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);
145 buildSortByAnnotationScoresMenu();
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;
1054 * @return alignment objects for all views
1056 AlignmentI[] getViewAlignments()
1058 if (alignPanels!=null)
1060 Enumeration e = alignPanels.elements();
1061 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1062 for (int i=0; e.hasMoreElements(); i++)
1064 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1070 return new AlignmentI[] { viewport.alignment };
1077 * @param e DOCUMENT ME!
1079 protected void undoMenuItem_actionPerformed(ActionEvent e)
1081 if (viewport.historyList.empty())
1083 CommandI command = (CommandI)viewport.historyList.pop();
1084 viewport.redoList.push(command);
1085 command.undoCommand(getViewAlignments());
1087 AlignViewport originalSource = getOriginatingSource(command);
1088 updateEditMenuBar();
1090 if(originalSource!=null)
1092 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1093 originalSource.firePropertyChange("alignment",
1095 originalSource.alignment.getSequences());
1102 * @param e DOCUMENT ME!
1104 protected void redoMenuItem_actionPerformed(ActionEvent e)
1106 if(viewport.redoList.size()<1)
1111 CommandI command = (CommandI) viewport.redoList.pop();
1112 viewport.historyList.push(command);
1113 command.doCommand(getViewAlignments());
1115 AlignViewport originalSource = getOriginatingSource(command);
1116 updateEditMenuBar();
1118 if(originalSource!=null)
1120 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1121 originalSource.firePropertyChange("alignment",
1123 originalSource.alignment.getSequences());
1127 AlignViewport getOriginatingSource(CommandI command)
1129 AlignViewport originalSource = null;
1130 //For sequence removal and addition, we need to fire
1131 //the property change event FROM the viewport where the
1132 //original alignment was altered
1134 if (command instanceof EditCommand)
1136 EditCommand editCommand = (EditCommand) command;
1137 al = editCommand.getAlignment();
1138 Vector comps = (Vector) PaintRefresher.components
1139 .get(viewport.getSequenceSetId());
1141 for (int i = 0; i < comps.size(); i++)
1143 if (comps.elementAt(i) instanceof AlignmentPanel)
1145 if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
1147 originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
1154 if (originalSource == null)
1156 //The original view is closed, we must validate
1157 //the current view against the closed view first
1160 PaintRefresher.validateSequences(al, viewport.alignment);
1163 originalSource = viewport;
1166 return originalSource;
1172 * @param up DOCUMENT ME!
1174 public void moveSelectedSequences(boolean up)
1176 SequenceGroup sg = viewport.getSelectionGroup();
1185 for (int i = 1; i < viewport.alignment.getHeight(); 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);
1207 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1209 SequenceI seq = viewport.alignment.getSequenceAt(i);
1211 if (!sg.getSequences(null).contains(seq))
1216 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1218 if (sg.getSequences(null).contains(temp))
1223 viewport.alignment.getSequences().setElementAt(temp, i);
1224 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1228 alignPanel.paintAlignment(true);
1234 synchronized void slideSequences(boolean right, int size)
1236 Vector sg = new Vector();
1237 if(viewport.cursorMode)
1239 sg.addElement(viewport.alignment.getSequenceAt(
1240 alignPanel.seqPanel.seqCanvas.cursorY));
1242 else if(viewport.getSelectionGroup()!=null
1243 && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight())
1245 sg = viewport.getSelectionGroup().getSequences(
1246 viewport.hiddenRepSequences);
1254 Vector invertGroup = new Vector();
1256 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1258 if(!sg.contains(viewport.alignment.getSequenceAt(i)))
1259 invertGroup.add(viewport.alignment.getSequenceAt(i));
1262 SequenceI[] seqs1 = new SequenceI[sg.size()];
1263 for (int i = 0; i < sg.size(); i++)
1264 seqs1[i] = (SequenceI) sg.elementAt(i);
1266 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1267 for (int i = 0; i < invertGroup.size(); i++)
1268 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1270 SlideSequencesCommand ssc;
1272 ssc = new SlideSequencesCommand("Slide Sequences",
1274 viewport.getGapCharacter()
1277 ssc = new SlideSequencesCommand("Slide Sequences",
1279 viewport.getGapCharacter()
1282 int groupAdjustment = 0;
1283 if (ssc.getGapsInsertedBegin() && right)
1285 if (viewport.cursorMode)
1286 alignPanel.seqPanel.moveCursor(size, 0);
1288 groupAdjustment = size;
1290 else if (!ssc.getGapsInsertedBegin() && !right)
1292 if (viewport.cursorMode)
1293 alignPanel.seqPanel.moveCursor( -size, 0);
1295 groupAdjustment = -size;
1298 if (groupAdjustment != 0)
1300 viewport.getSelectionGroup().setStartRes(
1301 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1302 viewport.getSelectionGroup().setEndRes(
1303 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1307 boolean appendHistoryItem = false;
1308 if(viewport.historyList!=null
1309 && viewport.historyList.size()>0
1310 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1312 appendHistoryItem = ssc.appendSlideCommand(
1313 (SlideSequencesCommand)viewport.historyList.peek())
1317 if(!appendHistoryItem)
1318 addHistoryItem(ssc);
1327 * @param e DOCUMENT ME!
1329 protected void copy_actionPerformed(ActionEvent e)
1332 if (viewport.getSelectionGroup() == null)
1336 // TODO: preserve the ordering of displayed alignment annotation in any internal paste (particularly sequence associated annotation)
1337 SequenceI [] seqs = viewport.getSelectionAsNewSequence();
1338 String[] omitHidden = null;
1340 if (viewport.hasHiddenColumns)
1342 omitHidden = viewport.getViewAsString(true);
1345 String output = new FormatAdapter().formatSequences(
1350 StringSelection ss = new StringSelection(output);
1354 jalview.gui.Desktop.internalCopy = true;
1355 //Its really worth setting the clipboard contents
1356 //to empty before setting the large StringSelection!!
1357 Toolkit.getDefaultToolkit().getSystemClipboard()
1358 .setContents(new StringSelection(""), null);
1360 Toolkit.getDefaultToolkit().getSystemClipboard()
1361 .setContents(ss, Desktop.instance);
1363 catch (OutOfMemoryError er)
1365 er.printStackTrace();
1366 javax.swing.SwingUtilities.invokeLater(new Runnable()
1370 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1371 "Out of memory copying region!!"
1373 "\nSee help files for increasing Java Virtual Machine memory."
1375 javax.swing.JOptionPane.WARNING_MESSAGE);
1382 Vector hiddenColumns = null;
1383 if(viewport.hasHiddenColumns)
1385 hiddenColumns =new Vector();
1386 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1387 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
1390 int[] region = (int[])
1391 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
1393 hiddenColumns.addElement(new int[]
1394 {region[0] - hiddenOffset,
1395 region[1]-hiddenOffset});
1399 Desktop.jalviewClipboard = new Object[]
1402 viewport.alignment.getDataset(),
1404 statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
1410 * @param e DOCUMENT ME!
1412 protected void pasteNew_actionPerformed(ActionEvent e)
1420 * @param e DOCUMENT ME!
1422 protected void pasteThis_actionPerformed(ActionEvent e)
1430 * @param newAlignment DOCUMENT ME!
1432 void paste(boolean newAlignment)
1434 boolean externalPaste=true;
1437 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1438 Transferable contents = c.getContents(this);
1440 if (contents == null)
1448 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1449 if (str.length() < 1)
1454 format = new IdentifyFile().Identify(str, "Paste");
1457 catch (OutOfMemoryError er)
1459 er.printStackTrace();
1460 javax.swing.SwingUtilities.invokeLater(new Runnable()
1464 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1465 "Out of memory pasting sequences!!"
1467 "\nSee help files for increasing Java Virtual Machine memory."
1469 javax.swing.JOptionPane.WARNING_MESSAGE);
1476 SequenceI[] sequences;
1477 boolean annotationAdded = false;
1478 AlignmentI alignment = null;
1480 if(Desktop.jalviewClipboard!=null)
1482 // The clipboard was filled from within Jalview, we must use the sequences
1483 // And dataset from the copied alignment
1484 SequenceI[] newseq = (SequenceI[])Desktop.jalviewClipboard[0];
1485 // be doubly sure that we create *new* sequence objects.
1486 sequences = new SequenceI[newseq.length];
1487 for (int i=0;i<newseq.length;i++) {
1488 sequences[i] = new Sequence(newseq[i]);
1490 alignment = new Alignment(sequences);
1491 externalPaste = false;
1495 // parse the clipboard as an alignment.
1496 alignment = new FormatAdapter().readFile(str, "Paste", format);
1497 sequences = alignment.getSequencesArray();
1505 if (Desktop.jalviewClipboard != null)
1507 // dataset is inherited
1508 alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
1512 // new dataset is constructed
1513 alignment.setDataset(null);
1515 alwidth = alignment.getWidth()+1;
1519 AlignmentI pastedal = alignment; // preserve pasted alignment object
1520 // Add pasted sequences and dataset into existing alignment.
1521 alignment = viewport.getAlignment();
1522 alwidth = alignment.getWidth()+1;
1523 // decide if we need to import sequences from an existing dataset
1524 boolean importDs = Desktop.jalviewClipboard != null
1525 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1526 // importDs==true instructs us to copy over new dataset sequences from
1527 // an existing alignment
1528 Vector newDs = (importDs) ? new Vector() : null; // used to create
1529 // minimum dataset set
1531 for (int i = 0; i < sequences.length; i++)
1535 newDs.addElement(null);
1537 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1539 if (importDs && ds != null)
1541 if (!newDs.contains(ds))
1543 newDs.setElementAt(ds, i);
1544 ds = new Sequence(ds);
1545 // update with new dataset sequence
1546 sequences[i].setDatasetSequence(ds);
1550 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1555 // copy and derive new dataset sequence
1556 sequences[i] = sequences[i].deriveSequence();
1557 alignment.getDataset().addSequence(sequences[i].getDatasetSequence());
1558 // TODO: avoid creation of duplicate dataset sequences with a
1559 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1561 alignment.addSequence(sequences[i]); // merges dataset
1565 newDs.clear(); // tidy up
1567 if (pastedal.getAlignmentAnnotation()!=null) {
1568 // Add any annotation attached to alignment.
1569 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1570 for (int i=0; i<alann.length; i++)
1572 annotationAdded=true;
1573 if (alann[i].sequenceRef==null && !alann[i].autoCalculated) {
1574 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1575 newann.padAnnotation(alwidth);
1576 alignment.addAnnotation(newann);
1581 if (!newAlignment) {
1585 addHistoryItem(new EditCommand(
1590 alignment.getWidth(),
1594 // Add any annotations attached to sequences
1595 for (int i = 0; i < sequences.length; i++)
1597 if (sequences[i].getAnnotation() != null)
1599 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1601 annotationAdded=true;
1602 sequences[i].getAnnotation()[a].adjustForAlignment();
1603 sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1604 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation was duplicated earlier
1605 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1609 if (!newAlignment) {
1611 // propagate alignment changed.
1612 viewport.setEndSeq(alignment.getHeight());
1613 if (annotationAdded)
1615 // Duplicate sequence annotation in all views.
1616 AlignmentI[] alview = this.getViewAlignments();
1617 for (int avnum=0;avnum<alview.length; avnum++)
1619 if (alview[avnum]!=alignment)
1621 // duplicate in a view other than the one with input focus
1622 int avwidth = alview[avnum].getWidth()+1;
1623 for (int i=0; i < sequences.length; i++)
1625 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1628 // this relies on sann being preserved after we modify the sequence's annotation array
1629 for (int a=0; a<sann.length; a++)
1631 AlignmentAnnotation newann = new AlignmentAnnotation(sann[a]);
1632 sequences[i].addAlignmentAnnotation(newann);
1633 newann.padAnnotation(avwidth);
1634 alview[avnum].addAnnotation(newann); // annotation was duplicated earlier
1635 alview[avnum].setAnnotationIndex(newann, a);
1640 buildSortByAnnotationScoresMenu();
1642 viewport.firePropertyChange("alignment", null, alignment.getSequences());
1645 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
1646 String newtitle = new String("Copied sequences");
1648 if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
1650 Vector hc = (Vector)Desktop.jalviewClipboard[2];
1651 for(int i=0; i<hc.size(); i++)
1653 int [] region = (int[]) hc.elementAt(i);
1654 af.viewport.hideColumns(region[0], region[1]);
1659 //>>>This is a fix for the moment, until a better solution is found!!<<<
1660 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
1661 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1663 // TODO: maintain provenance of an alignment, rather than just make the title a concatenation of operations.
1664 if (!externalPaste) {
1665 if (title.startsWith("Copied sequences"))
1671 newtitle = newtitle.concat("- from " + title);
1674 newtitle = new String("Pasted sequences");
1677 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1684 catch (Exception ex)
1686 ex.printStackTrace();
1687 System.out.println("Exception whilst pasting: "+ex);
1688 // could be anything being pasted in here
1697 * @param e DOCUMENT ME!
1699 protected void cut_actionPerformed(ActionEvent e)
1701 copy_actionPerformed(null);
1702 delete_actionPerformed(null);
1708 * @param e DOCUMENT ME!
1710 protected void delete_actionPerformed(ActionEvent evt)
1713 SequenceGroup sg = viewport.getSelectionGroup();
1719 Vector seqs = new Vector();
1721 for (int i = 0; i < sg.getSize(); i++)
1723 seq = sg.getSequenceAt(i);
1724 seqs.addElement(seq);
1728 // If the cut affects all sequences, remove highlighted columns
1729 if (sg.getSize() == viewport.alignment.getHeight())
1731 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1732 sg.getEndRes() + 1);
1736 SequenceI [] cut = new SequenceI[seqs.size()];
1737 for(int i=0; i<seqs.size(); i++)
1739 cut[i] = (SequenceI)seqs.elementAt(i);
1746 addHistoryItem(new EditCommand("Cut Sequences",
1750 sg.getEndRes()-sg.getStartRes()+1,
1751 viewport.alignment));
1754 viewport.setSelectionGroup(null);
1755 viewport.alignment.deleteGroup(sg);
1757 viewport.firePropertyChange("alignment", null,
1758 viewport.getAlignment().getSequences());
1760 if (viewport.getAlignment().getHeight() < 1)
1764 this.setClosed(true);
1766 catch (Exception ex)
1775 * @param e DOCUMENT ME!
1777 protected void deleteGroups_actionPerformed(ActionEvent e)
1779 viewport.alignment.deleteAllGroups();
1780 viewport.sequenceColours = null;
1781 viewport.setSelectionGroup(null);
1782 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1783 alignPanel.paintAlignment(true);
1789 * @param e DOCUMENT ME!
1791 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1793 SequenceGroup sg = new SequenceGroup();
1795 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1798 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1801 sg.setEndRes(viewport.alignment.getWidth() - 1);
1802 viewport.setSelectionGroup(sg);
1803 alignPanel.paintAlignment(true);
1804 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1810 * @param e DOCUMENT ME!
1812 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1814 if(viewport.cursorMode)
1816 alignPanel.seqPanel.keyboardNo1 = null;
1817 alignPanel.seqPanel.keyboardNo2 = null;
1819 viewport.setSelectionGroup(null);
1820 viewport.getColumnSelection().clear();
1821 viewport.setSelectionGroup(null);
1822 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1823 alignPanel.idPanel.idCanvas.searchResults = null;
1824 alignPanel.paintAlignment(true);
1825 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1831 * @param e DOCUMENT ME!
1833 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1835 SequenceGroup sg = viewport.getSelectionGroup();
1839 selectAllSequenceMenuItem_actionPerformed(null);
1844 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1847 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1850 alignPanel.paintAlignment(true);
1852 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1855 public void invertColSel_actionPerformed(ActionEvent e)
1857 viewport.invertColumnSelection();
1858 alignPanel.paintAlignment(true);
1865 * @param e DOCUMENT ME!
1867 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1869 trimAlignment(true);
1875 * @param e DOCUMENT ME!
1877 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
1879 trimAlignment(false);
1882 void trimAlignment(boolean trimLeft)
1884 ColumnSelection colSel = viewport.getColumnSelection();
1887 if (colSel.size() > 0)
1891 column = colSel.getMin();
1895 column = colSel.getMax();
1899 if(viewport.getSelectionGroup()!=null)
1901 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
1902 hiddenRepSequences);
1906 seqs = viewport.alignment.getSequencesArray();
1910 TrimRegionCommand trimRegion;
1913 trimRegion = new TrimRegionCommand("Remove Left",
1914 TrimRegionCommand.TRIM_LEFT,
1919 viewport.selectionGroup);
1920 viewport.setStartRes(0);
1924 trimRegion = new TrimRegionCommand("Remove Right",
1925 TrimRegionCommand.TRIM_RIGHT,
1930 viewport.selectionGroup);
1933 statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
1936 addHistoryItem(trimRegion);
1938 Vector groups = viewport.alignment.getGroups();
1940 for (int i = 0; i < groups.size(); i++)
1942 SequenceGroup sg = (SequenceGroup) groups.get(i);
1944 if ( (trimLeft && !sg.adjustForRemoveLeft(column))
1945 || (!trimLeft && !sg.adjustForRemoveRight(column)))
1947 viewport.alignment.deleteGroup(sg);
1951 viewport.firePropertyChange("alignment", null,
1952 viewport.getAlignment().getSequences());
1959 * @param e DOCUMENT ME!
1961 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1963 int start = 0, end = viewport.alignment.getWidth()-1;
1966 if (viewport.getSelectionGroup() != null)
1968 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
1969 hiddenRepSequences);
1970 start = viewport.getSelectionGroup().getStartRes();
1971 end = viewport.getSelectionGroup().getEndRes();
1975 seqs = viewport.alignment.getSequencesArray();
1979 RemoveGapColCommand removeGapCols =
1980 new RemoveGapColCommand("Remove Gapped Columns",
1983 viewport.alignment);
1985 addHistoryItem(removeGapCols);
1987 statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
1989 //This is to maintain viewport position on first residue
1991 SequenceI seq = viewport.alignment.getSequenceAt(0);
1992 int startRes = seq.findPosition(viewport.startRes);
1993 // ShiftList shifts;
1994 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
1995 // edit.alColumnChanges=shifts.getInverse();
1996 // if (viewport.hasHiddenColumns)
1997 // viewport.getColumnSelection().compensateForEdits(shifts);
1998 viewport.setStartRes(seq.findIndex(startRes)-1);
1999 viewport.firePropertyChange("alignment", null,
2000 viewport.getAlignment().getSequences());
2007 * @param e DOCUMENT ME!
2009 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2011 int start = 0, end = viewport.alignment.getWidth()-1;
2014 if (viewport.getSelectionGroup() != null)
2016 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
2017 hiddenRepSequences);
2018 start = viewport.getSelectionGroup().getStartRes();
2019 end = viewport.getSelectionGroup().getEndRes();
2023 seqs = viewport.alignment.getSequencesArray();
2026 //This is to maintain viewport position on first residue
2028 SequenceI seq = viewport.alignment.getSequenceAt(0);
2029 int startRes = seq.findPosition(viewport.startRes);
2031 addHistoryItem(new RemoveGapsCommand("Remove Gaps",
2034 viewport.alignment));
2036 viewport.setStartRes(seq.findIndex(startRes)-1);
2038 viewport.firePropertyChange("alignment", null,
2039 viewport.getAlignment().getSequences());
2046 * @param e DOCUMENT ME!
2048 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2050 viewport.padGaps = padGapsMenuitem.isSelected();
2052 viewport.firePropertyChange("alignment",
2054 viewport.getAlignment().getSequences());
2060 * @param e DOCUMENT ME!
2062 public void findMenuItem_actionPerformed(ActionEvent e)
2067 public void newView_actionPerformed(ActionEvent e)
2069 AlignmentPanel newap =
2070 new Jalview2XML().copyAlignPanel(alignPanel, true);
2072 newap.av.gatherViewsHere = false;
2074 if (viewport.viewName == null)
2076 viewport.viewName = "Original";
2079 newap.av.historyList = viewport.historyList;
2080 newap.av.redoList = viewport.redoList;
2082 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2083 String newViewName = "View " +index;
2085 Vector comps = (Vector) PaintRefresher.components.get(viewport.
2086 getSequenceSetId());
2087 Vector existingNames = new Vector();
2088 for(int i=0; i<comps.size(); i++)
2090 if(comps.elementAt(i) instanceof AlignmentPanel)
2092 AlignmentPanel ap = (AlignmentPanel)comps.elementAt(i);
2093 if(!existingNames.contains(ap.av.viewName))
2095 existingNames.addElement(ap.av.viewName);
2100 while(existingNames.contains(newViewName))
2102 newViewName = "View "+ (++index);
2105 newap.av.viewName = newViewName;
2107 addAlignmentPanel(newap, false);
2109 if(alignPanels.size()==2)
2111 viewport.gatherViewsHere = true;
2113 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2116 public void expandViews_actionPerformed(ActionEvent e)
2118 Desktop.instance.explodeViews(this);
2121 public void gatherViews_actionPerformed(ActionEvent e)
2123 Desktop.instance.gatherViews(this);
2131 * @param e DOCUMENT ME!
2133 public void font_actionPerformed(ActionEvent e)
2135 new FontChooser(alignPanel);
2142 * @param e DOCUMENT ME!
2144 protected void seqLimit_actionPerformed(ActionEvent e)
2146 viewport.setShowJVSuffix(seqLimits.isSelected());
2148 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
2149 alignPanel.paintAlignment(true);
2152 public void idRightAlign_actionPerformed(ActionEvent e)
2154 viewport.rightAlignIds = idRightAlign.isSelected();
2155 alignPanel.paintAlignment(true);
2163 * @param e DOCUMENT ME!
2165 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2167 viewport.setColourText(colourTextMenuItem.isSelected());
2168 alignPanel.paintAlignment(true);
2174 * @param e DOCUMENT ME!
2176 public void wrapMenuItem_actionPerformed(ActionEvent e)
2178 scaleAbove.setVisible(wrapMenuItem.isSelected());
2179 scaleLeft.setVisible(wrapMenuItem.isSelected());
2180 scaleRight.setVisible(wrapMenuItem.isSelected());
2181 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2182 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2185 public void showAllSeqs_actionPerformed(ActionEvent e)
2187 viewport.showAllHiddenSeqs();
2190 public void showAllColumns_actionPerformed(ActionEvent e)
2192 viewport.showAllHiddenColumns();
2196 public void hideSelSequences_actionPerformed(ActionEvent e)
2198 viewport.hideAllSelectedSeqs();
2199 alignPanel.paintAlignment(true);
2202 public void hideSelColumns_actionPerformed(ActionEvent e)
2204 viewport.hideSelectedColumns();
2205 alignPanel.paintAlignment(true);
2208 public void hiddenMarkers_actionPerformed(ActionEvent e)
2210 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2217 * @param e DOCUMENT ME!
2219 protected void scaleAbove_actionPerformed(ActionEvent e)
2221 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2222 alignPanel.paintAlignment(true);
2228 * @param e DOCUMENT ME!
2230 protected void scaleLeft_actionPerformed(ActionEvent e)
2232 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2233 alignPanel.paintAlignment(true);
2239 * @param e DOCUMENT ME!
2241 protected void scaleRight_actionPerformed(ActionEvent e)
2243 viewport.setScaleRightWrapped(scaleRight.isSelected());
2244 alignPanel.paintAlignment(true);
2250 * @param e DOCUMENT ME!
2252 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2254 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2255 alignPanel.paintAlignment(true);
2261 * @param e DOCUMENT ME!
2263 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2265 viewport.setShowText(viewTextMenuItem.isSelected());
2266 alignPanel.paintAlignment(true);
2272 * @param e DOCUMENT ME!
2274 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2276 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2277 alignPanel.paintAlignment(true);
2281 public FeatureSettings featureSettings;
2282 public void featureSettings_actionPerformed(ActionEvent e)
2284 if(featureSettings !=null )
2286 featureSettings.close();
2287 featureSettings = null;
2289 featureSettings = new FeatureSettings(this);
2295 * @param evt DOCUMENT ME!
2297 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2299 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2300 alignPanel.paintAlignment(true);
2301 if (alignPanel.getOverviewPanel() != null)
2303 alignPanel.getOverviewPanel().updateOverviewImage();
2310 * @param e DOCUMENT ME!
2312 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2314 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2315 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2318 public void alignmentProperties()
2320 JEditorPane editPane = new JEditorPane("text/html","");
2321 editPane.setEditable(false);
2322 StringBuffer contents = new StringBuffer("<html>");
2325 int min=Integer.MAX_VALUE, max=0;
2326 for(int i=0; i<viewport.alignment.getHeight(); i++)
2328 int size = viewport.alignment.getSequenceAt(i).getEnd()
2329 -viewport.alignment.getSequenceAt(i).getStart();
2336 avg = avg/(float)viewport.alignment.getHeight();
2338 contents.append("<br>Sequences: "+ viewport.alignment.getHeight());
2339 contents.append("<br>Minimum Sequence Length: "+min);
2340 contents.append("<br>Maximum Sequence Length: "+max);
2341 contents.append("<br>Average Length: "+(int)avg);
2343 if (((Alignment)viewport.alignment).getProperties() != null)
2345 Hashtable props = ((Alignment)viewport.alignment).getProperties();
2346 Enumeration en = props.keys();
2347 contents.append("<br><br><table border=\"1\">");
2348 while(en.hasMoreElements())
2350 String key = en.nextElement().toString();
2351 StringBuffer val = new StringBuffer();
2352 String vals = props.get(key).toString();
2355 npos = vals.indexOf("\n",pos);
2358 val.append(vals.substring(pos));
2360 val.append(vals.substring(pos, npos));
2365 contents.append("<tr><td>"+key+"</td><td>"+val+"</td></tr>");
2367 contents.append("</table>");
2369 editPane.setText(contents.toString()+"</html>");
2370 JInternalFrame frame = new JInternalFrame();
2371 frame.getContentPane().add(new JScrollPane(editPane));
2373 Desktop.instance.addInternalFrame(frame,"Alignment Properties: "+getTitle(),500,400);
2380 * @param e DOCUMENT ME!
2382 public void overviewMenuItem_actionPerformed(ActionEvent e)
2384 if (alignPanel.overviewPanel != null)
2389 JInternalFrame frame = new JInternalFrame();
2390 OverviewPanel overview = new OverviewPanel(alignPanel);
2391 frame.setContentPane(overview);
2392 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2393 frame.getWidth(), frame.getHeight());
2395 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2396 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2398 public void internalFrameClosed(
2399 javax.swing.event.InternalFrameEvent evt)
2401 alignPanel.setOverviewPanel(null);
2406 alignPanel.setOverviewPanel(overview);
2409 public void textColour_actionPerformed(ActionEvent e)
2411 new TextColourChooser().chooseColour(alignPanel, null);
2417 * @param e DOCUMENT ME!
2419 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2427 * @param e DOCUMENT ME!
2429 public void clustalColour_actionPerformed(ActionEvent e)
2431 changeColour(new ClustalxColourScheme(
2432 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
2438 * @param e DOCUMENT ME!
2440 public void zappoColour_actionPerformed(ActionEvent e)
2442 changeColour(new ZappoColourScheme());
2448 * @param e DOCUMENT ME!
2450 public void taylorColour_actionPerformed(ActionEvent e)
2452 changeColour(new TaylorColourScheme());
2458 * @param e DOCUMENT ME!
2460 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2462 changeColour(new HydrophobicColourScheme());
2468 * @param e DOCUMENT ME!
2470 public void helixColour_actionPerformed(ActionEvent e)
2472 changeColour(new HelixColourScheme());
2478 * @param e DOCUMENT ME!
2480 public void strandColour_actionPerformed(ActionEvent e)
2482 changeColour(new StrandColourScheme());
2488 * @param e DOCUMENT ME!
2490 public void turnColour_actionPerformed(ActionEvent e)
2492 changeColour(new TurnColourScheme());
2498 * @param e DOCUMENT ME!
2500 public void buriedColour_actionPerformed(ActionEvent e)
2502 changeColour(new BuriedColourScheme());
2508 * @param e DOCUMENT ME!
2510 public void nucleotideColour_actionPerformed(ActionEvent e)
2512 changeColour(new NucleotideColourScheme());
2515 public void annotationColour_actionPerformed(ActionEvent e)
2517 new AnnotationColourChooser(viewport, alignPanel);
2524 * @param e DOCUMENT ME!
2526 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2528 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2534 * @param cs DOCUMENT ME!
2536 public void changeColour(ColourSchemeI cs)
2542 if (viewport.getAbovePIDThreshold())
2544 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2547 cs.setThreshold(threshold,
2548 viewport.getIgnoreGapsConsensus());
2550 viewport.setGlobalColourScheme(cs);
2554 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2557 if (viewport.getConservationSelected())
2560 Alignment al = (Alignment) viewport.alignment;
2561 Conservation c = new Conservation("All",
2562 ResidueProperties.propHash, 3,
2563 al.getSequences(), 0,
2567 c.verdict(false, viewport.ConsPercGaps);
2569 cs.setConservation(c);
2571 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
2576 cs.setConservation(null);
2579 cs.setConsensus(viewport.hconsensus);
2582 viewport.setGlobalColourScheme(cs);
2584 if (viewport.getColourAppliesToAllGroups())
2586 Vector groups = viewport.alignment.getGroups();
2588 for (int i = 0; i < groups.size(); i++)
2590 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2598 if (cs instanceof ClustalxColourScheme)
2600 sg.cs = new ClustalxColourScheme(
2601 sg.getSequences(viewport.hiddenRepSequences), sg.getWidth());
2603 else if (cs instanceof UserColourScheme)
2605 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
2611 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2613 catch (Exception ex)
2618 if (viewport.getAbovePIDThreshold()
2619 || cs instanceof PIDColourScheme
2620 || cs instanceof Blosum62ColourScheme)
2622 sg.cs.setThreshold(threshold,
2623 viewport.getIgnoreGapsConsensus());
2625 sg.cs.setConsensus(AAFrequency.calculate(
2626 sg.getSequences(viewport.hiddenRepSequences), sg.getStartRes(),
2631 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2635 if (viewport.getConservationSelected())
2637 Conservation c = new Conservation("Group",
2638 ResidueProperties.propHash, 3,
2639 sg.getSequences(viewport.
2640 hiddenRepSequences),
2644 c.verdict(false, viewport.ConsPercGaps);
2645 sg.cs.setConservation(c);
2649 sg.cs.setConservation(null);
2654 if (alignPanel.getOverviewPanel() != null)
2656 alignPanel.getOverviewPanel().updateOverviewImage();
2662 alignPanel.paintAlignment(true);
2668 * @param e DOCUMENT ME!
2670 protected void modifyPID_actionPerformed(ActionEvent e)
2672 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
2674 SliderPanel.setPIDSliderSource(alignPanel,
2675 viewport.getGlobalColourScheme(),
2677 SliderPanel.showPIDSlider();
2684 * @param e DOCUMENT ME!
2686 protected void modifyConservation_actionPerformed(ActionEvent e)
2688 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
2690 SliderPanel.setConservationSlider(alignPanel,
2691 viewport.globalColourScheme,
2693 SliderPanel.showConservationSlider();
2700 * @param e DOCUMENT ME!
2702 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2704 viewport.setConservationSelected(conservationMenuItem.isSelected());
2706 viewport.setAbovePIDThreshold(false);
2707 abovePIDThreshold.setSelected(false);
2709 changeColour(viewport.getGlobalColourScheme());
2711 modifyConservation_actionPerformed(null);
2717 * @param e DOCUMENT ME!
2719 public void abovePIDThreshold_actionPerformed(ActionEvent e)
2721 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
2723 conservationMenuItem.setSelected(false);
2724 viewport.setConservationSelected(false);
2726 changeColour(viewport.getGlobalColourScheme());
2728 modifyPID_actionPerformed(null);
2734 * @param e DOCUMENT ME!
2736 public void userDefinedColour_actionPerformed(ActionEvent e)
2738 if (e.getActionCommand().equals("User Defined..."))
2740 new UserDefinedColours(alignPanel, null);
2744 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
2745 getUserColourSchemes().get(e.getActionCommand());
2751 public void updateUserColourMenu()
2754 Component[] menuItems = colourMenu.getMenuComponents();
2755 int i, iSize = menuItems.length;
2756 for (i = 0; i < iSize; i++)
2758 if (menuItems[i].getName() != null &&
2759 menuItems[i].getName().equals("USER_DEFINED"))
2761 colourMenu.remove(menuItems[i]);
2765 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
2767 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
2768 getUserColourSchemes().keys();
2770 while (userColours.hasMoreElements())
2772 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
2774 nextElement().toString());
2775 radioItem.setName("USER_DEFINED");
2776 radioItem.addMouseListener(new MouseAdapter()
2778 public void mousePressed(MouseEvent evt)
2780 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
2782 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
2784 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
2786 "Remove from default list?",
2787 "Remove user defined colour",
2788 JOptionPane.YES_NO_OPTION);
2789 if(option == JOptionPane.YES_OPTION)
2791 jalview.gui.UserDefinedColours.removeColourFromDefaults(
2792 radioItem.getText());
2793 colourMenu.remove(radioItem);
2797 radioItem.addActionListener(new ActionListener()
2799 public void actionPerformed(ActionEvent evt)
2801 userDefinedColour_actionPerformed(evt);
2808 radioItem.addActionListener(new ActionListener()
2810 public void actionPerformed(ActionEvent evt)
2812 userDefinedColour_actionPerformed(evt);
2816 colourMenu.insert(radioItem, 15);
2817 colours.add(radioItem);
2825 * @param e DOCUMENT ME!
2827 public void PIDColour_actionPerformed(ActionEvent e)
2829 changeColour(new PIDColourScheme());
2835 * @param e DOCUMENT ME!
2837 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
2839 changeColour(new Blosum62ColourScheme());
2845 * @param e DOCUMENT ME!
2847 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2849 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2850 AlignmentSorter.sortByPID(viewport.getAlignment(),
2851 viewport.getAlignment().getSequenceAt(0));
2852 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2853 viewport.alignment));
2854 alignPanel.paintAlignment(true);
2860 * @param e DOCUMENT ME!
2862 public void sortIDMenuItem_actionPerformed(ActionEvent e)
2864 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2865 AlignmentSorter.sortByID(viewport.getAlignment());
2866 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
2867 alignPanel.paintAlignment(true);
2873 * @param e DOCUMENT ME!
2875 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
2877 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2878 AlignmentSorter.sortByGroup(viewport.getAlignment());
2879 addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
2881 alignPanel.paintAlignment(true);
2886 * @param e DOCUMENT ME!
2888 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2890 new RedundancyPanel(alignPanel, this);
2897 * @param e DOCUMENT ME!
2899 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2901 if ( (viewport.getSelectionGroup() == null) ||
2902 (viewport.getSelectionGroup().getSize() < 2))
2904 JOptionPane.showInternalMessageDialog(this,
2905 "You must select at least 2 sequences.",
2906 "Invalid Selection",
2907 JOptionPane.WARNING_MESSAGE);
2911 JInternalFrame frame = new JInternalFrame();
2912 frame.setContentPane(new PairwiseAlignPanel(viewport));
2913 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
2920 * @param e DOCUMENT ME!
2922 public void PCAMenuItem_actionPerformed(ActionEvent e)
2924 if ( ( (viewport.getSelectionGroup() != null) &&
2925 (viewport.getSelectionGroup().getSize() < 4) &&
2926 (viewport.getSelectionGroup().getSize() > 0)) ||
2927 (viewport.getAlignment().getHeight() < 4))
2929 JOptionPane.showInternalMessageDialog(this,
2930 "Principal component analysis must take\n" +
2931 "at least 4 input sequences.",
2932 "Sequence selection insufficient",
2933 JOptionPane.WARNING_MESSAGE);
2938 new PCAPanel(alignPanel);
2942 public void autoCalculate_actionPerformed(ActionEvent e)
2944 viewport.autoCalculateConsensus = autoCalculate.isSelected();
2945 if(viewport.autoCalculateConsensus)
2947 viewport.firePropertyChange("alignment",
2949 viewport.getAlignment().getSequences());
2957 * @param e DOCUMENT ME!
2959 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2961 NewTreePanel("AV", "PID", "Average distance tree using PID");
2967 * @param e DOCUMENT ME!
2969 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2971 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2977 * @param e DOCUMENT ME!
2979 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2981 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2987 * @param e DOCUMENT ME!
2989 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2991 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2997 * @param type DOCUMENT ME!
2998 * @param pwType DOCUMENT ME!
2999 * @param title DOCUMENT ME!
3001 void NewTreePanel(String type, String pwType, String title)
3005 if (viewport.getSelectionGroup() != null)
3007 if (viewport.getSelectionGroup().getSize() < 3)
3009 JOptionPane.showMessageDialog(Desktop.desktop,
3010 "You need to have more than two sequences selected to build a tree!",
3011 "Not enough sequences",
3012 JOptionPane.WARNING_MESSAGE);
3017 SequenceGroup sg = viewport.getSelectionGroup();
3019 /* Decide if the selection is a column region */
3020 while (s < sg.getSize())
3022 if ( ( (SequenceI) sg.getSequences(null).elementAt(s++)).getLength() <
3025 JOptionPane.showMessageDialog(Desktop.desktop,
3026 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
3027 "Try using the Pad function in the edit menu,\n" +
3028 "or one of the multiple sequence alignment web services.",
3029 "Sequences in selection are not aligned",
3030 JOptionPane.WARNING_MESSAGE);
3036 title = title + " on region";
3037 tp = new TreePanel(alignPanel, type, pwType);
3041 //are the sequences aligned?
3042 if (!viewport.alignment.isAligned())
3044 JOptionPane.showMessageDialog(Desktop.desktop,
3045 "The sequences must be aligned before creating a tree.\n" +
3046 "Try using the Pad function in the edit menu,\n" +
3047 "or one of the multiple sequence alignment web services.",
3048 "Sequences not aligned",
3049 JOptionPane.WARNING_MESSAGE);
3054 if(viewport.alignment.getHeight()<2)
3059 tp = new TreePanel(alignPanel, type, pwType);
3064 if(viewport.viewName!=null)
3066 title+= viewport.viewName+" of ";
3069 title += this.title;
3071 Desktop.addInternalFrame(tp, title, 600, 500);
3077 * @param title DOCUMENT ME!
3078 * @param order DOCUMENT ME!
3080 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
3082 final JMenuItem item = new JMenuItem("by " + title);
3084 item.addActionListener(new java.awt.event.ActionListener()
3086 public void actionPerformed(ActionEvent e)
3088 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
3090 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
3091 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3093 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3094 viewport.alignment));
3096 alignPanel.paintAlignment(true);
3101 * Add a new sort by annotation score menu item
3102 * @param sort the menu to add the option to
3103 * @param scoreLabel the label used to retrieve scores for each sequence on the alignment
3105 public void addSortByAnnotScoreMenuItem(JMenu sort, final String scoreLabel)
3107 final JMenuItem item = new JMenuItem(scoreLabel);
3109 item.addActionListener(new java.awt.event.ActionListener()
3111 public void actionPerformed(ActionEvent e)
3113 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
3114 AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport.getAlignment());
3115 addHistoryItem(new OrderCommand("Sort by "+scoreLabel, oldOrder, viewport.alignment));
3116 alignPanel.paintAlignment(true);
3121 * last hash for alignment's annotation array - used to minimise cost of rebuild.
3123 protected int _annotationScoreVectorHash;
3125 * search the alignment and rebuild the sort by annotation score submenu
3126 * the last alignment annotation vector hash is stored to minimize
3127 * cost of rebuilding in subsequence calls.
3130 public void buildSortByAnnotationScoresMenu()
3132 if (viewport.alignment.getAlignmentAnnotation().hashCode()!=_annotationScoreVectorHash)
3134 sortByAnnotScore.removeAll();
3135 // almost certainly a quicker way to do this - but we keep it simple
3136 Hashtable scoreSorts=new Hashtable();
3137 AlignmentAnnotation aann[];
3138 Enumeration sq = viewport.alignment.getSequences().elements();
3139 while (sq.hasMoreElements())
3141 aann = ((SequenceI) sq.nextElement()).getAnnotation();
3142 for (int i=0;aann!=null && i<aann.length; i++)
3144 if (aann[i].hasScore() && aann[i].sequenceRef!=null)
3146 scoreSorts.put(aann[i].label, aann[i].label);
3150 Enumeration labels = scoreSorts.keys();
3151 while (labels.hasMoreElements())
3153 addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels.nextElement());
3155 sortByAnnotScore.setVisible(scoreSorts.size()>0);
3161 * Maintain the Order by->Displayed Tree menu.
3162 * Creates a new menu item for a TreePanel with an appropriate
3163 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
3164 * to remove the menu item when the treePanel is closed, and adjust
3165 * the tree leaf to sequence mapping when the alignment is modified.
3166 * @param treePanel Displayed tree window.
3167 * @param title SortBy menu item title.
3169 public void buildTreeMenu()
3171 sortByTreeMenu.removeAll();
3173 Vector comps = (Vector) PaintRefresher.components.get(viewport.
3174 getSequenceSetId());
3175 Vector treePanels = new Vector();
3176 int i, iSize = comps.size();
3177 for(i=0; i<iSize; i++)
3179 if(comps.elementAt(i) instanceof TreePanel)
3181 treePanels.add(comps.elementAt(i));
3185 iSize = treePanels.size();
3189 sortByTreeMenu.setVisible(false);
3193 sortByTreeMenu.setVisible(true);
3195 for(i=0; i<treePanels.size(); i++)
3197 TreePanel tp = (TreePanel)treePanels.elementAt(i);
3198 final JMenuItem item = new JMenuItem(tp.getTitle());
3199 final NJTree tree = ((TreePanel)treePanels.elementAt(i)).getTree();
3200 item.addActionListener(new java.awt.event.ActionListener()
3202 public void actionPerformed(ActionEvent e)
3204 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3205 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
3207 addHistoryItem(new OrderCommand("Tree Sort",
3209 viewport.alignment));
3211 alignPanel.paintAlignment(true);
3215 sortByTreeMenu.add(item);
3220 * Work out whether the whole set of sequences
3221 * or just the selected set will be submitted for multiple alignment.
3224 private jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3226 // Now, check we have enough sequences
3227 AlignmentView msa = null;
3229 if ( (viewport.getSelectionGroup() != null) &&
3230 (viewport.getSelectionGroup().getSize() > 1))
3232 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
3233 /*SequenceGroup seqs = viewport.getSelectionGroup();
3235 msa = new SequenceI[sz = seqs.getSize(false)];
3237 for (int i = 0; i < sz; i++)
3239 msa[i] = (SequenceI) seqs.getSequenceAt(i);
3241 msa = viewport.getAlignmentView(true);
3245 /*Vector seqs = viewport.getAlignment().getSequences();
3247 if (seqs.size() > 1)
3249 msa = new SequenceI[seqs.size()];
3251 for (int i = 0; i < seqs.size(); i++)
3253 msa[i] = (SequenceI) seqs.elementAt(i);
3256 msa = viewport.getAlignmentView(false);
3262 * Decides what is submitted to a secondary structure prediction service,
3263 * the currently selected sequence, or the currently selected alignment
3264 * (where the first sequence in the set is the one that the prediction
3267 AlignmentView gatherSeqOrMsaForSecStrPrediction()
3269 AlignmentView seqs = null;
3271 if ( (viewport.getSelectionGroup() != null) &&
3272 (viewport.getSelectionGroup().getSize() > 0))
3274 seqs = viewport.getAlignmentView(true);
3278 seqs = viewport.getAlignmentView(false);
3280 // limit sequences - JBPNote in future - could spawn multiple prediction jobs
3281 // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3282 if (!viewport.alignment.isAligned())
3284 seqs.setSequences(new SeqCigar[]
3285 {seqs.getSequences()[0]});
3292 * @param e DOCUMENT ME!
3294 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3296 // Pick the tree file
3297 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
3300 chooser.setFileView(new JalviewFileView());
3301 chooser.setDialogTitle("Select a newick-like tree file");
3302 chooser.setToolTipText("Load a tree file");
3304 int value = chooser.showOpenDialog(null);
3306 if (value == JalviewFileChooser.APPROVE_OPTION)
3308 String choice = chooser.getSelectedFile().getPath();
3309 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3313 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
3315 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3317 catch (Exception ex)
3319 JOptionPane.showMessageDialog(Desktop.desktop,
3320 "Problem reading tree file",
3322 JOptionPane.WARNING_MESSAGE);
3323 ex.printStackTrace();
3329 public TreePanel ShowNewickTree(NewickFile nf, String title)
3331 return ShowNewickTree(nf,title,600,500,4,5);
3334 public TreePanel ShowNewickTree(NewickFile nf, String title,
3335 AlignmentView input)
3337 return ShowNewickTree(nf,title, input, 600,500,4,5);
3340 public TreePanel ShowNewickTree(NewickFile nf, String title, int w, int h,
3343 return ShowNewickTree(nf, title, null, w, h, x, y);
3346 * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
3348 * @param nf the tree
3349 * @param title tree viewer title
3350 * @param input Associated alignment input data (or null)
3355 * @return TreePanel handle
3357 public TreePanel ShowNewickTree(NewickFile nf, String title,
3358 AlignmentView input, int w, int h, int x,
3361 TreePanel tp = null;
3367 if (nf.getTree() != null)
3369 tp = new TreePanel(alignPanel,
3378 tp.setLocation(x,y);
3382 Desktop.addInternalFrame(tp, title, w, h);
3385 catch (Exception ex)
3387 ex.printStackTrace();
3395 * Generates menu items and listener event actions for web service clients
3398 public void BuildWebServiceMenu()
3400 if ( (Discoverer.services != null)
3401 && (Discoverer.services.size() > 0))
3403 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
3404 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
3405 Vector wsmenu = new Vector();
3406 final AlignFrame af = this;
3409 // Add any Multiple Sequence Alignment Services
3410 final JMenu msawsmenu = new JMenu("Alignment");
3411 for (int i = 0, j = msaws.size(); i < j; i++)
3413 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
3415 final JMenuItem method = new JMenuItem(sh.getName());
3416 method.addActionListener(new ActionListener()
3418 public void actionPerformed(ActionEvent e)
3420 AlignmentView msa = gatherSequencesForAlignment();
3421 new jalview.ws.MsaWSClient(sh, title, msa,
3423 viewport.getAlignment().getDataset(),
3429 msawsmenu.add(method);
3430 // Deal with services that we know accept partial alignments.
3431 if (sh.getName().indexOf("lustal") > -1)
3433 // We know that ClustalWS can accept partial alignments for refinement.
3434 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
3435 methodR.addActionListener(new ActionListener()
3437 public void actionPerformed(ActionEvent e)
3439 AlignmentView msa = gatherSequencesForAlignment();
3440 new jalview.ws.MsaWSClient(sh, title, msa,
3442 viewport.getAlignment().getDataset(),
3448 msawsmenu.add(methodR);
3452 wsmenu.add(msawsmenu);
3454 if (secstrpr != null)
3456 // Add any secondary structure prediction services
3457 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
3458 for (int i = 0, j = secstrpr.size(); i < j; i++)
3460 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
3462 final JMenuItem method = new JMenuItem(sh.getName());
3463 method.addActionListener(new ActionListener()
3465 public void actionPerformed(ActionEvent e)
3467 AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
3468 if (msa.getSequences().length == 1)
3470 // Single Sequence prediction
3471 new jalview.ws.JPredClient(sh, title, false, msa, af, true);
3475 if (msa.getSequences().length > 1)
3477 // Sequence profile based prediction
3478 new jalview.ws.JPredClient(sh,
3479 title, true, msa, af, true);
3484 secstrmenu.add(method);
3486 wsmenu.add(secstrmenu);
3488 resetWebServiceMenu();
3489 for (int i = 0, j = wsmenu.size(); i < j; i++)
3491 webService.add( (JMenu) wsmenu.get(i));
3496 resetWebServiceMenu();
3497 this.webService.add(this.webServiceNoServices);
3499 // TODO: add in rediscovery function
3500 // TODO: reduce code redundancy.
3501 // TODO: group services by location as well as function.
3506 * empty the web service menu and add any ad-hoc functions
3507 * not dynamically discovered.
3510 private void resetWebServiceMenu()
3512 webService.removeAll();
3513 // Temporary hack - DBRef Fetcher always top level ws entry.
3514 JMenuItem rfetch = new JMenuItem("Fetch DB References");
3515 rfetch.setToolTipText("Retrieve and parse uniprot records for the alignment or the currently selected sequences");
3516 webService.add(rfetch);
3517 rfetch.addActionListener(new ActionListener() {
3519 public void actionPerformed(ActionEvent e)
3521 new jalview.io.DBRefFetcher(
3522 alignPanel.av.getSequenceSelection(),
3523 alignPanel.alignFrame).fetchDBRefs(false);
3529 /* public void vamsasStore_actionPerformed(ActionEvent e)
3531 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
3532 getProperty("LAST_DIRECTORY"));
3534 chooser.setFileView(new JalviewFileView());
3535 chooser.setDialogTitle("Export to Vamsas file");
3536 chooser.setToolTipText("Export");
3538 int value = chooser.showSaveDialog(this);
3540 if (value == JalviewFileChooser.APPROVE_OPTION)
3542 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
3543 //vs.store(chooser.getSelectedFile().getAbsolutePath() );
3544 vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
3550 public void showTranslation_actionPerformed(ActionEvent e)
3552 ///////////////////////////////
3553 // Collect Data to be translated/transferred
3555 SequenceI [] selection = viewport.getSequenceSelection();
3556 String [] seqstring = viewport.getViewAsString(true);
3557 AlignmentI al = null;
3559 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring, viewport.getViewAsVisibleContigs(true),
3560 viewport.getGapCharacter(), viewport.alignment.getAlignmentAnnotation(),
3561 viewport.alignment.getWidth());
3562 } catch (Exception ex) {
3564 jalview.bin.Cache.log.debug("Exception during translation.",ex);
3568 JOptionPane.showMessageDialog(Desktop.desktop,
3569 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
3570 "Translation Failed",
3571 JOptionPane.WARNING_MESSAGE);
3573 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
3574 Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
3583 * @param String DOCUMENT ME!
3585 public boolean parseFeaturesFile(String file, String type)
3587 boolean featuresFile = false;
3590 featuresFile = new FeaturesFile(file,
3591 type).parse(viewport.alignment.getDataset(),
3592 alignPanel.seqPanel.seqCanvas.
3593 getFeatureRenderer().featureColours,
3598 ex.printStackTrace();
3603 viewport.showSequenceFeatures = true;
3604 showSeqFeatures.setSelected(true);
3605 alignPanel.paintAlignment(true);
3608 return featuresFile;
3611 public void dragEnter(DropTargetDragEvent evt)
3614 public void dragExit(DropTargetEvent evt)
3617 public void dragOver(DropTargetDragEvent evt)
3620 public void dropActionChanged(DropTargetDragEvent evt)
3623 public void drop(DropTargetDropEvent evt)
3625 Transferable t = evt.getTransferable();
3626 java.util.List files = null;
3630 DataFlavor uriListFlavor = new DataFlavor(
3631 "text/uri-list;class=java.lang.String");
3632 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
3634 //Works on Windows and MacOSX
3635 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3636 files = (java.util.List) t.getTransferData(DataFlavor.
3637 javaFileListFlavor);
3639 else if (t.isDataFlavorSupported(uriListFlavor))
3641 // This is used by Unix drag system
3642 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3643 String data = (String) t.getTransferData(uriListFlavor);
3644 files = new java.util.ArrayList(1);
3645 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
3648 st.hasMoreTokens(); )
3650 String s = st.nextToken();
3651 if (s.startsWith("#"))
3653 // the line is a comment (as per the RFC 2483)
3657 java.net.URI uri = new java.net.URI(s);
3658 java.io.File file = new java.io.File(uri);
3665 e.printStackTrace();
3672 for (int i = 0; i < files.size(); i++)
3674 loadJalviewDataFile(files.get(i).toString());
3677 catch (Exception ex)
3679 ex.printStackTrace();
3684 // This method will attempt to load a "dropped" file first by testing
3685 // whether its and Annotation file, then features file. If both are
3686 // false then the user may have dropped an alignment file onto this
3688 public void loadJalviewDataFile(String file)
3692 String protocol = "File";
3694 if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
3699 boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
3700 alignment, file, protocol);
3704 boolean isGroupsFile = parseFeaturesFile(file,protocol);
3707 String format = new IdentifyFile().Identify(file, protocol);
3709 if(format.equalsIgnoreCase("JnetFile"))
3711 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
3713 new JnetAnnotationMaker().add_annotation(predictions,
3714 viewport.getAlignment(),
3716 alignPanel.adjustAnnotationHeight();
3717 alignPanel.paintAlignment(true);
3721 new FileLoader().LoadFile(viewport, file, protocol, format);
3728 alignPanel.adjustAnnotationHeight();
3729 buildSortByAnnotationScoresMenu();
3733 catch (Exception ex)
3735 ex.printStackTrace();
3739 public void tabSelectionChanged(int index)
3743 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
3744 viewport = alignPanel.av;
3745 setMenusFromViewport(viewport);
3749 public void tabbedPane_mousePressed(MouseEvent e)
3751 if(SwingUtilities.isRightMouseButton(e))
3753 String reply = JOptionPane.showInternalInputDialog(this,
3756 JOptionPane.QUESTION_MESSAGE);
3760 viewport.viewName = reply;
3761 tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
3767 public AlignViewport getCurrentView()
3774 * Open the dialog for regex description parsing.
3776 protected void extractScores_actionPerformed(ActionEvent e)
3778 ParseProperties pp = new jalview.analysis.ParseProperties(viewport.alignment);
3779 if (pp.getScoresFromDescription("col", "score column ", "\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)")>0)
3781 buildSortByAnnotationScoresMenu();
3790 public PrintThread(AlignmentPanel ap)
3794 static PageFormat pf;
3797 PrinterJob printJob = PrinterJob.getPrinterJob();
3801 printJob.setPrintable(ap, pf);
3805 printJob.setPrintable(ap);
3808 if (printJob.printDialog())
3814 catch (Exception PrintException)
3816 PrintException.printStackTrace();