment(true);
3079 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3081 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3082 AlignmentSorter.sortByID(viewport.getAlignment());
3083 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
3084 alignPanel.paintAlignment(true);
3093 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3095 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3096 AlignmentSorter.sortByLength(viewport.getAlignment());
3097 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3098 viewport.alignment));
3099 alignPanel.paintAlignment(true);
3108 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3110 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3111 AlignmentSorter.sortByGroup(viewport.getAlignment());
3112 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3113 viewport.alignment));
3115 alignPanel.paintAlignment(true);
3124 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3126 new RedundancyPanel(alignPanel, this);
3135 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3137 if ((viewport.getSelectionGroup() == null)
3138 || (viewport.getSelectionGroup().getSize() < 2))
3140 JOptionPane.showInternalMessageDialog(this,
3141 "You must select at least 2 sequences.", "Invalid Selection",
3142 JOptionPane.WARNING_MESSAGE);
3146 JInternalFrame frame = new JInternalFrame();
3147 frame.setContentPane(new PairwiseAlignPanel(viewport));
3148 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
3158 public void PCAMenuItem_actionPerformed(ActionEvent e)
3160 if (((viewport.getSelectionGroup() != null)
3161 && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3162 .getSelectionGroup().getSize() > 0))
3163 || (viewport.getAlignment().getHeight() < 4))
3165 JOptionPane.showInternalMessageDialog(this,
3166 "Principal component analysis must take\n"
3167 + "at least 4 input sequences.",
3168 "Sequence selection insufficient",
3169 JOptionPane.WARNING_MESSAGE);
3174 new PCAPanel(alignPanel);
3177 public void autoCalculate_actionPerformed(ActionEvent e)
3179 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3180 if (viewport.autoCalculateConsensus)
3182 viewport.firePropertyChange("alignment", null, viewport
3183 .getAlignment().getSequences());
3193 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3195 NewTreePanel("AV", "PID", "Average distance tree using PID");
3204 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3206 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3215 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3217 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3226 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3228 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3241 void NewTreePanel(String type, String pwType, String title)
3245 if (viewport.getSelectionGroup() != null)
3247 if (viewport.getSelectionGroup().getSize() < 3)
3252 "You need to have more than two sequences selected to build a tree!",
3253 "Not enough sequences", JOptionPane.WARNING_MESSAGE);
3258 SequenceGroup sg = viewport.getSelectionGroup();
3260 /* Decide if the selection is a column region */
3261 while (s < sg.getSize())
3263 if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
3269 "The selected region to create a tree may\nonly contain residues or gaps.\n"
3270 + "Try using the Pad function in the edit menu,\n"
3271 + "or one of the multiple sequence alignment web services.",
3272 "Sequences in selection are not aligned",
3273 JOptionPane.WARNING_MESSAGE);
3279 title = title + " on region";
3280 tp = new TreePanel(alignPanel, type, pwType);
3284 // are the sequences aligned?
3285 if (!viewport.alignment.isAligned())
3290 "The sequences must be aligned before creating a tree.\n"
3291 + "Try using the Pad function in the edit menu,\n"
3292 + "or one of the multiple sequence alignment web services.",
3293 "Sequences not aligned",
3294 JOptionPane.WARNING_MESSAGE);
3299 if (viewport.alignment.getHeight() < 2)
3304 tp = new TreePanel(alignPanel, type, pwType);
3309 if (viewport.viewName != null)
3311 title += viewport.viewName + " of ";
3314 title += this.title;
3316 Desktop.addInternalFrame(tp, title, 600, 500);
3327 public void addSortByOrderMenuItem(String title,
3328 final AlignmentOrder order)
3330 final JMenuItem item = new JMenuItem("by " + title);
3332 item.addActionListener(new java.awt.event.ActionListener()
3334 public void actionPerformed(ActionEvent e)
3336 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3338 // TODO: JBPNote - have to map order entries to curent SequenceI
3340 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3342 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3343 viewport.alignment));
3345 alignPanel.paintAlignment(true);
3351 * Add a new sort by annotation score menu item
3354 * the menu to add the option to
3356 * the label used to retrieve scores for each sequence on the
3359 public void addSortByAnnotScoreMenuItem(JMenu sort,
3360 final String scoreLabel)
3362 final JMenuItem item = new JMenuItem(scoreLabel);
3364 item.addActionListener(new java.awt.event.ActionListener()
3366 public void actionPerformed(ActionEvent e)
3368 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3369 AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport
3370 .getAlignment());// ,viewport.getSelectionGroup());
3371 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3372 viewport.alignment));
3373 alignPanel.paintAlignment(true);
3379 * last hash for alignment's annotation array - used to minimise cost of
3382 protected int _annotationScoreVectorHash;
3385 * search the alignment and rebuild the sort by annotation score submenu the
3386 * last alignment annotation vector hash is stored to minimize cost of
3387 * rebuilding in subsequence calls.
3390 public void buildSortByAnnotationScoresMenu()
3392 if (viewport.alignment.getAlignmentAnnotation() == null)
3397 if (viewport.alignment.getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3399 sortByAnnotScore.removeAll();
3400 // almost certainly a quicker way to do this - but we keep it simple
3401 Hashtable scoreSorts = new Hashtable();
3402 AlignmentAnnotation aann[];
3403 Enumeration sq = viewport.alignment.getSequences().elements();
3404 while (sq.hasMoreElements())
3406 aann = ((SequenceI) sq.nextElement()).getAnnotation();
3407 for (int i = 0; aann != null && i < aann.length; i++)
3409 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3411 scoreSorts.put(aann[i].label, aann[i].label);
3415 Enumeration labels = scoreSorts.keys();
3416 while (labels.hasMoreElements())
3418 addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels
3421 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3424 _annotationScoreVectorHash = viewport.alignment
3425 .getAlignmentAnnotation().hashCode();
3430 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3431 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3432 * call. Listeners are added to remove the menu item when the treePanel is
3433 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3437 * Displayed tree window.
3439 * SortBy menu item title.
3441 public void buildTreeMenu()
3443 sortByTreeMenu.removeAll();
3445 Vector comps = (Vector) PaintRefresher.components.get(viewport
3446 .getSequenceSetId());
3447 Vector treePanels = new Vector();
3448 int i, iSize = comps.size();
3449 for (i = 0; i < iSize; i++)
3451 if (comps.elementAt(i) instanceof TreePanel)
3453 treePanels.add(comps.elementAt(i));
3457 iSize = treePanels.size();
3461 sortByTreeMenu.setVisible(false);
3465 sortByTreeMenu.setVisible(true);
3467 for (i = 0; i < treePanels.size(); i++)
3469 TreePanel tp = (TreePanel) treePanels.elementAt(i);
3470 final JMenuItem item = new JMenuItem(tp.getTitle());
3471 final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3472 item.addActionListener(new java.awt.event.ActionListener()
3474 public void actionPerformed(ActionEvent e)
3476 SequenceI[] oldOrder = viewport.getAlignment()
3477 .getSequencesArray();
3478 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
3480 addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
3481 viewport.alignment));
3483 alignPanel.paintAlignment(true);
3487 sortByTreeMenu.add(item);
3492 * Work out whether the whole set of sequences or just the selected set will
3493 * be submitted for multiple alignment.
3496 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3498 // Now, check we have enough sequences
3499 AlignmentView msa = null;
3501 if ((viewport.getSelectionGroup() != null)
3502 && (viewport.getSelectionGroup().getSize() > 1))
3504 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3505 // some common interface!
3507 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3508 * SequenceI[sz = seqs.getSize(false)];
3510 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3511 * seqs.getSequenceAt(i); }
3513 msa = viewport.getAlignmentView(true);
3518 * Vector seqs = viewport.getAlignment().getSequences();
3520 * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3522 * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3523 * seqs.elementAt(i); } }
3525 msa = viewport.getAlignmentView(false);
3531 * Decides what is submitted to a secondary structure prediction service: the
3532 * first sequence in the alignment, or in the current selection, or, if the
3533 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3534 * region or the whole alignment. (where the first sequence in the set is the
3535 * one that the prediction will be for).
3537 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3539 AlignmentView seqs = null;
3541 if ((viewport.getSelectionGroup() != null)
3542 && (viewport.getSelectionGroup().getSize() > 0))
3544 seqs = viewport.getAlignmentView(true);
3548 seqs = viewport.getAlignmentView(false);
3550 // limit sequences - JBPNote in future - could spawn multiple prediction
3552 // TODO: viewport.alignment.isAligned is a global state - the local
3553 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3554 if (!viewport.alignment.isAligned())
3556 seqs.setSequences(new SeqCigar[]
3557 { seqs.getSequences()[0] });
3568 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3570 // Pick the tree file
3571 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
3572 .getProperty("LAST_DIRECTORY"));
3573 chooser.setFileView(new JalviewFileView());
3574 chooser.setDialogTitle("Select a newick-like tree file");
3575 chooser.setToolTipText("Load a tree file");
3577 int value = chooser.showOpenDialog(null);
3579 if (value == JalviewFileChooser.APPROVE_OPTION)
3581 String choice = chooser.getSelectedFile().getPath();
3582 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3583 jalview.io.NewickFile fin = null;
3586 fin = new jalview.io.NewickFile(choice, "File");
3587 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3588 } catch (Exception ex)
3590 JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3591 "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
3592 ex.printStackTrace();
3594 if (fin != null && fin.hasWarningMessage())
3596 JOptionPane.showMessageDialog(Desktop.desktop, fin
3597 .getWarningMessage(), "Possible problem with tree file",
3598 JOptionPane.WARNING_MESSAGE);
3603 public TreePanel ShowNewickTree(NewickFile nf, String title)
3605 return ShowNewickTree(nf, title, 600, 500, 4, 5);
3608 public TreePanel ShowNewickTree(NewickFile nf, String title,
3609 AlignmentView input)
3611 return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
3614 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
3615 int h, int x, int y)
3617 return ShowNewickTree(nf, title, null, w, h, x, y);
3621 * Add a treeviewer for the tree extracted from a newick file object to the
3622 * current alignment view
3629 * Associated alignment input data (or null)
3638 * @return TreePanel handle
3640 public TreePanel ShowNewickTree(NewickFile nf, String title,
3641 AlignmentView input, int w, int h, int x, int y)
3643 TreePanel tp = null;
3649 if (nf.getTree() != null)
3651 tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
3657 tp.setLocation(x, y);
3660 Desktop.addInternalFrame(tp, title, w, h);
3662 } catch (Exception ex)
3664 ex.printStackTrace();
3671 * Generates menu items and listener event actions for web service clients
3674 public void BuildWebServiceMenu()
3676 // TODO: add support for context dependent disabling of services based on
3677 // alignment and current selection
3678 // TODO: add additional serviceHandle parameter to specify abstract handler
3679 // class independently of AbstractName
3680 // TODO: add in rediscovery GUI function to restart discoverer
3681 // TODO: group services by location as well as function and/or introduce
3682 // object broker mechanism.
3683 if ((Discoverer.services != null) && (Discoverer.services.size() > 0))
3685 // TODO: refactor to allow list of AbstractName/Handler bindings to be
3686 // stored or retrieved from elsewhere
3687 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
3688 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
3689 Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
3690 // TODO: move GUI generation code onto service implementation - so a
3691 // client instance attaches itself to the GUI with method call like
3692 // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
3694 Vector wsmenu = new Vector();
3695 final IProgressIndicator af = this;
3698 // Add any Multiple Sequence Alignment Services
3699 final JMenu msawsmenu = new JMenu("Alignment");
3700 for (int i = 0, j = msaws.size(); i < j; i++)
3702 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
3704 jalview.ws.WSClient impl = jalview.ws.Discoverer
3705 .getServiceClient(sh);
3706 impl.attachWSMenuEntry(msawsmenu, this);
3709 wsmenu.add(msawsmenu);
3711 if (secstrpr != null)
3713 // Add any secondary structure prediction services
3714 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
3715 for (int i = 0, j = secstrpr.size(); i < j; i++)
3717 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
3719 jalview.ws.WSClient impl = jalview.ws.Discoverer
3720 .getServiceClient(sh);
3721 impl.attachWSMenuEntry(secstrmenu, this);
3723 wsmenu.add(secstrmenu);
3725 if (seqsrch != null)
3727 // Add any sequence search services
3728 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
3729 for (int i = 0, j = seqsrch.size(); i < j; i++)
3731 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
3733 jalview.ws.WSClient impl = jalview.ws.Discoverer
3734 .getServiceClient(sh);
3735 impl.attachWSMenuEntry(seqsrchmenu, this);
3737 // finally, add the whole shebang onto the webservices menu
3738 wsmenu.add(seqsrchmenu);
3740 resetWebServiceMenu();
3741 for (int i = 0, j = wsmenu.size(); i < j; i++)
3743 webService.add((JMenu) wsmenu.get(i));
3748 resetWebServiceMenu();
3749 this.webService.add(this.webServiceNoServices);
3754 * empty the web service menu and add any ad-hoc functions not dynamically
3758 private void resetWebServiceMenu()
3760 webService.removeAll();
3761 build_fetchdbmenu(webService);
3765 * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
3766 * chooser = new JalviewFileChooser(jalview.bin.Cache.
3767 * getProperty("LAST_DIRECTORY"));
3769 * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
3770 * to Vamsas file"); chooser.setToolTipText("Export");
3772 * int value = chooser.showSaveDialog(this);
3774 * if (value == JalviewFileChooser.APPROVE_OPTION) {
3775 * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
3776 * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
3777 * chooser.getSelectedFile().getAbsolutePath(), this); } }
3780 * prototype of an automatically enabled/disabled analysis function
3783 protected void setShowProductsEnabled()
3785 SequenceI[] selection = viewport.getSequenceSelection();
3786 if (canShowProducts(selection, viewport.getSelectionGroup() != null,
3787 viewport.getAlignment().getDataset()))
3789 showProducts.setEnabled(true);
3794 showProducts.setEnabled(false);
3799 * search selection for sequence xRef products and build the show products
3804 * @return true if showProducts menu should be enabled.
3806 public boolean canShowProducts(SequenceI[] selection,
3807 boolean isRegionSelection, Alignment dataset)
3809 boolean showp = false;
3812 showProducts.removeAll();
3813 final boolean dna = viewport.getAlignment().isNucleotide();
3814 final Alignment ds = dataset;
3815 String[] ptypes = (selection == null || selection.length == 0) ? null
3816 : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
3818 // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
3819 // selection, dataset, true);
3820 final SequenceI[] sel = selection;
3821 for (int t = 0; ptypes != null && t < ptypes.length; t++)
3824 final boolean isRegSel = isRegionSelection;
3825 final AlignFrame af = this;
3826 final String source = ptypes[t];
3827 JMenuItem xtype = new JMenuItem(ptypes[t]);
3828 xtype.addActionListener(new ActionListener()
3831 public void actionPerformed(ActionEvent e)
3833 // TODO: new thread for this call with vis-delay
3834 af.showProductsFor(af.viewport.getSequenceSelection(), ds,
3835 isRegSel, dna, source);
3839 showProducts.add(xtype);
3841 showProducts.setVisible(showp);
3842 showProducts.setEnabled(showp);
3843 } catch (Exception e)
3845 jalview.bin.Cache.log
3847 "canTranslate threw an exception - please report to help@jalview.org",
3854 protected void showProductsFor(SequenceI[] sel, Alignment ds,
3855 boolean isRegSel, boolean dna, String source)
3857 final boolean fisRegSel = isRegSel;
3858 final boolean fdna = dna;
3859 final String fsrc = source;
3860 final AlignFrame ths = this;
3861 final SequenceI[] fsel = sel;
3862 Runnable foo = new Runnable()
3867 final long sttime = System.currentTimeMillis();
3868 ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
3871 Alignment ds = ths.getViewport().alignment.getDataset(); // update
3875 Alignment prods = CrossRef
3876 .findXrefSequences(fsel, fdna, fsrc, ds);
3879 SequenceI[] sprods = new SequenceI[prods.getHeight()];
3880 for (int s = 0; s < sprods.length; s++)
3882 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
3883 if (ds.getSequences() == null
3884 || !ds.getSequences().contains(
3885 sprods[s].getDatasetSequence()))
3886 ds.addSequence(sprods[s].getDatasetSequence());
3887 sprods[s].updatePDBIds();
3889 Alignment al = new Alignment(sprods);
3890 AlignedCodonFrame[] cf = prods.getCodonFrames();
3892 for (int s = 0; cf != null && s < cf.length; s++)
3894 al.addCodonFrame(cf[s]);
3897 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
3899 String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
3900 + " for " + ((fisRegSel) ? "selected region of " : "")
3902 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
3907 System.err.println("No Sequences generated for xRef type "
3910 } catch (Exception e)
3912 jalview.bin.Cache.log.error(
3913 "Exception when finding crossreferences", e);
3914 } catch (OutOfMemoryError e)
3916 new OOMWarning("whilst fetching crossreferences", e);
3919 jalview.bin.Cache.log.error("Error when finding crossreferences",
3922 ths.setProgressBar("Finished searching for sequences from " + fsrc,
3927 Thread frunner = new Thread(foo);
3931 public boolean canShowTranslationProducts(SequenceI[] selection,
3932 AlignmentI alignment)
3937 return (jalview.analysis.Dna.canTranslate(selection, viewport
3938 .getViewAsVisibleContigs(true)));
3939 } catch (Exception e)
3941 jalview.bin.Cache.log
3943 "canTranslate threw an exception - please report to help@jalview.org",
3949 public void showProducts_actionPerformed(ActionEvent e)
3951 // /////////////////////////////
3952 // Collect Data to be translated/transferred
3954 SequenceI[] selection = viewport.getSequenceSelection();
3955 AlignmentI al = null;
3958 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
3959 .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
3960 viewport.getAlignment().getDataset());
3961 } catch (Exception ex)
3964 jalview.bin.Cache.log.debug("Exception during translation.", ex);
3971 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
3972 "Translation Failed", JOptionPane.WARNING_MESSAGE);
3976 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
3977 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
3978 DEFAULT_WIDTH, DEFAULT_HEIGHT);
3982 public void showTranslation_actionPerformed(ActionEvent e)
3984 // /////////////////////////////
3985 // Collect Data to be translated/transferred
3987 SequenceI[] selection = viewport.getSequenceSelection();
3988 String[] seqstring = viewport.getViewAsString(true);
3989 AlignmentI al = null;
3992 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
3993 viewport.getViewAsVisibleContigs(true), viewport
3994 .getGapCharacter(), viewport.alignment
3995 .getAlignmentAnnotation(), viewport.alignment
3996 .getWidth(), viewport.getAlignment().getDataset());
3997 } catch (Exception ex)
4000 jalview.bin.Cache.log.debug("Exception during translation.", ex);
4007 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4008 "Translation Failed", JOptionPane.WARNING_MESSAGE);
4012 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4013 Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4014 DEFAULT_WIDTH, DEFAULT_HEIGHT);
4019 * Try to load a features file onto the alignment.
4022 * contents or path to retrieve file
4024 * access mode of file (see jalview.io.AlignFile)
4025 * @return true if features file was parsed corectly.
4027 public boolean parseFeaturesFile(String file, String type)
4029 boolean featuresFile = false;
4032 featuresFile = new FeaturesFile(file, type).parse(viewport.alignment
4033 .getDataset(), alignPanel.seqPanel.seqCanvas
4034 .getFeatureRenderer().featureColours, false);
4035 } catch (Exception ex)
4037 ex.printStackTrace();
4042 viewport.showSequenceFeatures = true;
4043 showSeqFeatures.setSelected(true);
4044 if (alignPanel.seqPanel.seqCanvas.fr != null)
4046 // update the min/max ranges where necessary
4047 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4049 alignPanel.paintAlignment(true);
4052 return featuresFile;
4055 public void dragEnter(DropTargetDragEvent evt)
4059 public void dragExit(DropTargetEvent evt)
4063 public void dragOver(DropTargetDragEvent evt)
4067 public void dropActionChanged(DropTargetDragEvent evt)
4071 public void drop(DropTargetDropEvent evt)
4073 Transferable t = evt.getTransferable();
4074 java.util.List files = null;
4078 DataFlavor uriListFlavor = new DataFlavor(
4079 "text/uri-list;class=java.lang.String");
4080 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4082 // Works on Windows and MacOSX
4083 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4084 files = (java.util.List) t
4085 .getTransferData(DataFlavor.javaFileListFlavor);
4087 else if (t.isDataFlavorSupported(uriListFlavor))
4089 // This is used by Unix drag system
4090 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4091 String data = (String) t.getTransferData(uriListFlavor);
4092 files = new java.util.ArrayList(1);
4093 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4094 data, "\r\n"); st.hasMoreTokens();)
4096 String s = st.nextToken();
4097 if (s.startsWith("#"))
4099 // the line is a comment (as per the RFC 2483)
4103 java.net.URI uri = new java.net.URI(s);
4104 // check to see if we can handle this kind of URI
4105 if (uri.getScheme().toLowerCase().startsWith("http"))
4107 files.add(uri.toString());
4111 // otherwise preserve old behaviour: catch all for file objects
4112 java.io.File file = new java.io.File(uri);
4113 files.add(file.toString());
4117 } catch (Exception e)
4119 e.printStackTrace();
4126 for (int i = 0; i < files.size(); i++)
4128 loadJalviewDataFile(files.get(i).toString());
4130 } catch (Exception ex)
4132 ex.printStackTrace();
4138 * Attempt to load a "dropped" file or URL string: First by testing whether it's and
4139 * Annotation file, then a JNet file, and finally a features file. If all are
4140 * false then the user may have dropped an alignment file onto this
4144 * either a filename or a URL string.
4146 public void loadJalviewDataFile(String file)
4150 String protocol = jalview.io.FormatAdapter.FILE;
4151 String f=file.toLowerCase();
4152 if (f.indexOf("http:") == 0 || f.indexOf("https:")==0 || f.indexOf("file:") == 0)
4154 protocol = jalview.io.FormatAdapter.URL;
4157 boolean isAnnotation = new AnnotationFile().readAnnotationFile(
4158 viewport.alignment, file, protocol);
4162 // try to see if its a JNet 'concise' style annotation file *before* we
4163 // try to parse it as a features file
4164 String format = new IdentifyFile().Identify(file, protocol);
4165 if (format.equalsIgnoreCase("JnetFile"))
4167 jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
4169 new JnetAnnotationMaker().add_annotation(predictions, viewport
4170 .getAlignment(), 0, false);
4171 isAnnotation = true;
4175 // try to parse it as a features file
4176 boolean isGroupsFile = parseFeaturesFile(file, protocol);
4177 // if it wasn't a features file then we just treat it as a general
4178 // alignment file to load into the current view.
4181 new FileLoader().LoadFile(viewport, file, protocol, format);
4185 alignPanel.paintAlignment(true);
4192 alignPanel.adjustAnnotationHeight();
4193 viewport.updateSequenceIdColours();
4194 buildSortByAnnotationScoresMenu();
4195 alignPanel.paintAlignment(true);
4197 } catch (Exception ex)
4199 ex.printStackTrace();
4203 public void tabSelectionChanged(int index)
4207 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
4208 viewport = alignPanel.av;
4209 setMenusFromViewport(viewport);
4213 public void tabbedPane_mousePressed(MouseEvent e)
4215 if (SwingUtilities.isRightMouseButton(e))
4217 String reply = JOptionPane.showInternalInputDialog(this,
4218 "Enter View Name", "Edit View Name",
4219 JOptionPane.QUESTION_MESSAGE);
4223 viewport.viewName = reply;
4224 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4229 public AlignViewport getCurrentView()
4235 * Open the dialog for regex description parsing.
4237 protected void extractScores_actionPerformed(ActionEvent e)
4239 ParseProperties pp = new jalview.analysis.ParseProperties(
4240 viewport.alignment);
4241 // TODO: verify regex and introduce GUI dialog for version 2.5
4242 // if (pp.getScoresFromDescription("col", "score column ",
4243 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4245 if (pp.getScoresFromDescription("description column",
4246 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4248 buildSortByAnnotationScoresMenu();
4256 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4259 protected void showDbRefs_actionPerformed(ActionEvent e)
4261 viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
4267 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4270 protected void showNpFeats_actionPerformed(ActionEvent e)
4272 viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
4276 * find the viewport amongst the tabs in this alignment frame and close that
4281 public boolean closeView(AlignViewport av)
4285 this.closeMenuItem_actionPerformed(false);
4288 Component[] comp = tabbedPane.getComponents();
4289 for (int i = 0; comp != null && i < comp.length; i++)
4291 if (comp[i] instanceof AlignmentPanel)
4293 if (((AlignmentPanel) comp[i]).av == av)
4296 closeView((AlignmentPanel) comp[i]);
4304 protected void build_fetchdbmenu(JMenu webService)
4306 // Temporary hack - DBRef Fetcher always top level ws entry.
4307 // TODO We probably want to store a sequence database checklist in
4308 // preferences and have checkboxes.. rather than individual sources selected
4310 JMenu rfetch = new JMenu("Fetch DB References");
4312 .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
4313 webService.add(rfetch);
4315 JMenuItem fetchr = new JMenuItem("Standard Databases");
4317 .setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
4318 fetchr.addActionListener(new ActionListener()
4321 public void actionPerformed(ActionEvent e)
4323 new Thread(new Runnable()
4328 new jalview.ws.DBRefFetcher(alignPanel.av
4329 .getSequenceSelection(), alignPanel.alignFrame)
4330 .fetchDBRefs(false);
4338 JMenu dfetch = new JMenu();
4340 jalview.ws.SequenceFetcher sf = SequenceFetcher
4341 .getSequenceFetcherSingleton(this);
4342 String[] otherdb = sf.getOrderedSupportedSources();
4343 // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4344 // jalview.util.QuickSort.sort(otherdb, otherdb);
4345 int comp = 0, mcomp = 15;
4346 String mname = null;
4347 if (otherdb != null && otherdb.length > 0)
4349 for (int i = 0; i < otherdb.length; i++)
4351 String dbname = sf.getSourceProxy(otherdb[i]).getDbName();
4354 mname = "from '" + dbname + "'";
4356 fetchr = new JMenuItem(otherdb[i]);
4357 final String[] dassource = new String[]
4359 fetchr.addActionListener(new ActionListener()
4362 public void actionPerformed(ActionEvent e)
4364 new Thread(new Runnable()
4369 new jalview.ws.DBRefFetcher(alignPanel.av
4370 .getSequenceSelection(), alignPanel.alignFrame,
4371 dassource).fetchDBRefs(false);
4377 fetchr.setToolTipText("Retrieve from " + dbname);
4379 if (comp++ == mcomp || i == (otherdb.length - 1))
4381 dfetch.setText(mname + " to '" + dbname + "'");
4383 dfetch = new JMenu();
4392 * Left justify the whole alignment.
4394 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
4396 AlignmentI al = viewport.getAlignment();
4398 viewport.firePropertyChange("alignment", null, al);
4402 * Right justify the whole alignment.
4404 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
4406 AlignmentI al = viewport.getAlignment();
4408 viewport.firePropertyChange("alignment", null, al);
4411 public void setShowSeqFeatures(boolean b)
4413 showSeqFeatures.setSelected(true);
4414 viewport.setShowSequenceFeatures(true);
4421 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
4422 * awt.event.ActionEvent)
4424 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
4426 viewport.setShowUnconserved(showUnconservedMenuItem.getState());
4427 alignPanel.paintAlignment(true);
4431 * @see jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event.ActionEvent)
4433 protected void showGroupConsensus_actionPerformed(ActionEvent e)
4435 viewport.setShowGroupConsensus(showGroupConsensus.getState());
4436 alignPanel.updateAnnotation();
4441 * @see jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt.event.ActionEvent)
4443 protected void showGroupConservation_actionPerformed(ActionEvent e)
4445 viewport.setShowGroupConservation(showGroupConservation.getState());
4446 alignPanel.updateAnnotation();
4450 class PrintThread extends Thread
4454 public PrintThread(AlignmentPanel ap)
4459 static PageFormat pf;
4463 PrinterJob printJob = PrinterJob.getPrinterJob();
4467 printJob.setPrintable(ap, pf);
4471 printJob.setPrintable(ap);
4474 if (printJob.printDialog())
4479 } catch (Exception PrintException)
4481 PrintException.printStackTrace();