2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2007 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 Softwarechang
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
48 extends GAlignFrame implements DropTargetListener
51 public static final int DEFAULT_WIDTH = 700;
54 public static final int DEFAULT_HEIGHT = 500;
55 public AlignmentPanel alignPanel;
57 AlignViewport viewport;
59 Vector alignPanels = new Vector();
63 String currentFileFormat = null;
65 String fileName = null;
69 * Creates a new AlignFrame object.
71 * @param al DOCUMENT ME!
73 public AlignFrame(AlignmentI al, int width, int height)
75 this(al, null, width, height);
80 * new alignment window with hidden columns
81 * @param al AlignmentI
82 * @param hiddenColumns ColumnSelection or null
84 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
85 int width, int height)
87 this.setSize(width, height);
88 viewport = new AlignViewport(al, hiddenColumns);
90 alignPanel = new AlignmentPanel(this, viewport);
92 if(al.getDataset()==null)
97 addAlignmentPanel(alignPanel, true);
102 * Make a new AlignFrame from exisiting alignmentPanels
103 * @param ap AlignmentPanel
104 * @param av AlignViewport
106 public AlignFrame(AlignmentPanel ap)
110 addAlignmentPanel(ap, false);
116 if (viewport.conservation == null)
118 BLOSUM62Colour.setEnabled(false);
119 conservationMenuItem.setEnabled(false);
120 modifyConservation.setEnabled(false);
121 // PIDColour.setEnabled(false);
122 // abovePIDThreshold.setEnabled(false);
123 // modifyPID.setEnabled(false);
126 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
128 if (sortby.equals("Id"))
130 sortIDMenuItem_actionPerformed(null);
132 else if (sortby.equals("Pairwise Identity"))
134 sortPairwiseMenuItem_actionPerformed(null);
137 if (Desktop.desktop != null)
139 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
140 addServiceListeners();
141 setGUINucleotide(viewport.alignment.isNucleotide());
144 setMenusFromViewport(viewport);
146 if (viewport.wrapAlignment)
148 wrapMenuItem_actionPerformed(null);
151 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW",false))
153 this.overviewMenuItem_actionPerformed(null);
160 public void setFileName(String file, String format)
163 currentFileFormat = format;
164 reload.setEnabled(true);
167 void addKeyListener()
169 addKeyListener(new KeyAdapter()
171 public void keyPressed(KeyEvent evt)
173 if (viewport.cursorMode &&
174 ( (evt.getKeyCode() >= KeyEvent.VK_0 &&
175 evt.getKeyCode() <= KeyEvent.VK_9)
177 (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 &&
178 evt.getKeyCode() <= KeyEvent.VK_NUMPAD9)
180 && Character.isDigit(evt.getKeyChar()))
181 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
183 switch (evt.getKeyCode())
186 case 27: // escape key
187 deselectAllSequenceMenuItem_actionPerformed(null);
191 case KeyEvent.VK_DOWN:
192 if (evt.isAltDown() || !viewport.cursorMode)
193 moveSelectedSequences(false);
194 if (viewport.cursorMode)
195 alignPanel.seqPanel.moveCursor(0, 1);
199 if (evt.isAltDown() || !viewport.cursorMode)
200 moveSelectedSequences(true);
201 if (viewport.cursorMode)
202 alignPanel.seqPanel.moveCursor(0, -1);
206 case KeyEvent.VK_LEFT:
207 if (evt.isAltDown() || !viewport.cursorMode)
208 slideSequences(false,
209 alignPanel.seqPanel.getKeyboardNo1());
211 alignPanel.seqPanel.moveCursor( -1, 0);
216 case KeyEvent.VK_RIGHT:
217 if (evt.isAltDown() || !viewport.cursorMode)
219 alignPanel.seqPanel.getKeyboardNo1());
221 alignPanel.seqPanel.moveCursor(1, 0);
224 case KeyEvent.VK_SPACE:
225 if (viewport.cursorMode)
227 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
233 case KeyEvent.VK_DELETE:
234 case KeyEvent.VK_BACK_SPACE:
235 if (!viewport.cursorMode)
237 cut_actionPerformed(null);
241 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
249 if (viewport.cursorMode)
251 alignPanel.seqPanel.setCursorRow();
255 if (viewport.cursorMode && !evt.isControlDown())
257 alignPanel.seqPanel.setCursorColumn();
261 if (viewport.cursorMode)
263 alignPanel.seqPanel.setCursorPosition();
267 case KeyEvent.VK_ENTER:
268 case KeyEvent.VK_COMMA:
269 if (viewport.cursorMode)
271 alignPanel.seqPanel.setCursorRowAndColumn();
276 if (viewport.cursorMode)
278 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
282 if (viewport.cursorMode)
284 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
289 viewport.cursorMode = !viewport.cursorMode;
290 statusBar.setText("Keyboard editing mode is " +
291 (viewport.cursorMode ? "on" : "off"));
292 if (viewport.cursorMode)
294 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
295 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
297 alignPanel.seqPanel.seqCanvas.repaint();
303 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
304 java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
305 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
307 javax.help.HelpBroker hb = hs.createHelpBroker();
308 hb.setCurrentID("home");
309 hb.setDisplayed(true);
313 ex.printStackTrace();
319 boolean toggleSeqs = !evt.isControlDown();
320 boolean toggleCols = !evt.isShiftDown();
322 boolean hide = false;
324 SequenceGroup sg = viewport.getSelectionGroup();
327 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
329 hideSelSequences_actionPerformed(null);
332 else if (! (toggleCols &&
333 viewport.colSel.getSelected().size() > 0))
335 showAllSeqs_actionPerformed(null);
341 if (viewport.colSel.getSelected().size() > 0)
343 hideSelColumns_actionPerformed(null);
346 viewport.selectionGroup = sg;
351 showAllColumns_actionPerformed(null);
356 case KeyEvent.VK_PAGE_UP:
357 if (viewport.wrapAlignment)
359 alignPanel.scrollUp(true);
363 alignPanel.setScrollValues(viewport.startRes,
365 - viewport.endSeq + viewport.startSeq);
368 case KeyEvent.VK_PAGE_DOWN:
369 if (viewport.wrapAlignment)
371 alignPanel.scrollUp(false);
375 alignPanel.setScrollValues(viewport.startRes,
377 + viewport.endSeq - viewport.startSeq);
383 public void keyReleased(KeyEvent evt)
385 switch(evt.getKeyCode())
387 case KeyEvent.VK_LEFT:
388 if (evt.isAltDown() || !viewport.cursorMode)
389 viewport.firePropertyChange("alignment", null,
390 viewport.getAlignment().getSequences());
393 case KeyEvent.VK_RIGHT:
394 if (evt.isAltDown() || !viewport.cursorMode)
395 viewport.firePropertyChange("alignment", null,
396 viewport.getAlignment().getSequences());
404 public void addAlignmentPanel(final AlignmentPanel ap,
407 ap.alignFrame = this;
409 alignPanels.addElement(ap);
411 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
413 int aSize = alignPanels.size();
415 tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
417 if (aSize == 1 && ap.av.viewName==null)
419 this.getContentPane().add(ap, BorderLayout.CENTER);
425 setInitialTabVisible();
428 expandViews.setEnabled(true);
429 gatherViews.setEnabled(true);
430 tabbedPane.addTab(ap.av.viewName, ap);
432 ap.setVisible(false);
439 ap.av.alignment.padGaps();
441 ap.av.updateConservation(ap);
442 ap.av.updateConsensus(ap);
446 public void setInitialTabVisible()
448 expandViews.setEnabled(true);
449 gatherViews.setEnabled(true);
450 tabbedPane.setVisible(true);
451 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
452 tabbedPane.addTab(first.av.viewName,first);
453 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
457 public AlignViewport getViewport()
462 /* Set up intrinsic listeners for dynamically generated GUI bits. */
463 private void addServiceListeners()
465 final java.beans.PropertyChangeListener thisListener;
466 // Do this once to get current state
467 BuildWebServiceMenu();
468 Desktop.discoverer.addPropertyChangeListener(
469 thisListener = new java.beans.PropertyChangeListener()
471 public void propertyChange(PropertyChangeEvent evt)
473 // System.out.println("Discoverer property change.");
474 if (evt.getPropertyName().equals("services"))
476 // System.out.println("Rebuilding web service menu");
477 BuildWebServiceMenu();
482 addInternalFrameListener(new javax.swing.event.
483 InternalFrameAdapter()
485 public void internalFrameClosed(
486 javax.swing.event.InternalFrameEvent evt)
488 // System.out.println("deregistering discoverer listener");
489 Desktop.discoverer.removePropertyChangeListener(thisListener);
490 closeMenuItem_actionPerformed(true);
496 public void setGUINucleotide(boolean nucleotide)
498 showTranslation.setVisible( nucleotide );
499 conservationMenuItem.setEnabled( !nucleotide );
500 modifyConservation.setEnabled( !nucleotide );
502 //Remember AlignFrame always starts as protein
505 calculateMenu.remove(calculateMenu.getItemCount()-2);
510 * Need to call this method when tabs are selected for multiple views,
511 * or when loading from Jalview2XML.java
512 * @param av AlignViewport
514 void setMenusFromViewport(AlignViewport av)
516 padGapsMenuitem.setSelected(av.padGaps);
517 colourTextMenuItem.setSelected(av.showColourText);
518 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
519 conservationMenuItem.setSelected(av.getConservationSelected());
520 seqLimits.setSelected(av.getShowJVSuffix());
521 idRightAlign.setSelected(av.rightAlignIds);
522 renderGapsMenuItem.setSelected(av.renderGaps);
523 wrapMenuItem.setSelected(av.wrapAlignment);
524 scaleAbove.setVisible(av.wrapAlignment);
525 scaleLeft.setVisible(av.wrapAlignment);
526 scaleRight.setVisible(av.wrapAlignment);
527 annotationPanelMenuItem.setState(av.showAnnotation);
528 viewBoxesMenuItem.setSelected(av.showBoxes);
529 viewTextMenuItem.setSelected(av.showText);
531 setColourSelected(ColourSchemeProperty.
532 getColourName(av.getGlobalColourScheme()));
534 showSeqFeatures.setSelected(av.showSequenceFeatures);
535 hiddenMarkers.setState(av.showHiddenMarkers);
536 applyToAllGroups.setState(av.colourAppliesToAllGroups);
542 Hashtable progressBars;
543 public void setProgressBar(String message, long id)
545 if(progressBars == null)
547 progressBars = new Hashtable();
550 JPanel progressPanel;
551 GridLayout layout = (GridLayout) statusPanel.getLayout();
552 if(progressBars.get( new Long(id) )!=null)
554 progressPanel = (JPanel)progressBars.get( new Long(id) );
555 statusPanel.remove(progressPanel);
556 progressBars.remove( progressPanel );
557 progressPanel = null;
560 statusBar.setText(message);
563 layout.setRows(layout.getRows() - 1);
567 progressPanel = new JPanel(new BorderLayout(10, 5));
569 JProgressBar progressBar = new JProgressBar();
570 progressBar.setIndeterminate(true);
572 progressPanel.add(new JLabel(message), BorderLayout.WEST);
573 progressPanel.add(progressBar, BorderLayout.CENTER);
575 layout.setRows(layout.getRows() + 1);
576 statusPanel.add(progressPanel);
578 progressBars.put(new Long(id), progressPanel);
588 Added so Castor Mapping file can obtain Jalview Version
590 public String getVersion()
592 return jalview.bin.Cache.getProperty("VERSION");
595 public FeatureRenderer getFeatureRenderer()
597 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
601 public void fetchSequence_actionPerformed(ActionEvent e)
603 new SequenceFetcher(this);
606 public void addFromFile_actionPerformed(ActionEvent e)
608 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
611 public void reload_actionPerformed(ActionEvent e)
615 if(currentFileFormat.equals("Jalview"))
617 JInternalFrame [] frames = Desktop.desktop.getAllFrames();
618 for(int i=0; i<frames.length; i++)
620 if (frames[i] instanceof AlignFrame
622 && ( (AlignFrame) frames[i]).fileName.equals(fileName))
626 frames[i].setSelected(true);
627 Desktop.instance.closeAssociatedWindows();
629 catch (java.beans.PropertyVetoException ex)
634 Desktop.instance.closeAssociatedWindows();
636 FileLoader loader = new FileLoader();
637 String protocol = fileName.startsWith("http:")? "URL":"File";
638 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
642 Rectangle bounds = this.getBounds();
644 FileLoader loader = new FileLoader();
645 String protocol = fileName.startsWith("http:") ? "URL" : "File";
646 AlignFrame newframe =
647 loader.LoadFileWaitTillLoaded(fileName, protocol, currentFileFormat);
649 newframe.setBounds(bounds);
651 this.closeMenuItem_actionPerformed(true);
657 public void addFromText_actionPerformed(ActionEvent e)
659 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
662 public void addFromURL_actionPerformed(ActionEvent e)
664 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
668 public void save_actionPerformed(ActionEvent e)
671 || currentFileFormat==null
672 || fileName.startsWith("http")
675 saveAs_actionPerformed(null);
679 saveAlignment(fileName, currentFileFormat);
686 * @param e DOCUMENT ME!
688 public void saveAs_actionPerformed(ActionEvent e)
690 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
691 getProperty( "LAST_DIRECTORY"),
693 { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" },
695 { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
700 chooser.setFileView(new JalviewFileView());
701 chooser.setDialogTitle("Save Alignment to file");
702 chooser.setToolTipText("Save");
704 int value = chooser.showSaveDialog(this);
706 if (value == JalviewFileChooser.APPROVE_OPTION)
708 currentFileFormat = chooser.getSelectedFormat();
709 if (currentFileFormat == null)
711 JOptionPane.showInternalMessageDialog(Desktop.desktop,
712 "You must select a file format before saving!",
713 "File format not specified",
714 JOptionPane.WARNING_MESSAGE);
715 value = chooser.showSaveDialog(this);
719 fileName = chooser.getSelectedFile().getPath();
721 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
724 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
726 saveAlignment(fileName, currentFileFormat);
730 public boolean saveAlignment(String file, String format)
732 boolean success = true;
734 if (format.equalsIgnoreCase("Jalview"))
736 String shortName = title;
738 if (shortName.indexOf(java.io.File.separatorChar) > -1)
740 shortName = shortName.substring(shortName.lastIndexOf(
741 java.io.File.separatorChar) + 1);
744 success = new Jalview2XML().SaveAlignment(this, file, shortName);
746 statusBar.setText("Successfully saved to file: "
748 +format +" format.");
754 String[] omitHidden = null;
756 if (viewport.hasHiddenColumns)
758 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
759 "The Alignment contains hidden columns."
760 + "\nDo you want to save only the visible alignment?",
761 "Save / Omit Hidden Columns",
762 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
764 if (reply == JOptionPane.YES_OPTION)
766 omitHidden = viewport.getViewAsString(false);
770 String output = new FormatAdapter().formatSequences(
772 viewport.alignment.getSequencesArray(),
783 java.io.PrintWriter out = new java.io.PrintWriter(
784 new java.io.FileWriter(file));
789 statusBar.setText("Successfully saved to file: "
791 + format + " format.");
796 ex.printStackTrace();
803 JOptionPane.showInternalMessageDialog(
804 this, "Couldn't save file: " + fileName,
806 JOptionPane.WARNING_MESSAGE);
815 * @param e DOCUMENT ME!
817 protected void outputText_actionPerformed(ActionEvent e)
819 String [] omitHidden = null;
821 if(viewport.hasHiddenColumns)
823 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
824 "The Alignment contains hidden columns."
825 +"\nDo you want to output only the visible alignment?",
826 "Save / Omit Hidden Columns",
827 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
829 if(reply==JOptionPane.YES_OPTION)
831 omitHidden = viewport.getViewAsString(false);
835 CutAndPasteTransfer cap = new CutAndPasteTransfer();
836 cap.setForInput(null);
837 Desktop.addInternalFrame(cap,
838 "Alignment output - " + e.getActionCommand(), 600,
842 cap.setText(new FormatAdapter().formatSequences(
843 e.getActionCommand(),
844 viewport.alignment.getSequencesArray(),
851 * @param e DOCUMENT ME!
853 protected void htmlMenuItem_actionPerformed(ActionEvent e)
855 new HTMLOutput(alignPanel,
856 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
857 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
860 public void createImageMap(File file, String image)
862 alignPanel.makePNGImageMap(file, image);
868 * @param e DOCUMENT ME!
870 public void createPNG(File f)
872 alignPanel.makePNG(f);
878 * @param e DOCUMENT ME!
880 public void createEPS(File f)
882 alignPanel.makeEPS(f);
886 public void pageSetup_actionPerformed(ActionEvent e)
888 PrinterJob printJob = PrinterJob.getPrinterJob();
889 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
895 * @param e DOCUMENT ME!
897 public void printMenuItem_actionPerformed(ActionEvent e)
899 //Putting in a thread avoids Swing painting problems
900 PrintThread thread = new PrintThread(alignPanel);
904 public void exportFeatures_actionPerformed(ActionEvent e)
906 new AnnotationExporter().exportFeatures(alignPanel);
910 public void exportAnnotations_actionPerformed(ActionEvent e)
912 new AnnotationExporter().exportAnnotations(
914 viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
915 viewport.alignment.getGroups(),
916 ((Alignment)viewport.alignment).alignmentProperties
921 public void associatedData_actionPerformed(ActionEvent e)
923 // Pick the tree file
924 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
927 chooser.setFileView(new JalviewFileView());
928 chooser.setDialogTitle("Load Jalview Annotations or Features File");
929 chooser.setToolTipText("Load Jalview Annotations / Features file");
931 int value = chooser.showOpenDialog(null);
933 if (value == JalviewFileChooser.APPROVE_OPTION)
935 String choice = chooser.getSelectedFile().getPath();
936 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
937 loadJalviewDataFile(choice);
946 * @param e DOCUMENT ME!
948 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
950 if(alignPanels!=null && alignPanels.size()<2)
957 if(alignPanels!=null)
961 for (int i = 0; i < alignPanels.size(); i++)
963 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
964 jalview.structure.StructureSelectionManager.getStructureSelectionManager()
965 .removeStructureViewerListener(ap.seqPanel, null);
966 PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
967 PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
968 PaintRefresher.RemoveComponent(ap);
969 ap.av.alignment = null;
974 int index = tabbedPane.getSelectedIndex();
976 alignPanels.removeElement(alignPanel);
977 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
978 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
979 PaintRefresher.RemoveComponent(alignPanel);
980 viewport.alignment = null;
984 tabbedPane.removeTabAt(index);
985 tabbedPane.validate();
987 if(index==tabbedPane.getTabCount())
992 this.tabSelectionChanged(index);
998 this.setClosed(true);
1001 catch (Exception ex)
1003 ex.printStackTrace();
1011 void updateEditMenuBar()
1014 if (viewport.historyList.size() > 0)
1016 undoMenuItem.setEnabled(true);
1017 CommandI command = (CommandI) viewport.historyList.peek();
1018 undoMenuItem.setText("Undo " + command.getDescription());
1022 undoMenuItem.setEnabled(false);
1023 undoMenuItem.setText("Undo");
1026 if (viewport.redoList.size() > 0)
1028 redoMenuItem.setEnabled(true);
1030 CommandI command = (CommandI) viewport.redoList.peek();
1031 redoMenuItem.setText("Redo " + command.getDescription());
1035 redoMenuItem.setEnabled(false);
1036 redoMenuItem.setText("Redo");
1041 public void addHistoryItem(CommandI command)
1043 if(command.getSize()>0)
1045 viewport.historyList.push(command);
1046 viewport.redoList.clear();
1047 updateEditMenuBar();
1048 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1057 * @param e DOCUMENT ME!
1059 protected void undoMenuItem_actionPerformed(ActionEvent e)
1061 CommandI command = (CommandI)viewport.historyList.pop();
1062 viewport.redoList.push(command);
1063 command.undoCommand();
1065 AlignViewport originalSource = getOriginatingSource(command);
1066 updateEditMenuBar();
1068 if(originalSource!=null)
1070 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1071 originalSource.firePropertyChange("alignment",
1073 originalSource.alignment.getSequences());
1080 * @param e DOCUMENT ME!
1082 protected void redoMenuItem_actionPerformed(ActionEvent e)
1084 if(viewport.redoList.size()<1)
1089 CommandI command = (CommandI) viewport.redoList.pop();
1090 viewport.historyList.push(command);
1091 command.doCommand();
1093 AlignViewport originalSource = getOriginatingSource(command);
1094 updateEditMenuBar();
1096 if(originalSource!=null)
1098 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1099 originalSource.firePropertyChange("alignment",
1101 originalSource.alignment.getSequences());
1105 AlignViewport getOriginatingSource(CommandI command)
1107 AlignViewport originalSource = null;
1108 //For sequence removal and addition, we need to fire
1109 //the property change event FROM the viewport where the
1110 //original alignment was altered
1112 if (command instanceof EditCommand)
1114 EditCommand editCommand = (EditCommand) command;
1115 al = editCommand.getAlignment();
1116 Vector comps = (Vector) PaintRefresher.components
1117 .get(viewport.getSequenceSetId());
1119 for (int i = 0; i < comps.size(); i++)
1121 if (comps.elementAt(i) instanceof AlignmentPanel)
1123 if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
1125 originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
1132 if (originalSource == null)
1134 //The original view is closed, we must validate
1135 //the current view against the closed view first
1138 PaintRefresher.validateSequences(al, viewport.alignment);
1141 originalSource = viewport;
1144 return originalSource;
1150 * @param up DOCUMENT ME!
1152 public void moveSelectedSequences(boolean up)
1154 SequenceGroup sg = viewport.getSelectionGroup();
1163 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1165 SequenceI seq = viewport.alignment.getSequenceAt(i);
1167 if (!sg.getSequences(null).contains(seq))
1172 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1174 if (sg.getSequences(null).contains(temp))
1179 viewport.alignment.getSequences().setElementAt(temp, i);
1180 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1185 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1187 SequenceI seq = viewport.alignment.getSequenceAt(i);
1189 if (!sg.getSequences(null).contains(seq))
1194 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1196 if (sg.getSequences(null).contains(temp))
1201 viewport.alignment.getSequences().setElementAt(temp, i);
1202 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1206 alignPanel.paintAlignment(true);
1212 synchronized void slideSequences(boolean right, int size)
1214 Vector sg = new Vector();
1215 if(viewport.cursorMode)
1217 sg.addElement(viewport.alignment.getSequenceAt(
1218 alignPanel.seqPanel.seqCanvas.cursorY));
1220 else if(viewport.getSelectionGroup()!=null
1221 && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight())
1223 sg = viewport.getSelectionGroup().getSequences(
1224 viewport.hiddenRepSequences);
1232 Vector invertGroup = new Vector();
1234 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1236 if(!sg.contains(viewport.alignment.getSequenceAt(i)))
1237 invertGroup.add(viewport.alignment.getSequenceAt(i));
1240 SequenceI[] seqs1 = new SequenceI[sg.size()];
1241 for (int i = 0; i < sg.size(); i++)
1242 seqs1[i] = (SequenceI) sg.elementAt(i);
1244 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1245 for (int i = 0; i < invertGroup.size(); i++)
1246 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1248 SlideSequencesCommand ssc;
1250 ssc = new SlideSequencesCommand("Slide Sequences",
1252 viewport.getGapCharacter()
1255 ssc = new SlideSequencesCommand("Slide Sequences",
1257 viewport.getGapCharacter()
1260 int groupAdjustment = 0;
1261 if (ssc.getGapsInsertedBegin() && right)
1263 if (viewport.cursorMode)
1264 alignPanel.seqPanel.moveCursor(size, 0);
1266 groupAdjustment = size;
1268 else if (!ssc.getGapsInsertedBegin() && !right)
1270 if (viewport.cursorMode)
1271 alignPanel.seqPanel.moveCursor( -size, 0);
1273 groupAdjustment = -size;
1276 if (groupAdjustment != 0)
1278 viewport.getSelectionGroup().setStartRes(
1279 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1280 viewport.getSelectionGroup().setEndRes(
1281 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1285 boolean appendHistoryItem = false;
1286 if(viewport.historyList!=null
1287 && viewport.historyList.size()>0
1288 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1290 appendHistoryItem = ssc.appendSlideCommand(
1291 (SlideSequencesCommand)viewport.historyList.peek())
1295 if(!appendHistoryItem)
1296 addHistoryItem(ssc);
1305 * @param e DOCUMENT ME!
1307 protected void copy_actionPerformed(ActionEvent e)
1310 if (viewport.getSelectionGroup() == null)
1314 // TODO: preserve the ordering of displayed alignment annotation in any internal paste (particularly sequence associated annotation)
1315 SequenceI [] seqs = viewport.getSelectionAsNewSequence();
1316 String[] omitHidden = null;
1318 if (viewport.hasHiddenColumns)
1320 omitHidden = viewport.getViewAsString(true);
1323 String output = new FormatAdapter().formatSequences(
1328 StringSelection ss = new StringSelection(output);
1332 jalview.gui.Desktop.internalCopy = true;
1333 //Its really worth setting the clipboard contents
1334 //to empty before setting the large StringSelection!!
1335 Toolkit.getDefaultToolkit().getSystemClipboard()
1336 .setContents(new StringSelection(""), null);
1338 Toolkit.getDefaultToolkit().getSystemClipboard()
1339 .setContents(ss, Desktop.instance);
1341 catch (OutOfMemoryError er)
1343 er.printStackTrace();
1344 javax.swing.SwingUtilities.invokeLater(new Runnable()
1348 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1349 "Out of memory copying region!!"
1351 "\nSee help files for increasing Java Virtual Machine memory."
1353 javax.swing.JOptionPane.WARNING_MESSAGE);
1360 Vector hiddenColumns = null;
1361 if(viewport.hasHiddenColumns)
1363 hiddenColumns =new Vector();
1364 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1365 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
1368 int[] region = (int[])
1369 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
1371 hiddenColumns.addElement(new int[]
1372 {region[0] - hiddenOffset,
1373 region[1]-hiddenOffset});
1377 Desktop.jalviewClipboard = new Object[]
1380 viewport.alignment.getDataset(),
1382 statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
1388 * @param e DOCUMENT ME!
1390 protected void pasteNew_actionPerformed(ActionEvent e)
1398 * @param e DOCUMENT ME!
1400 protected void pasteThis_actionPerformed(ActionEvent e)
1408 * @param newAlignment DOCUMENT ME!
1410 void paste(boolean newAlignment)
1412 boolean externalPaste=true;
1415 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1416 Transferable contents = c.getContents(this);
1418 if (contents == null)
1426 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1427 if (str.length() < 1)
1432 format = new IdentifyFile().Identify(str, "Paste");
1435 catch (OutOfMemoryError er)
1437 er.printStackTrace();
1438 javax.swing.SwingUtilities.invokeLater(new Runnable()
1442 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1443 "Out of memory pasting sequences!!"
1445 "\nSee help files for increasing Java Virtual Machine memory."
1447 javax.swing.JOptionPane.WARNING_MESSAGE);
1454 SequenceI[] sequences;
1455 boolean annotationAdded = false;
1456 AlignmentI alignment = null;
1458 if(Desktop.jalviewClipboard!=null)
1460 // The clipboard was filled from within Jalview, we must use the sequences
1461 // And dataset from the copied alignment
1462 SequenceI[] newseq = (SequenceI[])Desktop.jalviewClipboard[0];
1463 // be doubly sure that we create *new* sequence objects.
1464 sequences = new SequenceI[newseq.length];
1465 for (int i=0;i<newseq.length;i++) {
1466 sequences[i] = new Sequence(newseq[i]);
1468 alignment = new Alignment(sequences);
1469 externalPaste = false;
1473 // parse the clipboard as an alignment.
1474 alignment = new FormatAdapter().readFile(str, "Paste", format);
1475 sequences = alignment.getSequencesArray();
1483 if (Desktop.jalviewClipboard != null)
1485 // dataset is inherited
1486 alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
1490 // new dataset is constructed
1491 alignment.setDataset(null);
1493 alwidth = alignment.getWidth()+1;
1497 AlignmentI pastedal = alignment; // preserve pasted alignment object
1498 // Add pasted sequences and dataset into existing alignment.
1499 alignment = viewport.getAlignment();
1500 alwidth = alignment.getWidth()+1;
1501 // decide if we need to import sequences from an existing dataset
1502 boolean importDs = Desktop.jalviewClipboard != null
1503 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1504 // importDs==true instructs us to copy over new dataset sequences from
1505 // an existing alignment
1506 Vector newDs = (importDs) ? new Vector() : null; // used to create
1507 // minimum dataset set
1509 for (int i = 0; i < sequences.length; i++)
1513 newDs.addElement(null);
1515 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1517 if (importDs && ds != null)
1519 if (!newDs.contains(ds))
1521 newDs.setElementAt(ds, i);
1522 ds = new Sequence(ds);
1523 // update with new dataset sequence
1524 sequences[i].setDatasetSequence(ds);
1528 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1533 // copy and derive new dataset sequence
1534 sequences[i] = sequences[i].deriveSequence();
1535 alignment.getDataset().addSequence(sequences[i].getDatasetSequence());
1536 // TODO: avoid creation of duplicate dataset sequences with a
1537 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1539 alignment.addSequence(sequences[i]); // merges dataset
1543 newDs.clear(); // tidy up
1545 if (pastedal.getAlignmentAnnotation()!=null) {
1546 // Add any annotation attached to alignment.
1547 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1548 for (int i=0; i<alann.length; i++)
1550 annotationAdded=true;
1551 if (alann[i].sequenceRef==null && !alann[i].autoCalculated) {
1552 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1553 newann.padAnnotation(alwidth);
1554 alignment.addAnnotation(newann);
1559 if (!newAlignment) {
1563 addHistoryItem(new EditCommand(
1568 alignment.getWidth(),
1572 // Add any annotations attached to sequences
1573 for (int i = 0; i < sequences.length; i++)
1575 if (sequences[i].getAnnotation() != null)
1577 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1579 annotationAdded=true;
1580 sequences[i].getAnnotation()[a].adjustForAlignment();
1581 sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1582 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation was duplicated earlier
1583 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1589 if (!newAlignment) {
1590 // propagate alignment changed.
1591 viewport.setEndSeq(alignment.getHeight());
1592 if (annotationAdded)
1594 alignPanel.annotationPanel.adjustPanelHeight();
1596 viewport.firePropertyChange("alignment", null, alignment.getSequences());
1598 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
1599 String newtitle = new String("Copied sequences");
1601 if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
1603 Vector hc = (Vector)Desktop.jalviewClipboard[2];
1604 for(int i=0; i<hc.size(); i++)
1606 int [] region = (int[]) hc.elementAt(i);
1607 af.viewport.hideColumns(region[0], region[1]);
1612 //>>>This is a fix for the moment, until a better solution is found!!<<<
1613 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
1614 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1616 // TODO: maintain provenance of an alignment, rather than just make the title a concatenation of operations.
1617 if (!externalPaste) {
1618 if (title.startsWith("Copied sequences"))
1624 newtitle = newtitle.concat("- from " + title);
1627 newtitle = new String("Pasted sequences");
1630 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1637 catch (Exception ex)
1639 ex.printStackTrace();
1640 System.out.println("Exception whilst pasting: "+ex);
1641 // could be anything being pasted in here
1650 * @param e DOCUMENT ME!
1652 protected void cut_actionPerformed(ActionEvent e)
1654 copy_actionPerformed(null);
1655 delete_actionPerformed(null);
1661 * @param e DOCUMENT ME!
1663 protected void delete_actionPerformed(ActionEvent evt)
1666 SequenceGroup sg = viewport.getSelectionGroup();
1672 Vector seqs = new Vector();
1674 for (int i = 0; i < sg.getSize(); i++)
1676 seq = sg.getSequenceAt(i);
1677 seqs.addElement(seq);
1681 // If the cut affects all sequences, remove highlighted columns
1682 if (sg.getSize() == viewport.alignment.getHeight())
1684 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1685 sg.getEndRes() + 1);
1689 SequenceI [] cut = new SequenceI[seqs.size()];
1690 for(int i=0; i<seqs.size(); i++)
1692 cut[i] = (SequenceI)seqs.elementAt(i);
1699 addHistoryItem(new EditCommand("Cut Sequences",
1703 sg.getEndRes()-sg.getStartRes()+1,
1704 viewport.alignment));
1707 viewport.setSelectionGroup(null);
1708 viewport.alignment.deleteGroup(sg);
1710 viewport.firePropertyChange("alignment", null,
1711 viewport.getAlignment().getSequences());
1713 if (viewport.getAlignment().getHeight() < 1)
1717 this.setClosed(true);
1719 catch (Exception ex)
1728 * @param e DOCUMENT ME!
1730 protected void deleteGroups_actionPerformed(ActionEvent e)
1732 viewport.alignment.deleteAllGroups();
1733 viewport.sequenceColours = null;
1734 viewport.setSelectionGroup(null);
1735 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1736 alignPanel.paintAlignment(true);
1742 * @param e DOCUMENT ME!
1744 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1746 SequenceGroup sg = new SequenceGroup();
1748 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1751 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1754 sg.setEndRes(viewport.alignment.getWidth() - 1);
1755 viewport.setSelectionGroup(sg);
1756 alignPanel.paintAlignment(true);
1757 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1763 * @param e DOCUMENT ME!
1765 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1767 if(viewport.cursorMode)
1769 alignPanel.seqPanel.keyboardNo1 = null;
1770 alignPanel.seqPanel.keyboardNo2 = null;
1772 viewport.setSelectionGroup(null);
1773 viewport.getColumnSelection().clear();
1774 viewport.setSelectionGroup(null);
1775 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1776 alignPanel.idPanel.idCanvas.searchResults = null;
1777 alignPanel.paintAlignment(true);
1778 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1784 * @param e DOCUMENT ME!
1786 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1788 SequenceGroup sg = viewport.getSelectionGroup();
1792 selectAllSequenceMenuItem_actionPerformed(null);
1797 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1800 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1803 alignPanel.paintAlignment(true);
1805 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1808 public void invertColSel_actionPerformed(ActionEvent e)
1810 viewport.invertColumnSelection();
1811 alignPanel.paintAlignment(true);
1818 * @param e DOCUMENT ME!
1820 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1822 trimAlignment(true);
1828 * @param e DOCUMENT ME!
1830 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
1832 trimAlignment(false);
1835 void trimAlignment(boolean trimLeft)
1837 ColumnSelection colSel = viewport.getColumnSelection();
1840 if (colSel.size() > 0)
1844 column = colSel.getMin();
1848 column = colSel.getMax();
1852 if(viewport.getSelectionGroup()!=null)
1854 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
1855 hiddenRepSequences);
1859 seqs = viewport.alignment.getSequencesArray();
1863 TrimRegionCommand trimRegion;
1866 trimRegion = new TrimRegionCommand("Remove Left",
1867 TrimRegionCommand.TRIM_LEFT,
1872 viewport.selectionGroup);
1873 viewport.setStartRes(0);
1877 trimRegion = new TrimRegionCommand("Remove Right",
1878 TrimRegionCommand.TRIM_RIGHT,
1883 viewport.selectionGroup);
1886 statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
1889 addHistoryItem(trimRegion);
1891 Vector groups = viewport.alignment.getGroups();
1893 for (int i = 0; i < groups.size(); i++)
1895 SequenceGroup sg = (SequenceGroup) groups.get(i);
1897 if ( (trimLeft && !sg.adjustForRemoveLeft(column))
1898 || (!trimLeft && !sg.adjustForRemoveRight(column)))
1900 viewport.alignment.deleteGroup(sg);
1904 viewport.firePropertyChange("alignment", null,
1905 viewport.getAlignment().getSequences());
1912 * @param e DOCUMENT ME!
1914 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1916 int start = 0, end = viewport.alignment.getWidth()-1;
1919 if (viewport.getSelectionGroup() != null)
1921 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
1922 hiddenRepSequences);
1923 start = viewport.getSelectionGroup().getStartRes();
1924 end = viewport.getSelectionGroup().getEndRes();
1928 seqs = viewport.alignment.getSequencesArray();
1932 RemoveGapColCommand removeGapCols =
1933 new RemoveGapColCommand("Remove Gapped Columns",
1936 viewport.alignment);
1938 addHistoryItem(removeGapCols);
1940 statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
1942 //This is to maintain viewport position on first residue
1944 SequenceI seq = viewport.alignment.getSequenceAt(0);
1945 int startRes = seq.findPosition(viewport.startRes);
1946 // ShiftList shifts;
1947 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
1948 // edit.alColumnChanges=shifts.getInverse();
1949 // if (viewport.hasHiddenColumns)
1950 // viewport.getColumnSelection().compensateForEdits(shifts);
1951 viewport.setStartRes(seq.findIndex(startRes)-1);
1952 viewport.firePropertyChange("alignment", null,
1953 viewport.getAlignment().getSequences());
1960 * @param e DOCUMENT ME!
1962 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1964 int start = 0, end = viewport.alignment.getWidth()-1;
1967 if (viewport.getSelectionGroup() != null)
1969 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
1970 hiddenRepSequences);
1971 start = viewport.getSelectionGroup().getStartRes();
1972 end = viewport.getSelectionGroup().getEndRes();
1976 seqs = viewport.alignment.getSequencesArray();
1979 //This is to maintain viewport position on first residue
1981 SequenceI seq = viewport.alignment.getSequenceAt(0);
1982 int startRes = seq.findPosition(viewport.startRes);
1984 addHistoryItem(new RemoveGapsCommand("Remove Gaps",
1987 viewport.alignment));
1989 viewport.setStartRes(seq.findIndex(startRes)-1);
1991 viewport.firePropertyChange("alignment", null,
1992 viewport.getAlignment().getSequences());
1999 * @param e DOCUMENT ME!
2001 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2003 viewport.padGaps = padGapsMenuitem.isSelected();
2005 viewport.firePropertyChange("alignment",
2007 viewport.getAlignment().getSequences());
2013 * @param e DOCUMENT ME!
2015 public void findMenuItem_actionPerformed(ActionEvent e)
2020 public void newView_actionPerformed(ActionEvent e)
2022 AlignmentPanel newap =
2023 new Jalview2XML().copyAlignPanel(alignPanel, true);
2025 newap.av.gatherViewsHere = false;
2027 if (viewport.viewName == null)
2029 viewport.viewName = "Original";
2032 newap.av.historyList = viewport.historyList;
2033 newap.av.redoList = viewport.redoList;
2035 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2036 String newViewName = "View " +index;
2038 Vector comps = (Vector) PaintRefresher.components.get(viewport.
2039 getSequenceSetId());
2040 Vector existingNames = new Vector();
2041 for(int i=0; i<comps.size(); i++)
2043 if(comps.elementAt(i) instanceof AlignmentPanel)
2045 AlignmentPanel ap = (AlignmentPanel)comps.elementAt(i);
2046 if(!existingNames.contains(ap.av.viewName))
2048 existingNames.addElement(ap.av.viewName);
2053 while(existingNames.contains(newViewName))
2055 newViewName = "View "+ (++index);
2058 newap.av.viewName = newViewName;
2060 addAlignmentPanel(newap, false);
2062 if(alignPanels.size()==2)
2064 viewport.gatherViewsHere = true;
2066 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2069 public void expandViews_actionPerformed(ActionEvent e)
2071 Desktop.instance.explodeViews(this);
2074 public void gatherViews_actionPerformed(ActionEvent e)
2076 Desktop.instance.gatherViews(this);
2084 * @param e DOCUMENT ME!
2086 public void font_actionPerformed(ActionEvent e)
2088 new FontChooser(alignPanel);
2095 * @param e DOCUMENT ME!
2097 protected void seqLimit_actionPerformed(ActionEvent e)
2099 viewport.setShowJVSuffix(seqLimits.isSelected());
2101 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
2102 alignPanel.paintAlignment(true);
2105 public void idRightAlign_actionPerformed(ActionEvent e)
2107 viewport.rightAlignIds = idRightAlign.isSelected();
2108 alignPanel.paintAlignment(true);
2116 * @param e DOCUMENT ME!
2118 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2120 viewport.setColourText(colourTextMenuItem.isSelected());
2121 alignPanel.paintAlignment(true);
2127 * @param e DOCUMENT ME!
2129 public void wrapMenuItem_actionPerformed(ActionEvent e)
2131 scaleAbove.setVisible(wrapMenuItem.isSelected());
2132 scaleLeft.setVisible(wrapMenuItem.isSelected());
2133 scaleRight.setVisible(wrapMenuItem.isSelected());
2134 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2135 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2138 public void showAllSeqs_actionPerformed(ActionEvent e)
2140 viewport.showAllHiddenSeqs();
2143 public void showAllColumns_actionPerformed(ActionEvent e)
2145 viewport.showAllHiddenColumns();
2149 public void hideSelSequences_actionPerformed(ActionEvent e)
2151 viewport.hideAllSelectedSeqs();
2152 alignPanel.paintAlignment(true);
2155 public void hideSelColumns_actionPerformed(ActionEvent e)
2157 viewport.hideSelectedColumns();
2158 alignPanel.paintAlignment(true);
2161 public void hiddenMarkers_actionPerformed(ActionEvent e)
2163 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2170 * @param e DOCUMENT ME!
2172 protected void scaleAbove_actionPerformed(ActionEvent e)
2174 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2175 alignPanel.paintAlignment(true);
2181 * @param e DOCUMENT ME!
2183 protected void scaleLeft_actionPerformed(ActionEvent e)
2185 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2186 alignPanel.paintAlignment(true);
2192 * @param e DOCUMENT ME!
2194 protected void scaleRight_actionPerformed(ActionEvent e)
2196 viewport.setScaleRightWrapped(scaleRight.isSelected());
2197 alignPanel.paintAlignment(true);
2203 * @param e DOCUMENT ME!
2205 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2207 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2208 alignPanel.paintAlignment(true);
2214 * @param e DOCUMENT ME!
2216 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2218 viewport.setShowText(viewTextMenuItem.isSelected());
2219 alignPanel.paintAlignment(true);
2225 * @param e DOCUMENT ME!
2227 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2229 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2230 alignPanel.paintAlignment(true);
2234 public FeatureSettings featureSettings;
2235 public void featureSettings_actionPerformed(ActionEvent e)
2237 if(featureSettings !=null )
2239 featureSettings.close();
2240 featureSettings = null;
2242 featureSettings = new FeatureSettings(this);
2248 * @param evt DOCUMENT ME!
2250 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2252 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2253 alignPanel.paintAlignment(true);
2254 if (alignPanel.getOverviewPanel() != null)
2256 alignPanel.getOverviewPanel().updateOverviewImage();
2263 * @param e DOCUMENT ME!
2265 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2267 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2268 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2271 public void alignmentProperties()
2273 JEditorPane editPane = new JEditorPane("text/html","");
2274 editPane.setEditable(false);
2275 StringBuffer contents = new StringBuffer("<html>");
2278 int min=Integer.MAX_VALUE, max=0;
2279 for(int i=0; i<viewport.alignment.getHeight(); i++)
2281 int size = viewport.alignment.getSequenceAt(i).getEnd()
2282 -viewport.alignment.getSequenceAt(i).getStart();
2289 avg = avg/(float)viewport.alignment.getHeight();
2291 contents.append("<br>Sequences: "+ viewport.alignment.getHeight());
2292 contents.append("<br>Minimum Sequence Length: "+min);
2293 contents.append("<br>Maximum Sequence Length: "+max);
2294 contents.append("<br>Average Length: "+(int)avg);
2296 if (((Alignment)viewport.alignment).getProperties() != null)
2298 Hashtable props = ((Alignment)viewport.alignment).getProperties();
2299 Enumeration en = props.keys();
2300 contents.append("<br><br><table border=\"1\">");
2301 while(en.hasMoreElements())
2303 String key = en.nextElement().toString();
2304 StringBuffer val = new StringBuffer();
2305 String vals = props.get(key).toString();
2308 npos = vals.indexOf("\n",pos);
2311 val.append(vals.substring(pos));
2313 val.append(vals.substring(pos, npos));
2318 contents.append("<tr><td>"+key+"</td><td>"+val+"</td></tr>");
2320 contents.append("</table>");
2322 editPane.setText(contents.toString()+"</html>");
2323 JInternalFrame frame = new JInternalFrame();
2324 frame.getContentPane().add(editPane);
2325 Desktop.instance.addInternalFrame(frame,"Alignment Properties: "+getTitle(),500,400);
2332 * @param e DOCUMENT ME!
2334 public void overviewMenuItem_actionPerformed(ActionEvent e)
2336 if (alignPanel.overviewPanel != null)
2341 JInternalFrame frame = new JInternalFrame();
2342 OverviewPanel overview = new OverviewPanel(alignPanel);
2343 frame.setContentPane(overview);
2344 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2345 frame.getWidth(), frame.getHeight());
2347 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2348 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2350 public void internalFrameClosed(
2351 javax.swing.event.InternalFrameEvent evt)
2353 alignPanel.setOverviewPanel(null);
2358 alignPanel.setOverviewPanel(overview);
2361 public void textColour_actionPerformed(ActionEvent e)
2363 new TextColourChooser().chooseColour(alignPanel, null);
2369 * @param e DOCUMENT ME!
2371 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2379 * @param e DOCUMENT ME!
2381 public void clustalColour_actionPerformed(ActionEvent e)
2383 changeColour(new ClustalxColourScheme(
2384 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
2390 * @param e DOCUMENT ME!
2392 public void zappoColour_actionPerformed(ActionEvent e)
2394 changeColour(new ZappoColourScheme());
2400 * @param e DOCUMENT ME!
2402 public void taylorColour_actionPerformed(ActionEvent e)
2404 changeColour(new TaylorColourScheme());
2410 * @param e DOCUMENT ME!
2412 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2414 changeColour(new HydrophobicColourScheme());
2420 * @param e DOCUMENT ME!
2422 public void helixColour_actionPerformed(ActionEvent e)
2424 changeColour(new HelixColourScheme());
2430 * @param e DOCUMENT ME!
2432 public void strandColour_actionPerformed(ActionEvent e)
2434 changeColour(new StrandColourScheme());
2440 * @param e DOCUMENT ME!
2442 public void turnColour_actionPerformed(ActionEvent e)
2444 changeColour(new TurnColourScheme());
2450 * @param e DOCUMENT ME!
2452 public void buriedColour_actionPerformed(ActionEvent e)
2454 changeColour(new BuriedColourScheme());
2460 * @param e DOCUMENT ME!
2462 public void nucleotideColour_actionPerformed(ActionEvent e)
2464 changeColour(new NucleotideColourScheme());
2467 public void annotationColour_actionPerformed(ActionEvent e)
2469 new AnnotationColourChooser(viewport, alignPanel);
2476 * @param e DOCUMENT ME!
2478 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2480 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2486 * @param cs DOCUMENT ME!
2488 public void changeColour(ColourSchemeI cs)
2494 if (viewport.getAbovePIDThreshold())
2496 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2499 cs.setThreshold(threshold,
2500 viewport.getIgnoreGapsConsensus());
2502 viewport.setGlobalColourScheme(cs);
2506 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2509 if (viewport.getConservationSelected())
2512 Alignment al = (Alignment) viewport.alignment;
2513 Conservation c = new Conservation("All",
2514 ResidueProperties.propHash, 3,
2515 al.getSequences(), 0,
2519 c.verdict(false, viewport.ConsPercGaps);
2521 cs.setConservation(c);
2523 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
2528 cs.setConservation(null);
2531 cs.setConsensus(viewport.hconsensus);
2534 viewport.setGlobalColourScheme(cs);
2536 if (viewport.getColourAppliesToAllGroups())
2538 Vector groups = viewport.alignment.getGroups();
2540 for (int i = 0; i < groups.size(); i++)
2542 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2550 if (cs instanceof ClustalxColourScheme)
2552 sg.cs = new ClustalxColourScheme(
2553 sg.getSequences(viewport.hiddenRepSequences), sg.getWidth());
2555 else if (cs instanceof UserColourScheme)
2557 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
2563 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2565 catch (Exception ex)
2570 if (viewport.getAbovePIDThreshold()
2571 || cs instanceof PIDColourScheme
2572 || cs instanceof Blosum62ColourScheme)
2574 sg.cs.setThreshold(threshold,
2575 viewport.getIgnoreGapsConsensus());
2577 sg.cs.setConsensus(AAFrequency.calculate(
2578 sg.getSequences(viewport.hiddenRepSequences), sg.getStartRes(),
2583 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2587 if (viewport.getConservationSelected())
2589 Conservation c = new Conservation("Group",
2590 ResidueProperties.propHash, 3,
2591 sg.getSequences(viewport.
2592 hiddenRepSequences),
2596 c.verdict(false, viewport.ConsPercGaps);
2597 sg.cs.setConservation(c);
2601 sg.cs.setConservation(null);
2606 if (alignPanel.getOverviewPanel() != null)
2608 alignPanel.getOverviewPanel().updateOverviewImage();
2614 alignPanel.paintAlignment(true);
2620 * @param e DOCUMENT ME!
2622 protected void modifyPID_actionPerformed(ActionEvent e)
2624 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
2626 SliderPanel.setPIDSliderSource(alignPanel,
2627 viewport.getGlobalColourScheme(),
2629 SliderPanel.showPIDSlider();
2636 * @param e DOCUMENT ME!
2638 protected void modifyConservation_actionPerformed(ActionEvent e)
2640 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
2642 SliderPanel.setConservationSlider(alignPanel,
2643 viewport.globalColourScheme,
2645 SliderPanel.showConservationSlider();
2652 * @param e DOCUMENT ME!
2654 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2656 viewport.setConservationSelected(conservationMenuItem.isSelected());
2658 viewport.setAbovePIDThreshold(false);
2659 abovePIDThreshold.setSelected(false);
2661 changeColour(viewport.getGlobalColourScheme());
2663 modifyConservation_actionPerformed(null);
2669 * @param e DOCUMENT ME!
2671 public void abovePIDThreshold_actionPerformed(ActionEvent e)
2673 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
2675 conservationMenuItem.setSelected(false);
2676 viewport.setConservationSelected(false);
2678 changeColour(viewport.getGlobalColourScheme());
2680 modifyPID_actionPerformed(null);
2686 * @param e DOCUMENT ME!
2688 public void userDefinedColour_actionPerformed(ActionEvent e)
2690 if (e.getActionCommand().equals("User Defined..."))
2692 new UserDefinedColours(alignPanel, null);
2696 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
2697 getUserColourSchemes().get(e.getActionCommand());
2703 public void updateUserColourMenu()
2706 Component[] menuItems = colourMenu.getMenuComponents();
2707 int i, iSize = menuItems.length;
2708 for (i = 0; i < iSize; i++)
2710 if (menuItems[i].getName() != null &&
2711 menuItems[i].getName().equals("USER_DEFINED"))
2713 colourMenu.remove(menuItems[i]);
2717 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
2719 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
2720 getUserColourSchemes().keys();
2722 while (userColours.hasMoreElements())
2724 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
2726 nextElement().toString());
2727 radioItem.setName("USER_DEFINED");
2728 radioItem.addMouseListener(new MouseAdapter()
2730 public void mousePressed(MouseEvent evt)
2732 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
2734 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
2736 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
2738 "Remove from default list?",
2739 "Remove user defined colour",
2740 JOptionPane.YES_NO_OPTION);
2741 if(option == JOptionPane.YES_OPTION)
2743 jalview.gui.UserDefinedColours.removeColourFromDefaults(
2744 radioItem.getText());
2745 colourMenu.remove(radioItem);
2749 radioItem.addActionListener(new ActionListener()
2751 public void actionPerformed(ActionEvent evt)
2753 userDefinedColour_actionPerformed(evt);
2760 radioItem.addActionListener(new ActionListener()
2762 public void actionPerformed(ActionEvent evt)
2764 userDefinedColour_actionPerformed(evt);
2768 colourMenu.insert(radioItem, 15);
2769 colours.add(radioItem);
2777 * @param e DOCUMENT ME!
2779 public void PIDColour_actionPerformed(ActionEvent e)
2781 changeColour(new PIDColourScheme());
2787 * @param e DOCUMENT ME!
2789 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
2791 changeColour(new Blosum62ColourScheme());
2797 * @param e DOCUMENT ME!
2799 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2801 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2802 AlignmentSorter.sortByPID(viewport.getAlignment(),
2803 viewport.getAlignment().getSequenceAt(0));
2804 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2805 viewport.alignment));
2806 alignPanel.paintAlignment(true);
2812 * @param e DOCUMENT ME!
2814 public void sortIDMenuItem_actionPerformed(ActionEvent e)
2816 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2817 AlignmentSorter.sortByID(viewport.getAlignment());
2818 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
2819 alignPanel.paintAlignment(true);
2825 * @param e DOCUMENT ME!
2827 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
2829 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2830 AlignmentSorter.sortByGroup(viewport.getAlignment());
2831 addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
2833 alignPanel.paintAlignment(true);
2838 * @param e DOCUMENT ME!
2840 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2842 new RedundancyPanel(alignPanel, this);
2849 * @param e DOCUMENT ME!
2851 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2853 if ( (viewport.getSelectionGroup() == null) ||
2854 (viewport.getSelectionGroup().getSize() < 2))
2856 JOptionPane.showInternalMessageDialog(this,
2857 "You must select at least 2 sequences.",
2858 "Invalid Selection",
2859 JOptionPane.WARNING_MESSAGE);
2863 JInternalFrame frame = new JInternalFrame();
2864 frame.setContentPane(new PairwiseAlignPanel(viewport));
2865 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
2872 * @param e DOCUMENT ME!
2874 public void PCAMenuItem_actionPerformed(ActionEvent e)
2876 if ( ( (viewport.getSelectionGroup() != null) &&
2877 (viewport.getSelectionGroup().getSize() < 4) &&
2878 (viewport.getSelectionGroup().getSize() > 0)) ||
2879 (viewport.getAlignment().getHeight() < 4))
2881 JOptionPane.showInternalMessageDialog(this,
2882 "Principal component analysis must take\n" +
2883 "at least 4 input sequences.",
2884 "Sequence selection insufficient",
2885 JOptionPane.WARNING_MESSAGE);
2890 new PCAPanel(alignPanel);
2894 public void autoCalculate_actionPerformed(ActionEvent e)
2896 viewport.autoCalculateConsensus = autoCalculate.isSelected();
2897 if(viewport.autoCalculateConsensus)
2899 viewport.firePropertyChange("alignment",
2901 viewport.getAlignment().getSequences());
2909 * @param e DOCUMENT ME!
2911 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2913 NewTreePanel("AV", "PID", "Average distance tree using PID");
2919 * @param e DOCUMENT ME!
2921 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2923 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2929 * @param e DOCUMENT ME!
2931 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2933 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2939 * @param e DOCUMENT ME!
2941 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2943 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2949 * @param type DOCUMENT ME!
2950 * @param pwType DOCUMENT ME!
2951 * @param title DOCUMENT ME!
2953 void NewTreePanel(String type, String pwType, String title)
2957 if (viewport.getSelectionGroup() != null)
2959 if (viewport.getSelectionGroup().getSize() < 3)
2961 JOptionPane.showMessageDialog(Desktop.desktop,
2962 "You need to have more than two sequences selected to build a tree!",
2963 "Not enough sequences",
2964 JOptionPane.WARNING_MESSAGE);
2969 SequenceGroup sg = viewport.getSelectionGroup();
2971 /* Decide if the selection is a column region */
2972 while (s < sg.getSize())
2974 if ( ( (SequenceI) sg.getSequences(null).elementAt(s++)).getLength() <
2977 JOptionPane.showMessageDialog(Desktop.desktop,
2978 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
2979 "Try using the Pad function in the edit menu,\n" +
2980 "or one of the multiple sequence alignment web services.",
2981 "Sequences in selection are not aligned",
2982 JOptionPane.WARNING_MESSAGE);
2988 title = title + " on region";
2989 tp = new TreePanel(alignPanel, type, pwType);
2993 //are the sequences aligned?
2994 if (!viewport.alignment.isAligned())
2996 JOptionPane.showMessageDialog(Desktop.desktop,
2997 "The sequences must be aligned before creating a tree.\n" +
2998 "Try using the Pad function in the edit menu,\n" +
2999 "or one of the multiple sequence alignment web services.",
3000 "Sequences not aligned",
3001 JOptionPane.WARNING_MESSAGE);
3006 if(viewport.alignment.getHeight()<2)
3011 tp = new TreePanel(alignPanel, type, pwType);
3016 if(viewport.viewName!=null)
3018 title+= viewport.viewName+" of ";
3021 title += this.title;
3023 Desktop.addInternalFrame(tp, title, 600, 500);
3029 * @param title DOCUMENT ME!
3030 * @param order DOCUMENT ME!
3032 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
3034 final JMenuItem item = new JMenuItem("by " + title);
3036 item.addActionListener(new java.awt.event.ActionListener()
3038 public void actionPerformed(ActionEvent e)
3040 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
3042 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
3043 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3045 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3046 viewport.alignment));
3048 alignPanel.paintAlignment(true);
3053 * Add a new sort by annotation score menu item
3054 * @param sort the menu to add the option to
3055 * @param scoreLabel the label used to retrieve scores for each sequence on the alignment
3057 public void addSortByAnnotScoreMenuItem(JMenu sort, final String scoreLabel)
3059 final JMenuItem item = new JMenuItem(scoreLabel);
3061 item.addActionListener(new java.awt.event.ActionListener()
3063 public void actionPerformed(ActionEvent e)
3065 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
3066 AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport.getAlignment());
3067 addHistoryItem(new OrderCommand("Sort by "+scoreLabel, oldOrder, viewport.alignment));
3068 alignPanel.paintAlignment(true);
3073 * last hash for alignment's annotation array - used to minimise cost of rebuild.
3075 protected int _annotationScoreVectorHash;
3077 * search the alignment and rebuild the sort by annotation score submenu
3078 * the last alignment annotation vector hash is stored to minimize
3079 * cost of rebuilding in subsequence calls.
3082 public void buildSortByAnnotationScoresMenu()
3084 if (viewport.alignment.getAlignmentAnnotation().hashCode()!=_annotationScoreVectorHash)
3086 sortByAnnotScore.removeAll();
3087 // almost certainly a quicker way to do this - but we keep it simple
3088 Hashtable scoreSorts=new Hashtable();
3089 AlignmentAnnotation aann[] = viewport.alignment.getAlignmentAnnotation();
3090 for (int i=0;i<aann.length; i++)
3092 if (aann[i].hasScore() && aann[i].sequenceRef!=null)
3094 scoreSorts.put(aann[i].label, aann[i].label);
3097 Enumeration labels = scoreSorts.keys();
3098 while (labels.hasMoreElements())
3100 addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels.nextElement());
3102 sortByAnnotScore.setVisible(scoreSorts.size()>0);
3108 * Maintain the Order by->Displayed Tree menu.
3109 * Creates a new menu item for a TreePanel with an appropriate
3110 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
3111 * to remove the menu item when the treePanel is closed, and adjust
3112 * the tree leaf to sequence mapping when the alignment is modified.
3113 * @param treePanel Displayed tree window.
3114 * @param title SortBy menu item title.
3116 public void buildTreeMenu()
3118 sortByTreeMenu.removeAll();
3120 Vector comps = (Vector) PaintRefresher.components.get(viewport.
3121 getSequenceSetId());
3122 Vector treePanels = new Vector();
3123 int i, iSize = comps.size();
3124 for(i=0; i<iSize; i++)
3126 if(comps.elementAt(i) instanceof TreePanel)
3128 treePanels.add(comps.elementAt(i));
3132 iSize = treePanels.size();
3136 sortByTreeMenu.setVisible(false);
3140 sortByTreeMenu.setVisible(true);
3142 for(i=0; i<treePanels.size(); i++)
3144 TreePanel tp = (TreePanel)treePanels.elementAt(i);
3145 final JMenuItem item = new JMenuItem(tp.getTitle());
3146 final NJTree tree = ((TreePanel)treePanels.elementAt(i)).getTree();
3147 item.addActionListener(new java.awt.event.ActionListener()
3149 public void actionPerformed(ActionEvent e)
3151 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3152 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
3154 addHistoryItem(new OrderCommand("Tree Sort",
3156 viewport.alignment));
3158 alignPanel.paintAlignment(true);
3162 sortByTreeMenu.add(item);
3167 * Work out whether the whole set of sequences
3168 * or just the selected set will be submitted for multiple alignment.
3171 private jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3173 // Now, check we have enough sequences
3174 AlignmentView msa = null;
3176 if ( (viewport.getSelectionGroup() != null) &&
3177 (viewport.getSelectionGroup().getSize() > 1))
3179 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
3180 /*SequenceGroup seqs = viewport.getSelectionGroup();
3182 msa = new SequenceI[sz = seqs.getSize(false)];
3184 for (int i = 0; i < sz; i++)
3186 msa[i] = (SequenceI) seqs.getSequenceAt(i);
3188 msa = viewport.getAlignmentView(true);
3192 /*Vector seqs = viewport.getAlignment().getSequences();
3194 if (seqs.size() > 1)
3196 msa = new SequenceI[seqs.size()];
3198 for (int i = 0; i < seqs.size(); i++)
3200 msa[i] = (SequenceI) seqs.elementAt(i);
3203 msa = viewport.getAlignmentView(false);
3209 * Decides what is submitted to a secondary structure prediction service,
3210 * the currently selected sequence, or the currently selected alignment
3211 * (where the first sequence in the set is the one that the prediction
3214 AlignmentView gatherSeqOrMsaForSecStrPrediction()
3216 AlignmentView seqs = null;
3218 if ( (viewport.getSelectionGroup() != null) &&
3219 (viewport.getSelectionGroup().getSize() > 0))
3221 seqs = viewport.getAlignmentView(true);
3225 seqs = viewport.getAlignmentView(false);
3227 // limit sequences - JBPNote in future - could spawn multiple prediction jobs
3228 // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3229 if (!viewport.alignment.isAligned())
3231 seqs.setSequences(new SeqCigar[]
3232 {seqs.getSequences()[0]});
3239 * @param e DOCUMENT ME!
3241 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3243 // Pick the tree file
3244 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
3247 chooser.setFileView(new JalviewFileView());
3248 chooser.setDialogTitle("Select a newick-like tree file");
3249 chooser.setToolTipText("Load a tree file");
3251 int value = chooser.showOpenDialog(null);
3253 if (value == JalviewFileChooser.APPROVE_OPTION)
3255 String choice = chooser.getSelectedFile().getPath();
3256 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3260 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
3262 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3264 catch (Exception ex)
3266 JOptionPane.showMessageDialog(Desktop.desktop,
3267 "Problem reading tree file",
3269 JOptionPane.WARNING_MESSAGE);
3270 ex.printStackTrace();
3276 public TreePanel ShowNewickTree(NewickFile nf, String title)
3278 return ShowNewickTree(nf,title,600,500,4,5);
3281 public TreePanel ShowNewickTree(NewickFile nf, String title,
3282 AlignmentView input)
3284 return ShowNewickTree(nf,title, input, 600,500,4,5);
3287 public TreePanel ShowNewickTree(NewickFile nf, String title, int w, int h,
3290 return ShowNewickTree(nf, title, null, w, h, x, y);
3293 * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
3295 * @param nf the tree
3296 * @param title tree viewer title
3297 * @param input Associated alignment input data (or null)
3302 * @return TreePanel handle
3304 public TreePanel ShowNewickTree(NewickFile nf, String title,
3305 AlignmentView input, int w, int h, int x,
3308 TreePanel tp = null;
3314 if (nf.getTree() != null)
3316 tp = new TreePanel(alignPanel,
3325 tp.setLocation(x,y);
3329 Desktop.addInternalFrame(tp, title, w, h);
3332 catch (Exception ex)
3334 ex.printStackTrace();
3342 * Generates menu items and listener event actions for web service clients
3345 public void BuildWebServiceMenu()
3347 if ( (Discoverer.services != null)
3348 && (Discoverer.services.size() > 0))
3350 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
3351 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
3352 Vector wsmenu = new Vector();
3353 final AlignFrame af = this;
3356 // Add any Multiple Sequence Alignment Services
3357 final JMenu msawsmenu = new JMenu("Alignment");
3358 for (int i = 0, j = msaws.size(); i < j; i++)
3360 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
3362 final JMenuItem method = new JMenuItem(sh.getName());
3363 method.addActionListener(new ActionListener()
3365 public void actionPerformed(ActionEvent e)
3367 AlignmentView msa = gatherSequencesForAlignment();
3368 new jalview.ws.MsaWSClient(sh, title, msa,
3370 viewport.getAlignment().getDataset(),
3376 msawsmenu.add(method);
3377 // Deal with services that we know accept partial alignments.
3378 if (sh.getName().indexOf("lustal") > -1)
3380 // We know that ClustalWS can accept partial alignments for refinement.
3381 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
3382 methodR.addActionListener(new ActionListener()
3384 public void actionPerformed(ActionEvent e)
3386 AlignmentView msa = gatherSequencesForAlignment();
3387 new jalview.ws.MsaWSClient(sh, title, msa,
3389 viewport.getAlignment().getDataset(),
3395 msawsmenu.add(methodR);
3399 wsmenu.add(msawsmenu);
3401 if (secstrpr != null)
3403 // Add any secondary structure prediction services
3404 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
3405 for (int i = 0, j = secstrpr.size(); i < j; i++)
3407 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
3409 final JMenuItem method = new JMenuItem(sh.getName());
3410 method.addActionListener(new ActionListener()
3412 public void actionPerformed(ActionEvent e)
3414 AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
3415 if (msa.getSequences().length == 1)
3417 // Single Sequence prediction
3418 new jalview.ws.JPredClient(sh, title, false, msa, af, true);
3422 if (msa.getSequences().length > 1)
3424 // Sequence profile based prediction
3425 new jalview.ws.JPredClient(sh,
3426 title, true, msa, af, true);
3431 secstrmenu.add(method);
3433 wsmenu.add(secstrmenu);
3435 resetWebServiceMenu();
3436 for (int i = 0, j = wsmenu.size(); i < j; i++)
3438 webService.add( (JMenu) wsmenu.get(i));
3443 resetWebServiceMenu();
3444 this.webService.add(this.webServiceNoServices);
3446 // TODO: add in rediscovery function
3447 // TODO: reduce code redundancy.
3448 // TODO: group services by location as well as function.
3453 * empty the web service menu and add any ad-hoc functions
3454 * not dynamically discovered.
3457 private void resetWebServiceMenu()
3459 webService.removeAll();
3460 // Temporary hack - DBRef Fetcher always top level ws entry.
3461 JMenuItem rfetch = new JMenuItem("Fetch DB References");
3462 rfetch.setToolTipText("Retrieve and parse uniprot records for the alignment or the currently selected sequences");
3463 webService.add(rfetch);
3464 rfetch.addActionListener(new ActionListener() {
3466 public void actionPerformed(ActionEvent e)
3468 new jalview.io.DBRefFetcher(
3469 alignPanel.av.getSequenceSelection(),
3470 alignPanel.alignFrame).fetchDBRefs(false);
3476 /* public void vamsasStore_actionPerformed(ActionEvent e)
3478 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
3479 getProperty("LAST_DIRECTORY"));
3481 chooser.setFileView(new JalviewFileView());
3482 chooser.setDialogTitle("Export to Vamsas file");
3483 chooser.setToolTipText("Export");
3485 int value = chooser.showSaveDialog(this);
3487 if (value == JalviewFileChooser.APPROVE_OPTION)
3489 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
3490 //vs.store(chooser.getSelectedFile().getAbsolutePath() );
3491 vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
3497 public void showTranslation_actionPerformed(ActionEvent e)
3499 ///////////////////////////////
3500 // Collect Data to be translated/transferred
3502 SequenceI [] selection = viewport.getSequenceSelection();
3503 String [] seqstring = viewport.getViewAsString(true);
3504 AlignmentI al = null;
3506 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring, viewport.getViewAsVisibleContigs(true),
3507 viewport.getGapCharacter(), viewport.alignment.getAlignmentAnnotation(),
3508 viewport.alignment.getWidth());
3509 } catch (Exception ex) {
3511 jalview.bin.Cache.log.debug("Exception during translation.",ex);
3515 JOptionPane.showMessageDialog(Desktop.desktop,
3516 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
3517 "Translation Failed",
3518 JOptionPane.WARNING_MESSAGE);
3520 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
3521 Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
3530 * @param String DOCUMENT ME!
3532 public boolean parseFeaturesFile(String file, String type)
3534 boolean featuresFile = false;
3537 featuresFile = new FeaturesFile(file,
3538 type).parse(viewport.alignment.getDataset(),
3539 alignPanel.seqPanel.seqCanvas.
3540 getFeatureRenderer().featureColours,
3545 ex.printStackTrace();
3550 viewport.showSequenceFeatures = true;
3551 showSeqFeatures.setSelected(true);
3552 alignPanel.paintAlignment(true);
3555 return featuresFile;
3558 public void dragEnter(DropTargetDragEvent evt)
3561 public void dragExit(DropTargetEvent evt)
3564 public void dragOver(DropTargetDragEvent evt)
3567 public void dropActionChanged(DropTargetDragEvent evt)
3570 public void drop(DropTargetDropEvent evt)
3572 Transferable t = evt.getTransferable();
3573 java.util.List files = null;
3577 DataFlavor uriListFlavor = new DataFlavor(
3578 "text/uri-list;class=java.lang.String");
3579 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
3581 //Works on Windows and MacOSX
3582 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3583 files = (java.util.List) t.getTransferData(DataFlavor.
3584 javaFileListFlavor);
3586 else if (t.isDataFlavorSupported(uriListFlavor))
3588 // This is used by Unix drag system
3589 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3590 String data = (String) t.getTransferData(uriListFlavor);
3591 files = new java.util.ArrayList(1);
3592 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
3595 st.hasMoreTokens(); )
3597 String s = st.nextToken();
3598 if (s.startsWith("#"))
3600 // the line is a comment (as per the RFC 2483)
3604 java.net.URI uri = new java.net.URI(s);
3605 java.io.File file = new java.io.File(uri);
3612 e.printStackTrace();
3619 for (int i = 0; i < files.size(); i++)
3621 loadJalviewDataFile(files.get(i).toString());
3624 catch (Exception ex)
3626 ex.printStackTrace();
3631 // This method will attempt to load a "dropped" file first by testing
3632 // whether its and Annotation file, then features file. If both are
3633 // false then the user may have dropped an alignment file onto this
3635 public void loadJalviewDataFile(String file)
3639 String protocol = "File";
3641 if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
3646 boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
3647 alignment, file, protocol);
3651 boolean isGroupsFile = parseFeaturesFile(file,protocol);
3654 String format = new IdentifyFile().Identify(file, protocol);
3656 if(format.equalsIgnoreCase("JnetFile"))
3658 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
3660 new JnetAnnotationMaker().add_annotation(predictions,
3661 viewport.getAlignment(),
3663 alignPanel.adjustAnnotationHeight();
3664 alignPanel.paintAlignment(true);
3668 new FileLoader().LoadFile(viewport, file, protocol, format);
3675 alignPanel.adjustAnnotationHeight();
3679 catch (Exception ex)
3681 ex.printStackTrace();
3685 public void tabSelectionChanged(int index)
3689 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
3690 viewport = alignPanel.av;
3691 setMenusFromViewport(viewport);
3695 public void tabbedPane_mousePressed(MouseEvent e)
3697 if(SwingUtilities.isRightMouseButton(e))
3699 String reply = JOptionPane.showInternalInputDialog(this,
3702 JOptionPane.QUESTION_MESSAGE);
3706 viewport.viewName = reply;
3707 tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
3713 public AlignViewport getCurrentView()
3720 * Open the dialog for regex description parsing.
3722 protected void extractScores_actionPerformed(ActionEvent e)
3724 ParseProperties pp = new jalview.analysis.ParseProperties(viewport.alignment);
3725 if (pp.getScoresFromDescription("col", "score column ", "\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)")>0)
3727 buildSortByAnnotationScoresMenu();
3736 public PrintThread(AlignmentPanel ap)
3740 static PageFormat pf;
3743 PrinterJob printJob = PrinterJob.getPrinterJob();
3747 printJob.setPrintable(ap, pf);
3751 printJob.setPrintable(ap);
3754 if (printJob.printDialog())
3760 catch (Exception PrintException)
3762 PrintException.printStackTrace();