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.*;
32 import jalview.analysis.*;
33 import jalview.commands.*;
34 import jalview.datamodel.*;
36 import jalview.jbgui.*;
37 import jalview.schemes.*;
46 public class AlignFrame
47 extends GAlignFrame implements DropTargetListener
50 public static final int DEFAULT_WIDTH = 700;
53 public static final int DEFAULT_HEIGHT = 500;
54 public AlignmentPanel alignPanel;
56 AlignViewport viewport;
58 Vector alignPanels = new Vector();
62 String currentFileFormat = null;
64 String fileName = null;
68 * Creates a new AlignFrame object.
70 * @param al DOCUMENT ME!
72 public AlignFrame(AlignmentI al, int width, int height)
74 this(al, null, width, height);
79 * new alignment window with hidden columns
80 * @param al AlignmentI
81 * @param hiddenColumns ColumnSelection or null
83 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
84 int width, int height)
86 this.setSize(width, height);
87 viewport = new AlignViewport(al, hiddenColumns);
89 alignPanel = new AlignmentPanel(this, viewport);
91 if(al.getDataset()==null)
96 addAlignmentPanel(alignPanel, true);
101 * Make a new AlignFrame from exisiting alignmentPanels
102 * @param ap AlignmentPanel
103 * @param av AlignViewport
105 public AlignFrame(AlignmentPanel ap)
109 addAlignmentPanel(ap, false);
115 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
117 if (viewport.conservation == null)
119 BLOSUM62Colour.setEnabled(false);
120 conservationMenuItem.setEnabled(false);
121 modifyConservation.setEnabled(false);
122 // PIDColour.setEnabled(false);
123 // abovePIDThreshold.setEnabled(false);
124 // modifyPID.setEnabled(false);
127 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
129 if (sortby.equals("Id"))
131 sortIDMenuItem_actionPerformed(null);
133 else if (sortby.equals("Pairwise Identity"))
135 sortPairwiseMenuItem_actionPerformed(null);
138 if (Desktop.desktop != null)
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 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
180 switch (evt.getKeyCode())
183 case 27: // escape key
184 deselectAllSequenceMenuItem_actionPerformed(null);
188 case KeyEvent.VK_DOWN:
189 if (evt.isAltDown() || !viewport.cursorMode)
190 moveSelectedSequences(false);
191 if (viewport.cursorMode)
192 alignPanel.seqPanel.moveCursor(0, 1);
196 if (evt.isAltDown() || !viewport.cursorMode)
197 moveSelectedSequences(true);
198 if (viewport.cursorMode)
199 alignPanel.seqPanel.moveCursor(0, -1);
203 case KeyEvent.VK_LEFT:
204 if (evt.isAltDown() || !viewport.cursorMode)
205 slideSequences(false,
206 alignPanel.seqPanel.getKeyboardNo1());
208 alignPanel.seqPanel.moveCursor( -1, 0);
213 case KeyEvent.VK_RIGHT:
214 if (evt.isAltDown() || !viewport.cursorMode)
216 alignPanel.seqPanel.getKeyboardNo1());
218 alignPanel.seqPanel.moveCursor(1, 0);
221 case KeyEvent.VK_SPACE:
222 if (viewport.cursorMode)
224 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
230 case KeyEvent.VK_DELETE:
231 case KeyEvent.VK_BACK_SPACE:
232 if (!viewport.cursorMode)
234 cut_actionPerformed(null);
238 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
246 if (viewport.cursorMode)
248 alignPanel.seqPanel.setCursorRow();
252 if (viewport.cursorMode && !evt.isControlDown())
254 alignPanel.seqPanel.setCursorColumn();
258 if (viewport.cursorMode)
260 alignPanel.seqPanel.setCursorPosition();
264 case KeyEvent.VK_ENTER:
265 case KeyEvent.VK_COMMA:
266 if (viewport.cursorMode)
268 alignPanel.seqPanel.setCursorRowAndColumn();
273 if (viewport.cursorMode)
275 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
279 if (viewport.cursorMode)
281 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
286 viewport.cursorMode = !viewport.cursorMode;
287 statusBar.setText("Keyboard editing mode is " +
288 (viewport.cursorMode ? "on" : "off"));
289 if (viewport.cursorMode)
291 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
292 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
294 alignPanel.seqPanel.seqCanvas.repaint();
300 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
301 java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
302 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
304 javax.help.HelpBroker hb = hs.createHelpBroker();
305 hb.setCurrentID("home");
306 hb.setDisplayed(true);
310 ex.printStackTrace();
316 boolean toggleSeqs = !evt.isControlDown();
317 boolean toggleCols = !evt.isShiftDown();
319 boolean hide = false;
321 SequenceGroup sg = viewport.getSelectionGroup();
324 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
326 hideSelSequences_actionPerformed(null);
329 else if (! (toggleCols &&
330 viewport.colSel.getSelected().size() > 0))
332 showAllSeqs_actionPerformed(null);
338 if (viewport.colSel.getSelected().size() > 0)
340 hideSelColumns_actionPerformed(null);
343 viewport.selectionGroup = sg;
348 showAllColumns_actionPerformed(null);
353 case KeyEvent.VK_PAGE_UP:
354 if (viewport.wrapAlignment)
356 alignPanel.scrollUp(true);
360 alignPanel.setScrollValues(viewport.startRes,
362 - viewport.endSeq + viewport.startSeq);
365 case KeyEvent.VK_PAGE_DOWN:
366 if (viewport.wrapAlignment)
368 alignPanel.scrollUp(false);
372 alignPanel.setScrollValues(viewport.startRes,
374 + viewport.endSeq - viewport.startSeq);
380 public void keyReleased(KeyEvent evt)
382 switch(evt.getKeyCode())
384 case KeyEvent.VK_LEFT:
385 if (evt.isAltDown() || !viewport.cursorMode)
386 viewport.firePropertyChange("alignment", null,
387 viewport.getAlignment().getSequences());
390 case KeyEvent.VK_RIGHT:
391 if (evt.isAltDown() || !viewport.cursorMode)
392 viewport.firePropertyChange("alignment", null,
393 viewport.getAlignment().getSequences());
401 public void addAlignmentPanel(final AlignmentPanel ap,
404 ap.alignFrame = this;
406 alignPanels.addElement(ap);
408 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
410 int aSize = alignPanels.size();
412 tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
414 if (aSize == 1 && ap.av.viewName==null)
416 this.getContentPane().add(ap, BorderLayout.CENTER);
422 setInitialTabVisible();
425 expandViews.setEnabled(true);
426 gatherViews.setEnabled(true);
427 tabbedPane.addTab(ap.av.viewName, ap);
429 ap.setVisible(false);
436 ap.av.alignment.padGaps();
438 ap.av.updateConservation(ap);
439 ap.av.updateConsensus(ap);
443 public void setInitialTabVisible()
445 expandViews.setEnabled(true);
446 gatherViews.setEnabled(true);
447 tabbedPane.setVisible(true);
448 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
449 tabbedPane.addTab(first.av.viewName,first);
450 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
454 public AlignViewport getViewport()
459 /* Set up intrinsic listeners for dynamically generated GUI bits. */
460 private void addServiceListeners()
462 final java.beans.PropertyChangeListener thisListener;
463 // Do this once to get current state
464 BuildWebServiceMenu();
465 Desktop.discoverer.addPropertyChangeListener(
466 thisListener = new java.beans.PropertyChangeListener()
468 public void propertyChange(PropertyChangeEvent evt)
470 // System.out.println("Discoverer property change.");
471 if (evt.getPropertyName().equals("services"))
473 // System.out.println("Rebuilding web service menu");
474 BuildWebServiceMenu();
479 addInternalFrameListener(new javax.swing.event.
480 InternalFrameAdapter()
482 public void internalFrameClosed(
483 javax.swing.event.InternalFrameEvent evt)
485 // System.out.println("deregistering discoverer listener");
486 Desktop.discoverer.removePropertyChangeListener(thisListener);
487 closeMenuItem_actionPerformed(true);
493 public void setGUINucleotide(boolean nucleotide)
495 showTranslation.setVisible( nucleotide );
496 conservationMenuItem.setEnabled( !nucleotide );
497 modifyConservation.setEnabled( !nucleotide );
499 //Remember AlignFrame always starts as protein
502 calculateMenu.remove(calculateMenu.getItemCount()-2);
507 * Need to call this method when tabs are selected for multiple views,
508 * or when loading from Jalview2XML.java
509 * @param av AlignViewport
511 void setMenusFromViewport(AlignViewport av)
513 padGapsMenuitem.setSelected(av.padGaps);
514 colourTextMenuItem.setSelected(av.showColourText);
515 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
516 conservationMenuItem.setSelected(av.getConservationSelected());
517 seqLimits.setSelected(av.getShowJVSuffix());
518 idRightAlign.setSelected(av.rightAlignIds);
519 renderGapsMenuItem.setSelected(av.renderGaps);
520 wrapMenuItem.setSelected(av.wrapAlignment);
521 scaleAbove.setVisible(av.wrapAlignment);
522 scaleLeft.setVisible(av.wrapAlignment);
523 scaleRight.setVisible(av.wrapAlignment);
524 annotationPanelMenuItem.setState(av.showAnnotation);
525 viewBoxesMenuItem.setSelected(av.showBoxes);
526 viewTextMenuItem.setSelected(av.showText);
528 setColourSelected(ColourSchemeProperty.
529 getColourName(av.getGlobalColourScheme()));
531 showSeqFeatures.setSelected(av.showSequenceFeatures);
532 hiddenMarkers.setState(av.showHiddenMarkers);
533 applyToAllGroups.setState(av.colourAppliesToAllGroups);
539 Hashtable progressBars;
540 public void setProgressBar(String message, long id)
542 if(progressBars == null)
544 progressBars = new Hashtable();
547 JPanel progressPanel;
548 GridLayout layout = (GridLayout) statusPanel.getLayout();
549 if(progressBars.get( new Long(id) )!=null)
551 progressPanel = (JPanel)progressBars.get( new Long(id) );
552 statusPanel.remove(progressPanel);
553 progressBars.remove( progressPanel );
554 progressPanel = null;
557 statusBar.setText(message);
560 layout.setRows(layout.getRows() - 1);
564 progressPanel = new JPanel(new BorderLayout(10, 5));
566 JProgressBar progressBar = new JProgressBar();
567 progressBar.setIndeterminate(true);
569 progressPanel.add(new JLabel(message), BorderLayout.WEST);
570 progressPanel.add(progressBar, BorderLayout.CENTER);
572 layout.setRows(layout.getRows() + 1);
573 statusPanel.add(progressPanel);
575 progressBars.put(new Long(id), progressPanel);
585 Added so Castor Mapping file can obtain Jalview Version
587 public String getVersion()
589 return jalview.bin.Cache.getProperty("VERSION");
592 public FeatureRenderer getFeatureRenderer()
594 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
598 public void fetchSequence_actionPerformed(ActionEvent e)
600 new SequenceFetcher(this);
603 public void addFromFile_actionPerformed(ActionEvent e)
605 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
608 public void reload_actionPerformed(ActionEvent e)
612 if(currentFileFormat.equals("Jalview"))
614 JInternalFrame [] frames = Desktop.desktop.getAllFrames();
615 for(int i=0; i<frames.length; i++)
617 if (frames[i] instanceof AlignFrame
619 && ( (AlignFrame) frames[i]).fileName.equals(fileName))
623 frames[i].setSelected(true);
624 Desktop.instance.closeAssociatedWindows();
626 catch (java.beans.PropertyVetoException ex)
631 Desktop.instance.closeAssociatedWindows();
633 FileLoader loader = new FileLoader();
634 String protocol = fileName.startsWith("http:")? "URL":"File";
635 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
639 Rectangle bounds = this.getBounds();
641 FileLoader loader = new FileLoader();
642 String protocol = fileName.startsWith("http:") ? "URL" : "File";
643 AlignFrame newframe =
644 loader.LoadFileWaitTillLoaded(fileName, protocol, currentFileFormat);
646 newframe.setBounds(bounds);
648 this.closeMenuItem_actionPerformed(true);
654 public void addFromText_actionPerformed(ActionEvent e)
656 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
659 public void addFromURL_actionPerformed(ActionEvent e)
661 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
665 public void save_actionPerformed(ActionEvent e)
668 || currentFileFormat==null
669 || fileName.startsWith("http")
672 saveAs_actionPerformed(null);
676 saveAlignment(fileName, currentFileFormat);
683 * @param e DOCUMENT ME!
685 public void saveAs_actionPerformed(ActionEvent e)
687 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
688 getProperty( "LAST_DIRECTORY"),
690 { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" },
692 { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
697 chooser.setFileView(new JalviewFileView());
698 chooser.setDialogTitle("Save Alignment to file");
699 chooser.setToolTipText("Save");
701 int value = chooser.showSaveDialog(this);
703 if (value == JalviewFileChooser.APPROVE_OPTION)
705 currentFileFormat = chooser.getSelectedFormat();
706 if (currentFileFormat == null)
708 JOptionPane.showInternalMessageDialog(Desktop.desktop,
709 "You must select a file format before saving!",
710 "File format not specified",
711 JOptionPane.WARNING_MESSAGE);
712 value = chooser.showSaveDialog(this);
716 fileName = chooser.getSelectedFile().getPath();
718 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
721 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
723 saveAlignment(fileName, currentFileFormat);
727 public boolean saveAlignment(String file, String format)
729 boolean success = true;
731 if (format.equalsIgnoreCase("Jalview"))
733 String shortName = title;
735 if (shortName.indexOf(java.io.File.separatorChar) > -1)
737 shortName = shortName.substring(shortName.lastIndexOf(
738 java.io.File.separatorChar) + 1);
741 success = new Jalview2XML().SaveAlignment(this, file, shortName);
743 statusBar.setText("Successfully saved to file: "
745 +format +" format.");
751 String[] omitHidden = null;
753 if (viewport.hasHiddenColumns)
755 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
756 "The Alignment contains hidden columns."
757 + "\nDo you want to save only the visible alignment?",
758 "Save / Omit Hidden Columns",
759 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
761 if (reply == JOptionPane.YES_OPTION)
763 omitHidden = viewport.getViewAsString(false);
767 String output = new FormatAdapter().formatSequences(
769 viewport.alignment.getSequencesArray(),
780 java.io.PrintWriter out = new java.io.PrintWriter(
781 new java.io.FileWriter(file));
786 statusBar.setText("Successfully saved to file: "
788 + format + " format.");
793 ex.printStackTrace();
800 JOptionPane.showInternalMessageDialog(
801 this, "Couldn't save file: " + fileName,
803 JOptionPane.WARNING_MESSAGE);
812 * @param e DOCUMENT ME!
814 protected void outputText_actionPerformed(ActionEvent e)
816 String [] omitHidden = null;
818 if(viewport.hasHiddenColumns)
820 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
821 "The Alignment contains hidden columns."
822 +"\nDo you want to output only the visible alignment?",
823 "Save / Omit Hidden Columns",
824 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
826 if(reply==JOptionPane.YES_OPTION)
828 omitHidden = viewport.getViewAsString(false);
832 CutAndPasteTransfer cap = new CutAndPasteTransfer();
833 cap.setForInput(null);
834 Desktop.addInternalFrame(cap,
835 "Alignment output - " + e.getActionCommand(), 600,
839 cap.setText(new FormatAdapter().formatSequences(
840 e.getActionCommand(),
841 viewport.alignment.getSequencesArray(),
848 * @param e DOCUMENT ME!
850 protected void htmlMenuItem_actionPerformed(ActionEvent e)
852 new HTMLOutput(viewport,
853 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
854 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
857 public void createImageMap(File file, String image)
859 alignPanel.makePNGImageMap(file, image);
865 * @param e DOCUMENT ME!
867 public void createPNG(File f)
869 alignPanel.makePNG(f);
875 * @param e DOCUMENT ME!
877 public void createEPS(File f)
879 alignPanel.makeEPS(f);
883 public void pageSetup_actionPerformed(ActionEvent e)
885 PrinterJob printJob = PrinterJob.getPrinterJob();
886 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
892 * @param e DOCUMENT ME!
894 public void printMenuItem_actionPerformed(ActionEvent e)
896 //Putting in a thread avoids Swing painting problems
897 PrintThread thread = new PrintThread(alignPanel);
901 public void exportFeatures_actionPerformed(ActionEvent e)
903 new AnnotationExporter().exportFeatures(alignPanel);
907 public void exportAnnotations_actionPerformed(ActionEvent e)
909 new AnnotationExporter().exportAnnotations(
911 viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
912 viewport.alignment.getGroups()
917 public void associatedData_actionPerformed(ActionEvent e)
919 // Pick the tree file
920 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
923 chooser.setFileView(new JalviewFileView());
924 chooser.setDialogTitle("Load Jalview Annotations or Features File");
925 chooser.setToolTipText("Load Jalview Annotations / Features file");
927 int value = chooser.showOpenDialog(null);
929 if (value == JalviewFileChooser.APPROVE_OPTION)
931 String choice = chooser.getSelectedFile().getPath();
932 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
933 loadJalviewDataFile(choice);
942 * @param e DOCUMENT ME!
944 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
946 if(alignPanels!=null && alignPanels.size()<2)
953 if(alignPanels!=null)
957 for (int i = 0; i < alignPanels.size(); i++)
959 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
960 PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
961 PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
962 PaintRefresher.RemoveComponent(ap);
967 int index = tabbedPane.getSelectedIndex();
969 alignPanels.removeElement(alignPanel);
970 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
971 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
972 PaintRefresher.RemoveComponent(alignPanel);
976 tabbedPane.removeTabAt(index);
977 tabbedPane.validate();
979 if(index==tabbedPane.getTabCount())
984 this.tabSelectionChanged(index);
990 this.setClosed(true);
995 ex.printStackTrace();
1003 void updateEditMenuBar()
1006 if (viewport.historyList.size() > 0)
1008 undoMenuItem.setEnabled(true);
1009 CommandI command = (CommandI) viewport.historyList.peek();
1010 undoMenuItem.setText("Undo " + command.getDescription());
1014 undoMenuItem.setEnabled(false);
1015 undoMenuItem.setText("Undo");
1018 if (viewport.redoList.size() > 0)
1020 redoMenuItem.setEnabled(true);
1022 CommandI command = (CommandI) viewport.redoList.peek();
1023 redoMenuItem.setText("Redo " + command.getDescription());
1027 redoMenuItem.setEnabled(false);
1028 redoMenuItem.setText("Redo");
1033 public void addHistoryItem(CommandI command)
1035 if(command.getSize()>0)
1037 viewport.historyList.push(command);
1038 viewport.redoList.clear();
1039 updateEditMenuBar();
1040 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1049 * @param e DOCUMENT ME!
1051 protected void undoMenuItem_actionPerformed(ActionEvent e)
1053 CommandI command = (CommandI)viewport.historyList.pop();
1054 viewport.redoList.push(command);
1055 command.undoCommand();
1057 AlignViewport originalSource = getOriginatingSource(command);
1058 updateEditMenuBar();
1060 if(originalSource!=null)
1062 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1063 originalSource.firePropertyChange("alignment",
1065 originalSource.alignment.getSequences());
1072 * @param e DOCUMENT ME!
1074 protected void redoMenuItem_actionPerformed(ActionEvent e)
1076 if(viewport.redoList.size()<1)
1081 CommandI command = (CommandI) viewport.redoList.pop();
1082 viewport.historyList.push(command);
1083 command.doCommand();
1085 AlignViewport originalSource = getOriginatingSource(command);
1086 updateEditMenuBar();
1088 if(originalSource!=null)
1090 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1091 originalSource.firePropertyChange("alignment",
1093 originalSource.alignment.getSequences());
1097 AlignViewport getOriginatingSource(CommandI command)
1099 AlignViewport originalSource = null;
1100 //For sequence removal and addition, we need to fire
1101 //the property change event FROM the viewport where the
1102 //original alignment was altered
1104 if (command instanceof EditCommand)
1106 EditCommand editCommand = (EditCommand) command;
1107 al = editCommand.getAlignment();
1108 Vector comps = (Vector) PaintRefresher.components
1109 .get(viewport.getSequenceSetId());
1111 for (int i = 0; i < comps.size(); i++)
1113 if (comps.elementAt(i) instanceof AlignmentPanel)
1115 if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
1117 originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
1124 if (originalSource == null)
1126 //The original view is closed, we must validate
1127 //the current view against the closed view first
1130 PaintRefresher.validateSequences(al, viewport.alignment);
1133 originalSource = viewport;
1136 return originalSource;
1142 * @param up DOCUMENT ME!
1144 public void moveSelectedSequences(boolean up)
1146 SequenceGroup sg = viewport.getSelectionGroup();
1155 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1157 SequenceI seq = viewport.alignment.getSequenceAt(i);
1159 if (!sg.getSequences(null).contains(seq))
1164 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1166 if (sg.getSequences(null).contains(temp))
1171 viewport.alignment.getSequences().setElementAt(temp, i);
1172 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1177 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1179 SequenceI seq = viewport.alignment.getSequenceAt(i);
1181 if (!sg.getSequences(null).contains(seq))
1186 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1188 if (sg.getSequences(null).contains(temp))
1193 viewport.alignment.getSequences().setElementAt(temp, i);
1194 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1198 alignPanel.paintAlignment(true);
1204 synchronized void slideSequences(boolean right, int size)
1206 if(viewport.hasHiddenColumns)
1208 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1209 "Slide Sequences not available with hidden columns",
1210 "Slide Sequence not Available",
1211 JOptionPane.WARNING_MESSAGE);
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)
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)
1414 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1415 Transferable contents = c.getContents(this);
1417 if (contents == null)
1425 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1426 if (str.length() < 1)
1431 format = new IdentifyFile().Identify(str, "Paste");
1434 catch (OutOfMemoryError er)
1436 er.printStackTrace();
1437 javax.swing.SwingUtilities.invokeLater(new Runnable()
1441 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1442 "Out of memory pasting sequences!!"
1444 "\nSee help files for increasing Java Virtual Machine memory."
1446 javax.swing.JOptionPane.WARNING_MESSAGE);
1453 SequenceI[] sequences;
1456 if(Desktop.jalviewClipboard!=null)
1458 // The clipboard was filled from within Jalview, we must use the sequences
1459 // And dataset from the copied alignment
1460 sequences = (SequenceI[])Desktop.jalviewClipboard[0];
1464 sequences = new FormatAdapter().readFile(str, "Paste", format).
1465 getSequencesArray();
1468 AlignmentI alignment = null;
1472 alignment = new Alignment(sequences);
1474 if (Desktop.jalviewClipboard != null)
1476 alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
1480 alignment.setDataset(null);
1485 alignment = viewport.getAlignment();
1488 SequenceI [] newseqs = new SequenceI[sequences.length];
1489 for (int i = 0; i < sequences.length; i++)
1491 newseqs[i] = new Sequence(sequences[i].getName(),
1492 sequences[i].getSequence(),
1493 sequences[i].getStart(),
1494 sequences[i].getEnd());
1496 alignment.addSequence(newseqs[i]);
1502 addHistoryItem(new EditCommand(
1507 alignment.getWidth(),
1512 viewport.setEndSeq(alignment.getHeight());
1513 alignment.getWidth();
1514 viewport.firePropertyChange("alignment", null, alignment.getSequences());
1519 // Add any annotations attached to sequences
1520 for (int i = 0; i < sequences.length; i++)
1522 if (sequences[i].getAnnotation() != null)
1524 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1526 AlignmentAnnotation newAnnot =
1527 new AlignmentAnnotation(
1528 sequences[i].getAnnotation()[a].label,
1529 sequences[i].getAnnotation()[a].description,
1530 sequences[i].getAnnotation()[a].annotations,
1531 sequences[i].getAnnotation()[a].graphMin,
1532 sequences[i].getAnnotation()[a].graphMax,
1533 sequences[i].getAnnotation()[a].graph);
1535 sequences[i].getAnnotation()[a] = newAnnot;
1536 newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].
1538 newAnnot.sequenceRef = sequences[i];
1539 newAnnot.adjustForAlignment();
1540 alignment.addAnnotation(newAnnot);
1541 alignment.setAnnotationIndex(newAnnot, a);
1544 alignPanel.annotationPanel.adjustPanelHeight();
1550 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
1551 String newtitle = new String("Copied sequences");
1553 if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
1555 Vector hc = (Vector)Desktop.jalviewClipboard[2];
1556 for(int i=0; i<hc.size(); i++)
1558 int [] region = (int[]) hc.elementAt(i);
1559 af.viewport.hideColumns(region[0], region[1]);
1564 //>>>This is a fix for the moment, until a better solution is found!!<<<
1565 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
1566 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1569 if (title.startsWith("Copied sequences"))
1575 newtitle = newtitle.concat("- from " + title);
1578 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1585 catch (Exception ex)
1587 ex.printStackTrace();
1588 System.out.println("Exception whilst pasting: "+ex);
1589 // could be anything being pasted in here
1598 * @param e DOCUMENT ME!
1600 protected void cut_actionPerformed(ActionEvent e)
1602 copy_actionPerformed(null);
1603 delete_actionPerformed(null);
1609 * @param e DOCUMENT ME!
1611 protected void delete_actionPerformed(ActionEvent evt)
1614 SequenceGroup sg = viewport.getSelectionGroup();
1620 Vector seqs = new Vector();
1622 for (int i = 0; i < sg.getSize(); i++)
1624 seq = sg.getSequenceAt(i);
1625 seqs.addElement(seq);
1629 // If the cut affects all sequences, remove highlighted columns
1630 if (sg.getSize() == viewport.alignment.getHeight())
1632 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1633 sg.getEndRes() + 1);
1637 SequenceI [] cut = new SequenceI[seqs.size()];
1638 for(int i=0; i<seqs.size(); i++)
1640 cut[i] = (SequenceI)seqs.elementAt(i);
1647 addHistoryItem(new EditCommand("Cut Sequences",
1651 sg.getEndRes()-sg.getStartRes()+1,
1652 viewport.alignment));
1655 viewport.setSelectionGroup(null);
1656 viewport.alignment.deleteGroup(sg);
1658 viewport.firePropertyChange("alignment", null,
1659 viewport.getAlignment().getSequences());
1661 if (viewport.getAlignment().getHeight() < 1)
1665 this.setClosed(true);
1667 catch (Exception ex)
1676 * @param e DOCUMENT ME!
1678 protected void deleteGroups_actionPerformed(ActionEvent e)
1680 viewport.alignment.deleteAllGroups();
1681 viewport.sequenceColours = null;
1682 viewport.setSelectionGroup(null);
1683 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1684 alignPanel.paintAlignment(true);
1690 * @param e DOCUMENT ME!
1692 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1694 SequenceGroup sg = new SequenceGroup();
1696 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1699 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1702 sg.setEndRes(viewport.alignment.getWidth() - 1);
1703 viewport.setSelectionGroup(sg);
1704 alignPanel.paintAlignment(true);
1705 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1711 * @param e DOCUMENT ME!
1713 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1715 if(viewport.cursorMode)
1717 alignPanel.seqPanel.keyboardNo1 = null;
1718 alignPanel.seqPanel.keyboardNo2 = null;
1720 viewport.setSelectionGroup(null);
1721 viewport.getColumnSelection().clear();
1722 viewport.setSelectionGroup(null);
1723 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1724 alignPanel.idPanel.idCanvas.searchResults = null;
1725 alignPanel.paintAlignment(true);
1726 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1732 * @param e DOCUMENT ME!
1734 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1736 SequenceGroup sg = viewport.getSelectionGroup();
1740 selectAllSequenceMenuItem_actionPerformed(null);
1745 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1748 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1751 alignPanel.paintAlignment(true);
1753 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1756 public void invertColSel_actionPerformed(ActionEvent e)
1758 viewport.invertColumnSelection();
1759 alignPanel.paintAlignment(true);
1766 * @param e DOCUMENT ME!
1768 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1770 trimAlignment(true);
1776 * @param e DOCUMENT ME!
1778 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
1780 trimAlignment(false);
1783 void trimAlignment(boolean trimLeft)
1785 ColumnSelection colSel = viewport.getColumnSelection();
1788 if (colSel.size() > 0)
1792 column = colSel.getMin();
1796 column = colSel.getMax();
1800 if(viewport.getSelectionGroup()!=null)
1802 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
1803 hiddenRepSequences);
1807 seqs = viewport.alignment.getSequencesArray();
1811 TrimRegionCommand trimRegion;
1814 trimRegion = new TrimRegionCommand("Remove Left",
1815 TrimRegionCommand.TRIM_LEFT,
1820 viewport.selectionGroup);
1821 viewport.setStartRes(0);
1825 trimRegion = new TrimRegionCommand("Remove Right",
1826 TrimRegionCommand.TRIM_RIGHT,
1831 viewport.selectionGroup);
1834 statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
1837 addHistoryItem(trimRegion);
1839 Vector groups = viewport.alignment.getGroups();
1841 for (int i = 0; i < groups.size(); i++)
1843 SequenceGroup sg = (SequenceGroup) groups.get(i);
1845 if ( (trimLeft && !sg.adjustForRemoveLeft(column))
1846 || (!trimLeft && !sg.adjustForRemoveRight(column)))
1848 viewport.alignment.deleteGroup(sg);
1852 viewport.firePropertyChange("alignment", null,
1853 viewport.getAlignment().getSequences());
1860 * @param e DOCUMENT ME!
1862 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1864 int start = 0, end = viewport.alignment.getWidth()-1;
1867 if (viewport.getSelectionGroup() != null)
1869 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
1870 hiddenRepSequences);
1871 start = viewport.getSelectionGroup().getStartRes();
1872 end = viewport.getSelectionGroup().getEndRes();
1876 seqs = viewport.alignment.getSequencesArray();
1880 RemoveGapColCommand removeGapCols =
1881 new RemoveGapColCommand("Remove Gapped Columns",
1884 viewport.alignment);
1886 addHistoryItem(removeGapCols);
1888 statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
1890 //This is to maintain viewport position on first residue
1892 SequenceI seq = viewport.alignment.getSequenceAt(0);
1893 int startRes = seq.findPosition(viewport.startRes);
1894 // ShiftList shifts;
1895 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
1896 // edit.alColumnChanges=shifts.getInverse();
1897 // if (viewport.hasHiddenColumns)
1898 // viewport.getColumnSelection().compensateForEdits(shifts);
1899 viewport.setStartRes(seq.findIndex(startRes)-1);
1900 viewport.firePropertyChange("alignment", null,
1901 viewport.getAlignment().getSequences());
1908 * @param e DOCUMENT ME!
1910 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1912 int start = 0, end = viewport.alignment.getWidth()-1;
1915 if (viewport.getSelectionGroup() != null)
1917 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
1918 hiddenRepSequences);
1919 start = viewport.getSelectionGroup().getStartRes();
1920 end = viewport.getSelectionGroup().getEndRes();
1924 seqs = viewport.alignment.getSequencesArray();
1927 //This is to maintain viewport position on first residue
1929 SequenceI seq = viewport.alignment.getSequenceAt(0);
1930 int startRes = seq.findPosition(viewport.startRes);
1932 addHistoryItem(new RemoveGapsCommand("Remove Gaps",
1935 viewport.alignment));
1937 viewport.setStartRes(seq.findIndex(startRes)-1);
1939 viewport.firePropertyChange("alignment", null,
1940 viewport.getAlignment().getSequences());
1947 * @param e DOCUMENT ME!
1949 public void padGapsMenuitem_actionPerformed(ActionEvent e)
1951 viewport.padGaps = padGapsMenuitem.isSelected();
1953 viewport.firePropertyChange("alignment",
1955 viewport.getAlignment().getSequences());
1961 * @param e DOCUMENT ME!
1963 public void findMenuItem_actionPerformed(ActionEvent e)
1968 public void newView_actionPerformed(ActionEvent e)
1970 AlignmentPanel newap =
1971 new Jalview2XML().copyAlignPanel(alignPanel, true);
1973 if (viewport.viewName == null)
1975 viewport.viewName = "Original";
1978 newap.av.historyList = viewport.historyList;
1979 newap.av.redoList = viewport.redoList;
1981 int index = Desktop.getViewCount(viewport.getSequenceSetId());
1982 String newViewName = "View " +index;
1984 Vector comps = (Vector) PaintRefresher.components.get(viewport.
1985 getSequenceSetId());
1986 Vector existingNames = new Vector();
1987 for(int i=0; i<comps.size(); i++)
1989 if(comps.elementAt(i) instanceof AlignmentPanel)
1991 AlignmentPanel ap = (AlignmentPanel)comps.elementAt(i);
1992 if(!existingNames.contains(ap.av.viewName))
1994 existingNames.addElement(ap.av.viewName);
1999 while(existingNames.contains(newViewName))
2001 newViewName = "View "+ (++index);
2004 newap.av.viewName = newViewName;
2006 addAlignmentPanel(newap, false);
2008 if(alignPanels.size()==2)
2010 viewport.gatherViewsHere = true;
2012 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2015 public void expandViews_actionPerformed(ActionEvent e)
2017 Desktop.instance.explodeViews(this);
2020 public void gatherViews_actionPerformed(ActionEvent e)
2022 Desktop.instance.gatherViews(this);
2030 * @param e DOCUMENT ME!
2032 public void font_actionPerformed(ActionEvent e)
2034 new FontChooser(alignPanel);
2041 * @param e DOCUMENT ME!
2043 protected void seqLimit_actionPerformed(ActionEvent e)
2045 viewport.setShowJVSuffix(seqLimits.isSelected());
2047 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
2048 alignPanel.paintAlignment(true);
2051 public void idRightAlign_actionPerformed(ActionEvent e)
2053 viewport.rightAlignIds = idRightAlign.isSelected();
2054 alignPanel.paintAlignment(true);
2062 * @param e DOCUMENT ME!
2064 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2066 viewport.setColourText(colourTextMenuItem.isSelected());
2067 alignPanel.paintAlignment(true);
2073 * @param e DOCUMENT ME!
2075 public void wrapMenuItem_actionPerformed(ActionEvent e)
2077 scaleAbove.setVisible(wrapMenuItem.isSelected());
2078 scaleLeft.setVisible(wrapMenuItem.isSelected());
2079 scaleRight.setVisible(wrapMenuItem.isSelected());
2080 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2081 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2084 public void showAllSeqs_actionPerformed(ActionEvent e)
2086 viewport.showAllHiddenSeqs();
2089 public void showAllColumns_actionPerformed(ActionEvent e)
2091 viewport.showAllHiddenColumns();
2095 public void hideSelSequences_actionPerformed(ActionEvent e)
2097 viewport.hideAllSelectedSeqs();
2098 alignPanel.paintAlignment(true);
2101 public void hideSelColumns_actionPerformed(ActionEvent e)
2103 viewport.hideSelectedColumns();
2104 alignPanel.paintAlignment(true);
2107 public void hiddenMarkers_actionPerformed(ActionEvent e)
2109 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2116 * @param e DOCUMENT ME!
2118 protected void scaleAbove_actionPerformed(ActionEvent e)
2120 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2121 alignPanel.paintAlignment(true);
2127 * @param e DOCUMENT ME!
2129 protected void scaleLeft_actionPerformed(ActionEvent e)
2131 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2132 alignPanel.paintAlignment(true);
2138 * @param e DOCUMENT ME!
2140 protected void scaleRight_actionPerformed(ActionEvent e)
2142 viewport.setScaleRightWrapped(scaleRight.isSelected());
2143 alignPanel.paintAlignment(true);
2149 * @param e DOCUMENT ME!
2151 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2153 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2154 alignPanel.paintAlignment(true);
2160 * @param e DOCUMENT ME!
2162 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2164 viewport.setShowText(viewTextMenuItem.isSelected());
2165 alignPanel.paintAlignment(true);
2171 * @param e DOCUMENT ME!
2173 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2175 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2176 alignPanel.paintAlignment(true);
2180 public FeatureSettings featureSettings;
2181 public void featureSettings_actionPerformed(ActionEvent e)
2183 if(featureSettings !=null )
2185 featureSettings.close();
2186 featureSettings = null;
2188 featureSettings = new FeatureSettings(this);
2194 * @param evt DOCUMENT ME!
2196 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2198 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2199 alignPanel.paintAlignment(true);
2200 if (alignPanel.getOverviewPanel() != null)
2202 alignPanel.getOverviewPanel().updateOverviewImage();
2209 * @param e DOCUMENT ME!
2211 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2213 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2214 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2220 * @param e DOCUMENT ME!
2222 public void overviewMenuItem_actionPerformed(ActionEvent e)
2224 if (alignPanel.overviewPanel != null)
2229 JInternalFrame frame = new JInternalFrame();
2230 OverviewPanel overview = new OverviewPanel(alignPanel);
2231 frame.setContentPane(overview);
2232 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2233 frame.getWidth(), frame.getHeight());
2235 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2236 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2238 public void internalFrameClosed(
2239 javax.swing.event.InternalFrameEvent evt)
2241 alignPanel.setOverviewPanel(null);
2246 alignPanel.setOverviewPanel(overview);
2249 public void textColour_actionPerformed(ActionEvent e)
2251 new TextColourChooser().chooseColour(alignPanel, null);
2257 * @param e DOCUMENT ME!
2259 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2267 * @param e DOCUMENT ME!
2269 public void clustalColour_actionPerformed(ActionEvent e)
2271 changeColour(new ClustalxColourScheme(
2272 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
2278 * @param e DOCUMENT ME!
2280 public void zappoColour_actionPerformed(ActionEvent e)
2282 changeColour(new ZappoColourScheme());
2288 * @param e DOCUMENT ME!
2290 public void taylorColour_actionPerformed(ActionEvent e)
2292 changeColour(new TaylorColourScheme());
2298 * @param e DOCUMENT ME!
2300 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2302 changeColour(new HydrophobicColourScheme());
2308 * @param e DOCUMENT ME!
2310 public void helixColour_actionPerformed(ActionEvent e)
2312 changeColour(new HelixColourScheme());
2318 * @param e DOCUMENT ME!
2320 public void strandColour_actionPerformed(ActionEvent e)
2322 changeColour(new StrandColourScheme());
2328 * @param e DOCUMENT ME!
2330 public void turnColour_actionPerformed(ActionEvent e)
2332 changeColour(new TurnColourScheme());
2338 * @param e DOCUMENT ME!
2340 public void buriedColour_actionPerformed(ActionEvent e)
2342 changeColour(new BuriedColourScheme());
2348 * @param e DOCUMENT ME!
2350 public void nucleotideColour_actionPerformed(ActionEvent e)
2352 changeColour(new NucleotideColourScheme());
2355 public void annotationColour_actionPerformed(ActionEvent e)
2357 new AnnotationColourChooser(viewport, alignPanel);
2364 * @param e DOCUMENT ME!
2366 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2368 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2374 * @param cs DOCUMENT ME!
2376 public void changeColour(ColourSchemeI cs)
2382 if (viewport.getAbovePIDThreshold())
2384 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2387 cs.setThreshold(threshold,
2388 viewport.getIgnoreGapsConsensus());
2390 viewport.setGlobalColourScheme(cs);
2394 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2397 if (viewport.getConservationSelected())
2400 Alignment al = (Alignment) viewport.alignment;
2401 Conservation c = new Conservation("All",
2402 ResidueProperties.propHash, 3,
2403 al.getSequences(), 0,
2407 c.verdict(false, viewport.ConsPercGaps);
2409 cs.setConservation(c);
2411 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
2416 cs.setConservation(null);
2419 cs.setConsensus(viewport.hconsensus);
2422 viewport.setGlobalColourScheme(cs);
2424 if (viewport.getColourAppliesToAllGroups())
2426 Vector groups = viewport.alignment.getGroups();
2428 for (int i = 0; i < groups.size(); i++)
2430 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2438 if (cs instanceof ClustalxColourScheme)
2440 sg.cs = new ClustalxColourScheme(
2441 sg.getSequences(viewport.hiddenRepSequences), sg.getWidth());
2443 else if (cs instanceof UserColourScheme)
2445 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
2451 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2453 catch (Exception ex)
2458 if (viewport.getAbovePIDThreshold()
2459 || cs instanceof PIDColourScheme
2460 || cs instanceof Blosum62ColourScheme)
2462 sg.cs.setThreshold(threshold,
2463 viewport.getIgnoreGapsConsensus());
2465 sg.cs.setConsensus(AAFrequency.calculate(
2466 sg.getSequences(viewport.hiddenRepSequences), sg.getStartRes(),
2471 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2475 if (viewport.getConservationSelected())
2477 Conservation c = new Conservation("Group",
2478 ResidueProperties.propHash, 3,
2479 sg.getSequences(viewport.
2480 hiddenRepSequences),
2484 c.verdict(false, viewport.ConsPercGaps);
2485 sg.cs.setConservation(c);
2489 sg.cs.setConservation(null);
2494 if (alignPanel.getOverviewPanel() != null)
2496 alignPanel.getOverviewPanel().updateOverviewImage();
2502 alignPanel.paintAlignment(true);
2508 * @param e DOCUMENT ME!
2510 protected void modifyPID_actionPerformed(ActionEvent e)
2512 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
2514 SliderPanel.setPIDSliderSource(alignPanel,
2515 viewport.getGlobalColourScheme(),
2517 SliderPanel.showPIDSlider();
2524 * @param e DOCUMENT ME!
2526 protected void modifyConservation_actionPerformed(ActionEvent e)
2528 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
2530 SliderPanel.setConservationSlider(alignPanel,
2531 viewport.globalColourScheme,
2533 SliderPanel.showConservationSlider();
2540 * @param e DOCUMENT ME!
2542 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2544 viewport.setConservationSelected(conservationMenuItem.isSelected());
2546 viewport.setAbovePIDThreshold(false);
2547 abovePIDThreshold.setSelected(false);
2549 changeColour(viewport.getGlobalColourScheme());
2551 modifyConservation_actionPerformed(null);
2557 * @param e DOCUMENT ME!
2559 public void abovePIDThreshold_actionPerformed(ActionEvent e)
2561 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
2563 conservationMenuItem.setSelected(false);
2564 viewport.setConservationSelected(false);
2566 changeColour(viewport.getGlobalColourScheme());
2568 modifyPID_actionPerformed(null);
2574 * @param e DOCUMENT ME!
2576 public void userDefinedColour_actionPerformed(ActionEvent e)
2578 if (e.getActionCommand().equals("User Defined..."))
2580 new UserDefinedColours(alignPanel, null);
2584 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
2585 getUserColourSchemes().get(e.getActionCommand());
2591 public void updateUserColourMenu()
2594 Component[] menuItems = colourMenu.getMenuComponents();
2595 int i, iSize = menuItems.length;
2596 for (i = 0; i < iSize; i++)
2598 if (menuItems[i].getName() != null &&
2599 menuItems[i].getName().equals("USER_DEFINED"))
2601 colourMenu.remove(menuItems[i]);
2605 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
2607 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
2608 getUserColourSchemes().keys();
2610 while (userColours.hasMoreElements())
2612 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
2614 nextElement().toString());
2615 radioItem.setName("USER_DEFINED");
2616 radioItem.addMouseListener(new MouseAdapter()
2618 public void mousePressed(MouseEvent evt)
2620 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
2622 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
2624 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
2626 "Remove from default list?",
2627 "Remove user defined colour",
2628 JOptionPane.YES_NO_OPTION);
2629 if(option == JOptionPane.YES_OPTION)
2631 jalview.gui.UserDefinedColours.removeColourFromDefaults(
2632 radioItem.getText());
2633 colourMenu.remove(radioItem);
2637 radioItem.addActionListener(new ActionListener()
2639 public void actionPerformed(ActionEvent evt)
2641 userDefinedColour_actionPerformed(evt);
2648 radioItem.addActionListener(new ActionListener()
2650 public void actionPerformed(ActionEvent evt)
2652 userDefinedColour_actionPerformed(evt);
2656 colourMenu.insert(radioItem, 15);
2657 colours.add(radioItem);
2665 * @param e DOCUMENT ME!
2667 public void PIDColour_actionPerformed(ActionEvent e)
2669 changeColour(new PIDColourScheme());
2675 * @param e DOCUMENT ME!
2677 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
2679 changeColour(new Blosum62ColourScheme());
2685 * @param e DOCUMENT ME!
2687 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2689 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2690 AlignmentSorter.sortByPID(viewport.getAlignment(),
2691 viewport.getAlignment().getSequenceAt(0));
2692 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2693 viewport.alignment));
2694 alignPanel.paintAlignment(true);
2700 * @param e DOCUMENT ME!
2702 public void sortIDMenuItem_actionPerformed(ActionEvent e)
2704 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2705 AlignmentSorter.sortByID(viewport.getAlignment());
2706 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
2707 alignPanel.paintAlignment(true);
2713 * @param e DOCUMENT ME!
2715 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
2717 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2718 AlignmentSorter.sortByGroup(viewport.getAlignment());
2719 addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
2721 alignPanel.paintAlignment(true);
2727 * @param e DOCUMENT ME!
2729 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2731 new RedundancyPanel(alignPanel, this);
2738 * @param e DOCUMENT ME!
2740 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2742 if ( (viewport.getSelectionGroup() == null) ||
2743 (viewport.getSelectionGroup().getSize() < 2))
2745 JOptionPane.showInternalMessageDialog(this,
2746 "You must select at least 2 sequences.",
2747 "Invalid Selection",
2748 JOptionPane.WARNING_MESSAGE);
2752 JInternalFrame frame = new JInternalFrame();
2753 frame.setContentPane(new PairwiseAlignPanel(viewport));
2754 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
2761 * @param e DOCUMENT ME!
2763 public void PCAMenuItem_actionPerformed(ActionEvent e)
2765 if ( ( (viewport.getSelectionGroup() != null) &&
2766 (viewport.getSelectionGroup().getSize() < 4) &&
2767 (viewport.getSelectionGroup().getSize() > 0)) ||
2768 (viewport.getAlignment().getHeight() < 4))
2770 JOptionPane.showInternalMessageDialog(this,
2771 "Principal component analysis must take\n" +
2772 "at least 4 input sequences.",
2773 "Sequence selection insufficient",
2774 JOptionPane.WARNING_MESSAGE);
2779 new PCAPanel(alignPanel);
2783 public void autoCalculate_actionPerformed(ActionEvent e)
2785 viewport.autoCalculateConsensus = autoCalculate.isSelected();
2786 if(viewport.autoCalculateConsensus)
2788 viewport.firePropertyChange("alignment",
2790 viewport.getAlignment().getSequences());
2798 * @param e DOCUMENT ME!
2800 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2802 NewTreePanel("AV", "PID", "Average distance tree using PID");
2808 * @param e DOCUMENT ME!
2810 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2812 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2818 * @param e DOCUMENT ME!
2820 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2822 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2828 * @param e DOCUMENT ME!
2830 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2832 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2838 * @param type DOCUMENT ME!
2839 * @param pwType DOCUMENT ME!
2840 * @param title DOCUMENT ME!
2842 void NewTreePanel(String type, String pwType, String title)
2846 if (viewport.getSelectionGroup() != null)
2848 if (viewport.getSelectionGroup().getSize() < 3)
2850 JOptionPane.showMessageDialog(Desktop.desktop,
2851 "You need to have more than two sequences selected to build a tree!",
2852 "Not enough sequences",
2853 JOptionPane.WARNING_MESSAGE);
2858 SequenceGroup sg = viewport.getSelectionGroup();
2860 /* Decide if the selection is a column region */
2861 while (s < sg.getSize())
2863 if ( ( (SequenceI) sg.getSequences(null).elementAt(s++)).getLength() <
2866 JOptionPane.showMessageDialog(Desktop.desktop,
2867 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
2868 "Try using the Pad function in the edit menu,\n" +
2869 "or one of the multiple sequence alignment web services.",
2870 "Sequences in selection are not aligned",
2871 JOptionPane.WARNING_MESSAGE);
2877 title = title + " on region";
2878 tp = new TreePanel(alignPanel, type, pwType);
2882 //are the sequences aligned?
2883 if (!viewport.alignment.isAligned())
2885 JOptionPane.showMessageDialog(Desktop.desktop,
2886 "The sequences must be aligned before creating a tree.\n" +
2887 "Try using the Pad function in the edit menu,\n" +
2888 "or one of the multiple sequence alignment web services.",
2889 "Sequences not aligned",
2890 JOptionPane.WARNING_MESSAGE);
2895 if(viewport.alignment.getHeight()<2)
2900 tp = new TreePanel(alignPanel, type, pwType);
2905 if(viewport.viewName!=null)
2907 title+= viewport.viewName+" of ";
2910 title += this.title;
2912 Desktop.addInternalFrame(tp, title, 600, 500);
2918 * @param title DOCUMENT ME!
2919 * @param order DOCUMENT ME!
2921 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
2923 final JMenuItem item = new JMenuItem("by " + title);
2925 item.addActionListener(new java.awt.event.ActionListener()
2927 public void actionPerformed(ActionEvent e)
2929 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2931 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
2932 AlignmentSorter.sortBy(viewport.getAlignment(), order);
2934 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
2935 viewport.alignment));
2937 alignPanel.paintAlignment(true);
2943 * Maintain the Order by->Displayed Tree menu.
2944 * Creates a new menu item for a TreePanel with an appropriate
2945 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
2946 * to remove the menu item when the treePanel is closed, and adjust
2947 * the tree leaf to sequence mapping when the alignment is modified.
2948 * @param treePanel Displayed tree window.
2949 * @param title SortBy menu item title.
2951 public void buildTreeMenu()
2953 sortByTreeMenu.removeAll();
2955 Vector comps = (Vector) PaintRefresher.components.get(viewport.
2956 getSequenceSetId());
2957 Vector treePanels = new Vector();
2958 int i, iSize = comps.size();
2959 for(i=0; i<iSize; i++)
2961 if(comps.elementAt(i) instanceof TreePanel)
2963 treePanels.add(comps.elementAt(i));
2967 iSize = treePanels.size();
2971 sortByTreeMenu.setVisible(false);
2975 sortByTreeMenu.setVisible(true);
2977 for(i=0; i<treePanels.size(); i++)
2979 TreePanel tp = (TreePanel)treePanels.elementAt(i);
2980 final JMenuItem item = new JMenuItem(tp.getTitle());
2981 final NJTree tree = ((TreePanel)treePanels.elementAt(i)).getTree();
2982 item.addActionListener(new java.awt.event.ActionListener()
2984 public void actionPerformed(ActionEvent e)
2986 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2987 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
2989 addHistoryItem(new OrderCommand("Tree Sort",
2991 viewport.alignment));
2993 alignPanel.paintAlignment(true);
2997 sortByTreeMenu.add(item);
3002 * Work out whether the whole set of sequences
3003 * or just the selected set will be submitted for multiple alignment.
3006 private jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3008 // Now, check we have enough sequences
3009 AlignmentView msa = null;
3011 if ( (viewport.getSelectionGroup() != null) &&
3012 (viewport.getSelectionGroup().getSize() > 1))
3014 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
3015 /*SequenceGroup seqs = viewport.getSelectionGroup();
3017 msa = new SequenceI[sz = seqs.getSize(false)];
3019 for (int i = 0; i < sz; i++)
3021 msa[i] = (SequenceI) seqs.getSequenceAt(i);
3023 msa = viewport.getAlignmentView(true);
3027 /*Vector seqs = viewport.getAlignment().getSequences();
3029 if (seqs.size() > 1)
3031 msa = new SequenceI[seqs.size()];
3033 for (int i = 0; i < seqs.size(); i++)
3035 msa[i] = (SequenceI) seqs.elementAt(i);
3038 msa = viewport.getAlignmentView(false);
3044 * Decides what is submitted to a secondary structure prediction service,
3045 * the currently selected sequence, or the currently selected alignment
3046 * (where the first sequence in the set is the one that the prediction
3049 AlignmentView gatherSeqOrMsaForSecStrPrediction()
3051 AlignmentView seqs = null;
3053 if ( (viewport.getSelectionGroup() != null) &&
3054 (viewport.getSelectionGroup().getSize() > 0))
3056 seqs = viewport.getAlignmentView(true);
3060 seqs = viewport.getAlignmentView(false);
3062 // limit sequences - JBPNote in future - could spawn multiple prediction jobs
3063 // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3064 if (!viewport.alignment.isAligned())
3066 seqs.setSequences(new SeqCigar[]
3067 {seqs.getSequences()[0]});
3074 * @param e DOCUMENT ME!
3076 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3078 // Pick the tree file
3079 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
3082 chooser.setFileView(new JalviewFileView());
3083 chooser.setDialogTitle("Select a newick-like tree file");
3084 chooser.setToolTipText("Load a tree file");
3086 int value = chooser.showOpenDialog(null);
3088 if (value == JalviewFileChooser.APPROVE_OPTION)
3090 String choice = chooser.getSelectedFile().getPath();
3091 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3095 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
3097 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3099 catch (Exception ex)
3101 JOptionPane.showMessageDialog(Desktop.desktop,
3102 "Problem reading tree file",
3104 JOptionPane.WARNING_MESSAGE);
3105 ex.printStackTrace();
3111 public TreePanel ShowNewickTree(NewickFile nf, String title)
3113 return ShowNewickTree(nf,title,600,500,4,5);
3116 public TreePanel ShowNewickTree(NewickFile nf, String title,
3117 AlignmentView input)
3119 return ShowNewickTree(nf,title, input, 600,500,4,5);
3122 public TreePanel ShowNewickTree(NewickFile nf, String title, int w, int h,
3125 return ShowNewickTree(nf, title, null, w, h, x, y);
3128 * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
3130 * @param nf the tree
3131 * @param title tree viewer title
3132 * @param input Associated alignment input data (or null)
3137 * @return TreePanel handle
3139 public TreePanel ShowNewickTree(NewickFile nf, String title,
3140 AlignmentView input, int w, int h, int x,
3143 TreePanel tp = null;
3149 if (nf.getTree() != null)
3151 tp = new TreePanel(alignPanel,
3160 tp.setLocation(x,y);
3164 Desktop.addInternalFrame(tp, title, w, h);
3167 catch (Exception ex)
3169 ex.printStackTrace();
3177 * Generates menu items and listener event actions for web service clients
3180 public void BuildWebServiceMenu()
3182 if ( (Discoverer.services != null)
3183 && (Discoverer.services.size() > 0))
3185 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
3186 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
3187 Vector wsmenu = new Vector();
3188 final AlignFrame af = this;
3191 // Add any Multiple Sequence Alignment Services
3192 final JMenu msawsmenu = new JMenu("Alignment");
3193 for (int i = 0, j = msaws.size(); i < j; i++)
3195 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
3197 final JMenuItem method = new JMenuItem(sh.getName());
3198 method.addActionListener(new ActionListener()
3200 public void actionPerformed(ActionEvent e)
3202 AlignmentView msa = gatherSequencesForAlignment();
3203 new jalview.ws.MsaWSClient(sh, title, msa,
3205 viewport.getAlignment().getDataset(),
3211 msawsmenu.add(method);
3212 // Deal with services that we know accept partial alignments.
3213 if (sh.getName().indexOf("lustal") > -1)
3215 // We know that ClustalWS can accept partial alignments for refinement.
3216 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
3217 methodR.addActionListener(new ActionListener()
3219 public void actionPerformed(ActionEvent e)
3221 AlignmentView msa = gatherSequencesForAlignment();
3222 new jalview.ws.MsaWSClient(sh, title, msa,
3224 viewport.getAlignment().getDataset(),
3230 msawsmenu.add(methodR);
3234 wsmenu.add(msawsmenu);
3236 if (secstrpr != null)
3238 // Add any secondary structure prediction services
3239 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
3240 for (int i = 0, j = secstrpr.size(); i < j; i++)
3242 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
3244 final JMenuItem method = new JMenuItem(sh.getName());
3245 method.addActionListener(new ActionListener()
3247 public void actionPerformed(ActionEvent e)
3249 AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
3250 if (msa.getSequences().length == 1)
3252 // Single Sequence prediction
3253 new jalview.ws.JPredClient(sh, title, false, msa, af, true);
3257 if (msa.getSequences().length > 1)
3259 // Sequence profile based prediction
3260 new jalview.ws.JPredClient(sh,
3261 title, true, msa, af, true);
3266 secstrmenu.add(method);
3268 wsmenu.add(secstrmenu);
3270 this.webService.removeAll();
3271 for (int i = 0, j = wsmenu.size(); i < j; i++)
3273 webService.add( (JMenu) wsmenu.get(i));
3278 this.webService.removeAll();
3279 this.webService.add(this.webServiceNoServices);
3281 // TODO: add in rediscovery function
3282 // TODO: reduce code redundancy.
3283 // TODO: group services by location as well as function.
3286 /* public void vamsasStore_actionPerformed(ActionEvent e)
3288 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
3289 getProperty("LAST_DIRECTORY"));
3291 chooser.setFileView(new JalviewFileView());
3292 chooser.setDialogTitle("Export to Vamsas file");
3293 chooser.setToolTipText("Export");
3295 int value = chooser.showSaveDialog(this);
3297 if (value == JalviewFileChooser.APPROVE_OPTION)
3299 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
3300 //vs.store(chooser.getSelectedFile().getAbsolutePath() );
3301 vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
3308 public void showTranslation_actionPerformed(ActionEvent e)
3310 ///////////////////////////////
3311 // Collect Data to be translated/transferred
3313 SequenceI [] selection = viewport.getSelectionAsNewSequence();
3314 String [] seqstring = viewport.getViewAsString(true);
3315 AlignmentI al = null;
3317 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring, viewport.getViewAsVisibleContigs(true),
3318 viewport.getGapCharacter(), viewport.alignment.getAlignmentAnnotation(),
3319 viewport.alignment.getWidth());
3320 } catch (Exception ex) {
3322 jalview.bin.Cache.log.debug("Exception during translation.",ex);
3326 JOptionPane.showMessageDialog(Desktop.desktop,
3327 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
3328 "Translation Failed",
3329 JOptionPane.WARNING_MESSAGE);
3331 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
3332 Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
3341 * @param String DOCUMENT ME!
3343 public boolean parseFeaturesFile(String file, String type)
3345 boolean featuresFile = false;
3348 featuresFile = new FeaturesFile(file,
3349 type).parse(viewport.alignment.getDataset(),
3350 alignPanel.seqPanel.seqCanvas.
3351 getFeatureRenderer().featureColours,
3356 ex.printStackTrace();
3361 viewport.showSequenceFeatures = true;
3362 showSeqFeatures.setSelected(true);
3363 alignPanel.paintAlignment(true);
3366 return featuresFile;
3369 public void dragEnter(DropTargetDragEvent evt)
3372 public void dragExit(DropTargetEvent evt)
3375 public void dragOver(DropTargetDragEvent evt)
3378 public void dropActionChanged(DropTargetDragEvent evt)
3381 public void drop(DropTargetDropEvent evt)
3383 Transferable t = evt.getTransferable();
3384 java.util.List files = null;
3388 DataFlavor uriListFlavor = new DataFlavor(
3389 "text/uri-list;class=java.lang.String");
3390 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
3392 //Works on Windows and MacOSX
3393 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3394 files = (java.util.List) t.getTransferData(DataFlavor.
3395 javaFileListFlavor);
3397 else if (t.isDataFlavorSupported(uriListFlavor))
3399 // This is used by Unix drag system
3400 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3401 String data = (String) t.getTransferData(uriListFlavor);
3402 files = new java.util.ArrayList(1);
3403 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
3406 st.hasMoreTokens(); )
3408 String s = st.nextToken();
3409 if (s.startsWith("#"))
3411 // the line is a comment (as per the RFC 2483)
3415 java.net.URI uri = new java.net.URI(s);
3416 java.io.File file = new java.io.File(uri);
3423 e.printStackTrace();
3430 for (int i = 0; i < files.size(); i++)
3432 loadJalviewDataFile(files.get(i).toString());
3435 catch (Exception ex)
3437 ex.printStackTrace();
3442 // This method will attempt to load a "dropped" file first by testing
3443 // whether its and Annotation file, then features file. If both are
3444 // false then the user may have dropped an alignment file onto this
3446 public void loadJalviewDataFile(String file)
3450 String protocol = "File";
3452 if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
3457 boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
3458 alignment, file, protocol);
3462 boolean isGroupsFile = parseFeaturesFile(file,protocol);
3465 String format = new IdentifyFile().Identify(file, protocol);
3467 if(format.equalsIgnoreCase("JnetFile"))
3469 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
3471 new JnetAnnotationMaker().add_annotation(predictions,
3472 viewport.getAlignment(),
3474 alignPanel.adjustAnnotationHeight();
3475 alignPanel.paintAlignment(true);
3479 new FileLoader().LoadFile(viewport, file, protocol, format);
3486 alignPanel.adjustAnnotationHeight();
3490 catch (Exception ex)
3492 ex.printStackTrace();
3496 public void tabSelectionChanged(int index)
3500 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
3501 viewport = alignPanel.av;
3502 setMenusFromViewport(viewport);
3506 public void tabbedPane_mousePressed(MouseEvent e)
3508 if(SwingUtilities.isRightMouseButton(e))
3510 String reply = JOptionPane.showInternalInputDialog(this,
3513 JOptionPane.QUESTION_MESSAGE);
3517 viewport.viewName = reply;
3518 tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
3524 public AlignViewport getCurrentView()
3534 public PrintThread(AlignmentPanel ap)
3538 static PageFormat pf;
3541 PrinterJob printJob = PrinterJob.getPrinterJob();
3545 printJob.setPrintable(ap, pf);
3549 printJob.setPrintable(ap);
3552 if (printJob.printDialog())
3558 catch (Exception PrintException)
3560 PrintException.printStackTrace();