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 jalview.structure.StructureSelectionManager.getStructureSelectionManager()
961 .removeStructureViewerListener(ap.seqPanel, null);
962 PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
963 PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
964 PaintRefresher.RemoveComponent(ap);
965 ap.av.alignment.destroyAlignment();
970 int index = tabbedPane.getSelectedIndex();
972 alignPanels.removeElement(alignPanel);
973 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
974 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
975 PaintRefresher.RemoveComponent(alignPanel);
976 alignPanel.av.alignment.destroyAlignment();
980 tabbedPane.removeTabAt(index);
981 tabbedPane.validate();
983 if(index==tabbedPane.getTabCount())
988 this.tabSelectionChanged(index);
994 this.setClosed(true);
999 ex.printStackTrace();
1007 void updateEditMenuBar()
1010 if (viewport.historyList.size() > 0)
1012 undoMenuItem.setEnabled(true);
1013 CommandI command = (CommandI) viewport.historyList.peek();
1014 undoMenuItem.setText("Undo " + command.getDescription());
1018 undoMenuItem.setEnabled(false);
1019 undoMenuItem.setText("Undo");
1022 if (viewport.redoList.size() > 0)
1024 redoMenuItem.setEnabled(true);
1026 CommandI command = (CommandI) viewport.redoList.peek();
1027 redoMenuItem.setText("Redo " + command.getDescription());
1031 redoMenuItem.setEnabled(false);
1032 redoMenuItem.setText("Redo");
1037 public void addHistoryItem(CommandI command)
1039 if(command.getSize()>0)
1041 viewport.historyList.push(command);
1042 viewport.redoList.clear();
1043 updateEditMenuBar();
1044 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1053 * @param e DOCUMENT ME!
1055 protected void undoMenuItem_actionPerformed(ActionEvent e)
1057 CommandI command = (CommandI)viewport.historyList.pop();
1058 viewport.redoList.push(command);
1059 command.undoCommand();
1061 AlignViewport originalSource = getOriginatingSource(command);
1062 updateEditMenuBar();
1064 if(originalSource!=null)
1066 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1067 originalSource.firePropertyChange("alignment",
1069 originalSource.alignment.getSequences());
1076 * @param e DOCUMENT ME!
1078 protected void redoMenuItem_actionPerformed(ActionEvent e)
1080 if(viewport.redoList.size()<1)
1085 CommandI command = (CommandI) viewport.redoList.pop();
1086 viewport.historyList.push(command);
1087 command.doCommand();
1089 AlignViewport originalSource = getOriginatingSource(command);
1090 updateEditMenuBar();
1092 if(originalSource!=null)
1094 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1095 originalSource.firePropertyChange("alignment",
1097 originalSource.alignment.getSequences());
1101 AlignViewport getOriginatingSource(CommandI command)
1103 AlignViewport originalSource = null;
1104 //For sequence removal and addition, we need to fire
1105 //the property change event FROM the viewport where the
1106 //original alignment was altered
1108 if (command instanceof EditCommand)
1110 EditCommand editCommand = (EditCommand) command;
1111 al = editCommand.getAlignment();
1112 Vector comps = (Vector) PaintRefresher.components
1113 .get(viewport.getSequenceSetId());
1115 for (int i = 0; i < comps.size(); i++)
1117 if (comps.elementAt(i) instanceof AlignmentPanel)
1119 if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
1121 originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
1128 if (originalSource == null)
1130 //The original view is closed, we must validate
1131 //the current view against the closed view first
1134 PaintRefresher.validateSequences(al, viewport.alignment);
1137 originalSource = viewport;
1140 return originalSource;
1146 * @param up DOCUMENT ME!
1148 public void moveSelectedSequences(boolean up)
1150 SequenceGroup sg = viewport.getSelectionGroup();
1159 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1161 SequenceI seq = viewport.alignment.getSequenceAt(i);
1163 if (!sg.getSequences(null).contains(seq))
1168 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1170 if (sg.getSequences(null).contains(temp))
1175 viewport.alignment.getSequences().setElementAt(temp, i);
1176 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1181 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1183 SequenceI seq = viewport.alignment.getSequenceAt(i);
1185 if (!sg.getSequences(null).contains(seq))
1190 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1192 if (sg.getSequences(null).contains(temp))
1197 viewport.alignment.getSequences().setElementAt(temp, i);
1198 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1202 alignPanel.paintAlignment(true);
1208 synchronized void slideSequences(boolean right, int size)
1210 Vector sg = new Vector();
1211 if(viewport.cursorMode)
1213 sg.addElement(viewport.alignment.getSequenceAt(
1214 alignPanel.seqPanel.seqCanvas.cursorY));
1216 else if(viewport.getSelectionGroup()!=null
1217 && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight())
1219 sg = viewport.getSelectionGroup().getSequences(
1220 viewport.hiddenRepSequences);
1228 Vector invertGroup = new Vector();
1230 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1232 if(!sg.contains(viewport.alignment.getSequenceAt(i)))
1233 invertGroup.add(viewport.alignment.getSequenceAt(i));
1236 SequenceI[] seqs1 = new SequenceI[sg.size()];
1237 for (int i = 0; i < sg.size(); i++)
1238 seqs1[i] = (SequenceI) sg.elementAt(i);
1240 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1241 for (int i = 0; i < invertGroup.size(); i++)
1242 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1244 SlideSequencesCommand ssc;
1246 ssc = new SlideSequencesCommand("Slide Sequences",
1248 viewport.getGapCharacter()
1251 ssc = new SlideSequencesCommand("Slide Sequences",
1253 viewport.getGapCharacter()
1256 int groupAdjustment = 0;
1257 if (ssc.getGapsInsertedBegin() && right)
1259 if (viewport.cursorMode)
1260 alignPanel.seqPanel.moveCursor(size, 0);
1262 groupAdjustment = size;
1264 else if (!ssc.getGapsInsertedBegin() && !right)
1266 if (viewport.cursorMode)
1267 alignPanel.seqPanel.moveCursor( -size, 0);
1269 groupAdjustment = -size;
1272 if (groupAdjustment != 0)
1274 viewport.getSelectionGroup().setStartRes(
1275 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1276 viewport.getSelectionGroup().setEndRes(
1277 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1281 boolean appendHistoryItem = false;
1282 if(viewport.historyList!=null
1283 && viewport.historyList.size()>0
1284 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1286 appendHistoryItem = ssc.appendSlideCommand(
1287 (SlideSequencesCommand)viewport.historyList.peek())
1291 if(!appendHistoryItem)
1292 addHistoryItem(ssc);
1301 * @param e DOCUMENT ME!
1303 protected void copy_actionPerformed(ActionEvent e)
1306 if (viewport.getSelectionGroup() == null)
1311 SequenceI [] seqs = viewport.getSelectionAsNewSequence();
1312 String[] omitHidden = null;
1314 if (viewport.hasHiddenColumns)
1316 omitHidden = viewport.getViewAsString(true);
1319 String output = new FormatAdapter().formatSequences(
1324 StringSelection ss = new StringSelection(output);
1328 jalview.gui.Desktop.internalCopy = true;
1329 //Its really worth setting the clipboard contents
1330 //to empty before setting the large StringSelection!!
1331 Toolkit.getDefaultToolkit().getSystemClipboard()
1332 .setContents(new StringSelection(""), null);
1334 Toolkit.getDefaultToolkit().getSystemClipboard()
1335 .setContents(ss, Desktop.instance);
1337 catch (OutOfMemoryError er)
1339 er.printStackTrace();
1340 javax.swing.SwingUtilities.invokeLater(new Runnable()
1344 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1345 "Out of memory copying region!!"
1347 "\nSee help files for increasing Java Virtual Machine memory."
1349 javax.swing.JOptionPane.WARNING_MESSAGE);
1356 Vector hiddenColumns = null;
1357 if(viewport.hasHiddenColumns)
1359 hiddenColumns =new Vector();
1360 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1361 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
1364 int[] region = (int[])
1365 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
1367 hiddenColumns.addElement(new int[]
1368 {region[0] - hiddenOffset,
1369 region[1]-hiddenOffset});
1373 Desktop.jalviewClipboard = new Object[]
1376 viewport.alignment.getDataset(),
1378 statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
1384 * @param e DOCUMENT ME!
1386 protected void pasteNew_actionPerformed(ActionEvent e)
1394 * @param e DOCUMENT ME!
1396 protected void pasteThis_actionPerformed(ActionEvent e)
1404 * @param newAlignment DOCUMENT ME!
1406 void paste(boolean newAlignment)
1410 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1411 Transferable contents = c.getContents(this);
1413 if (contents == null)
1421 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1422 if (str.length() < 1)
1427 format = new IdentifyFile().Identify(str, "Paste");
1430 catch (OutOfMemoryError er)
1432 er.printStackTrace();
1433 javax.swing.SwingUtilities.invokeLater(new Runnable()
1437 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1438 "Out of memory pasting sequences!!"
1440 "\nSee help files for increasing Java Virtual Machine memory."
1442 javax.swing.JOptionPane.WARNING_MESSAGE);
1449 SequenceI[] sequences;
1452 if(Desktop.jalviewClipboard!=null)
1454 // The clipboard was filled from within Jalview, we must use the sequences
1455 // And dataset from the copied alignment
1456 sequences = (SequenceI[])Desktop.jalviewClipboard[0];
1460 sequences = new FormatAdapter().readFile(str, "Paste", format).
1461 getSequencesArray();
1464 AlignmentI alignment = null;
1468 alignment = new Alignment(sequences);
1470 if (Desktop.jalviewClipboard != null)
1472 alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
1476 alignment.setDataset(null);
1481 alignment = viewport.getAlignment();
1484 SequenceI [] newseqs = new SequenceI[sequences.length];
1485 for (int i = 0; i < sequences.length; i++)
1487 newseqs[i] = new Sequence(sequences[i].getName(),
1488 sequences[i].getSequence(),
1489 sequences[i].getStart(),
1490 sequences[i].getEnd());
1492 alignment.addSequence(newseqs[i]);
1498 addHistoryItem(new EditCommand(
1503 alignment.getWidth(),
1508 viewport.setEndSeq(alignment.getHeight());
1509 alignment.getWidth();
1510 viewport.firePropertyChange("alignment", null, alignment.getSequences());
1515 // Add any annotations attached to sequences
1516 for (int i = 0; i < sequences.length; i++)
1518 if (sequences[i].getAnnotation() != null)
1520 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1522 AlignmentAnnotation newAnnot =
1523 new AlignmentAnnotation(
1524 sequences[i].getAnnotation()[a].label,
1525 sequences[i].getAnnotation()[a].description,
1526 sequences[i].getAnnotation()[a].annotations,
1527 sequences[i].getAnnotation()[a].graphMin,
1528 sequences[i].getAnnotation()[a].graphMax,
1529 sequences[i].getAnnotation()[a].graph);
1531 sequences[i].getAnnotation()[a] = newAnnot;
1532 newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].
1534 newAnnot.sequenceRef = sequences[i];
1535 newAnnot.adjustForAlignment();
1536 alignment.addAnnotation(newAnnot);
1537 alignment.setAnnotationIndex(newAnnot, a);
1540 alignPanel.annotationPanel.adjustPanelHeight();
1546 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
1547 String newtitle = new String("Copied sequences");
1549 if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
1551 Vector hc = (Vector)Desktop.jalviewClipboard[2];
1552 for(int i=0; i<hc.size(); i++)
1554 int [] region = (int[]) hc.elementAt(i);
1555 af.viewport.hideColumns(region[0], region[1]);
1560 //>>>This is a fix for the moment, until a better solution is found!!<<<
1561 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
1562 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1565 if (title.startsWith("Copied sequences"))
1571 newtitle = newtitle.concat("- from " + title);
1574 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1581 catch (Exception ex)
1583 ex.printStackTrace();
1584 System.out.println("Exception whilst pasting: "+ex);
1585 // could be anything being pasted in here
1594 * @param e DOCUMENT ME!
1596 protected void cut_actionPerformed(ActionEvent e)
1598 copy_actionPerformed(null);
1599 delete_actionPerformed(null);
1605 * @param e DOCUMENT ME!
1607 protected void delete_actionPerformed(ActionEvent evt)
1610 SequenceGroup sg = viewport.getSelectionGroup();
1616 Vector seqs = new Vector();
1618 for (int i = 0; i < sg.getSize(); i++)
1620 seq = sg.getSequenceAt(i);
1621 seqs.addElement(seq);
1625 // If the cut affects all sequences, remove highlighted columns
1626 if (sg.getSize() == viewport.alignment.getHeight())
1628 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1629 sg.getEndRes() + 1);
1633 SequenceI [] cut = new SequenceI[seqs.size()];
1634 for(int i=0; i<seqs.size(); i++)
1636 cut[i] = (SequenceI)seqs.elementAt(i);
1643 addHistoryItem(new EditCommand("Cut Sequences",
1647 sg.getEndRes()-sg.getStartRes()+1,
1648 viewport.alignment));
1651 viewport.setSelectionGroup(null);
1652 viewport.alignment.deleteGroup(sg);
1654 viewport.firePropertyChange("alignment", null,
1655 viewport.getAlignment().getSequences());
1657 if (viewport.getAlignment().getHeight() < 1)
1661 this.setClosed(true);
1663 catch (Exception ex)
1672 * @param e DOCUMENT ME!
1674 protected void deleteGroups_actionPerformed(ActionEvent e)
1676 viewport.alignment.deleteAllGroups();
1677 viewport.sequenceColours = null;
1678 viewport.setSelectionGroup(null);
1679 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1680 alignPanel.paintAlignment(true);
1686 * @param e DOCUMENT ME!
1688 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1690 SequenceGroup sg = new SequenceGroup();
1692 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1695 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1698 sg.setEndRes(viewport.alignment.getWidth() - 1);
1699 viewport.setSelectionGroup(sg);
1700 alignPanel.paintAlignment(true);
1701 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1707 * @param e DOCUMENT ME!
1709 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1711 if(viewport.cursorMode)
1713 alignPanel.seqPanel.keyboardNo1 = null;
1714 alignPanel.seqPanel.keyboardNo2 = null;
1716 viewport.setSelectionGroup(null);
1717 viewport.getColumnSelection().clear();
1718 viewport.setSelectionGroup(null);
1719 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1720 alignPanel.idPanel.idCanvas.searchResults = null;
1721 alignPanel.paintAlignment(true);
1722 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1728 * @param e DOCUMENT ME!
1730 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1732 SequenceGroup sg = viewport.getSelectionGroup();
1736 selectAllSequenceMenuItem_actionPerformed(null);
1741 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1744 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1747 alignPanel.paintAlignment(true);
1749 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1752 public void invertColSel_actionPerformed(ActionEvent e)
1754 viewport.invertColumnSelection();
1755 alignPanel.paintAlignment(true);
1762 * @param e DOCUMENT ME!
1764 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1766 trimAlignment(true);
1772 * @param e DOCUMENT ME!
1774 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
1776 trimAlignment(false);
1779 void trimAlignment(boolean trimLeft)
1781 ColumnSelection colSel = viewport.getColumnSelection();
1784 if (colSel.size() > 0)
1788 column = colSel.getMin();
1792 column = colSel.getMax();
1796 if(viewport.getSelectionGroup()!=null)
1798 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
1799 hiddenRepSequences);
1803 seqs = viewport.alignment.getSequencesArray();
1807 TrimRegionCommand trimRegion;
1810 trimRegion = new TrimRegionCommand("Remove Left",
1811 TrimRegionCommand.TRIM_LEFT,
1816 viewport.selectionGroup);
1817 viewport.setStartRes(0);
1821 trimRegion = new TrimRegionCommand("Remove Right",
1822 TrimRegionCommand.TRIM_RIGHT,
1827 viewport.selectionGroup);
1830 statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
1833 addHistoryItem(trimRegion);
1835 Vector groups = viewport.alignment.getGroups();
1837 for (int i = 0; i < groups.size(); i++)
1839 SequenceGroup sg = (SequenceGroup) groups.get(i);
1841 if ( (trimLeft && !sg.adjustForRemoveLeft(column))
1842 || (!trimLeft && !sg.adjustForRemoveRight(column)))
1844 viewport.alignment.deleteGroup(sg);
1848 viewport.firePropertyChange("alignment", null,
1849 viewport.getAlignment().getSequences());
1856 * @param e DOCUMENT ME!
1858 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1860 int start = 0, end = viewport.alignment.getWidth()-1;
1863 if (viewport.getSelectionGroup() != null)
1865 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
1866 hiddenRepSequences);
1867 start = viewport.getSelectionGroup().getStartRes();
1868 end = viewport.getSelectionGroup().getEndRes();
1872 seqs = viewport.alignment.getSequencesArray();
1876 RemoveGapColCommand removeGapCols =
1877 new RemoveGapColCommand("Remove Gapped Columns",
1880 viewport.alignment);
1882 addHistoryItem(removeGapCols);
1884 statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
1886 //This is to maintain viewport position on first residue
1888 SequenceI seq = viewport.alignment.getSequenceAt(0);
1889 int startRes = seq.findPosition(viewport.startRes);
1890 // ShiftList shifts;
1891 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
1892 // edit.alColumnChanges=shifts.getInverse();
1893 // if (viewport.hasHiddenColumns)
1894 // viewport.getColumnSelection().compensateForEdits(shifts);
1895 viewport.setStartRes(seq.findIndex(startRes)-1);
1896 viewport.firePropertyChange("alignment", null,
1897 viewport.getAlignment().getSequences());
1904 * @param e DOCUMENT ME!
1906 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1908 int start = 0, end = viewport.alignment.getWidth()-1;
1911 if (viewport.getSelectionGroup() != null)
1913 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
1914 hiddenRepSequences);
1915 start = viewport.getSelectionGroup().getStartRes();
1916 end = viewport.getSelectionGroup().getEndRes();
1920 seqs = viewport.alignment.getSequencesArray();
1923 //This is to maintain viewport position on first residue
1925 SequenceI seq = viewport.alignment.getSequenceAt(0);
1926 int startRes = seq.findPosition(viewport.startRes);
1928 addHistoryItem(new RemoveGapsCommand("Remove Gaps",
1931 viewport.alignment));
1933 viewport.setStartRes(seq.findIndex(startRes)-1);
1935 viewport.firePropertyChange("alignment", null,
1936 viewport.getAlignment().getSequences());
1943 * @param e DOCUMENT ME!
1945 public void padGapsMenuitem_actionPerformed(ActionEvent e)
1947 viewport.padGaps = padGapsMenuitem.isSelected();
1949 viewport.firePropertyChange("alignment",
1951 viewport.getAlignment().getSequences());
1957 * @param e DOCUMENT ME!
1959 public void findMenuItem_actionPerformed(ActionEvent e)
1964 public void newView_actionPerformed(ActionEvent e)
1966 AlignmentPanel newap =
1967 new Jalview2XML().copyAlignPanel(alignPanel, true);
1969 newap.av.gatherViewsHere = false;
1971 if (viewport.viewName == null)
1973 viewport.viewName = "Original";
1976 newap.av.historyList = viewport.historyList;
1977 newap.av.redoList = viewport.redoList;
1979 int index = Desktop.getViewCount(viewport.getSequenceSetId());
1980 String newViewName = "View " +index;
1982 Vector comps = (Vector) PaintRefresher.components.get(viewport.
1983 getSequenceSetId());
1984 Vector existingNames = new Vector();
1985 for(int i=0; i<comps.size(); i++)
1987 if(comps.elementAt(i) instanceof AlignmentPanel)
1989 AlignmentPanel ap = (AlignmentPanel)comps.elementAt(i);
1990 if(!existingNames.contains(ap.av.viewName))
1992 existingNames.addElement(ap.av.viewName);
1997 while(existingNames.contains(newViewName))
1999 newViewName = "View "+ (++index);
2002 newap.av.viewName = newViewName;
2004 addAlignmentPanel(newap, false);
2006 if(alignPanels.size()==2)
2008 viewport.gatherViewsHere = true;
2010 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2013 public void expandViews_actionPerformed(ActionEvent e)
2015 Desktop.instance.explodeViews(this);
2018 public void gatherViews_actionPerformed(ActionEvent e)
2020 Desktop.instance.gatherViews(this);
2028 * @param e DOCUMENT ME!
2030 public void font_actionPerformed(ActionEvent e)
2032 new FontChooser(alignPanel);
2039 * @param e DOCUMENT ME!
2041 protected void seqLimit_actionPerformed(ActionEvent e)
2043 viewport.setShowJVSuffix(seqLimits.isSelected());
2045 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
2046 alignPanel.paintAlignment(true);
2049 public void idRightAlign_actionPerformed(ActionEvent e)
2051 viewport.rightAlignIds = idRightAlign.isSelected();
2052 alignPanel.paintAlignment(true);
2060 * @param e DOCUMENT ME!
2062 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2064 viewport.setColourText(colourTextMenuItem.isSelected());
2065 alignPanel.paintAlignment(true);
2071 * @param e DOCUMENT ME!
2073 public void wrapMenuItem_actionPerformed(ActionEvent e)
2075 scaleAbove.setVisible(wrapMenuItem.isSelected());
2076 scaleLeft.setVisible(wrapMenuItem.isSelected());
2077 scaleRight.setVisible(wrapMenuItem.isSelected());
2078 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2079 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2082 public void showAllSeqs_actionPerformed(ActionEvent e)
2084 viewport.showAllHiddenSeqs();
2087 public void showAllColumns_actionPerformed(ActionEvent e)
2089 viewport.showAllHiddenColumns();
2093 public void hideSelSequences_actionPerformed(ActionEvent e)
2095 viewport.hideAllSelectedSeqs();
2096 alignPanel.paintAlignment(true);
2099 public void hideSelColumns_actionPerformed(ActionEvent e)
2101 viewport.hideSelectedColumns();
2102 alignPanel.paintAlignment(true);
2105 public void hiddenMarkers_actionPerformed(ActionEvent e)
2107 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2114 * @param e DOCUMENT ME!
2116 protected void scaleAbove_actionPerformed(ActionEvent e)
2118 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2119 alignPanel.paintAlignment(true);
2125 * @param e DOCUMENT ME!
2127 protected void scaleLeft_actionPerformed(ActionEvent e)
2129 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2130 alignPanel.paintAlignment(true);
2136 * @param e DOCUMENT ME!
2138 protected void scaleRight_actionPerformed(ActionEvent e)
2140 viewport.setScaleRightWrapped(scaleRight.isSelected());
2141 alignPanel.paintAlignment(true);
2147 * @param e DOCUMENT ME!
2149 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2151 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2152 alignPanel.paintAlignment(true);
2158 * @param e DOCUMENT ME!
2160 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2162 viewport.setShowText(viewTextMenuItem.isSelected());
2163 alignPanel.paintAlignment(true);
2169 * @param e DOCUMENT ME!
2171 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2173 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2174 alignPanel.paintAlignment(true);
2178 public FeatureSettings featureSettings;
2179 public void featureSettings_actionPerformed(ActionEvent e)
2181 if(featureSettings !=null )
2183 featureSettings.close();
2184 featureSettings = null;
2186 featureSettings = new FeatureSettings(this);
2192 * @param evt DOCUMENT ME!
2194 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2196 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2197 alignPanel.paintAlignment(true);
2198 if (alignPanel.getOverviewPanel() != null)
2200 alignPanel.getOverviewPanel().updateOverviewImage();
2207 * @param e DOCUMENT ME!
2209 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2211 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2212 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2218 * @param e DOCUMENT ME!
2220 public void overviewMenuItem_actionPerformed(ActionEvent e)
2222 if (alignPanel.overviewPanel != null)
2227 JInternalFrame frame = new JInternalFrame();
2228 OverviewPanel overview = new OverviewPanel(alignPanel);
2229 frame.setContentPane(overview);
2230 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2231 frame.getWidth(), frame.getHeight());
2233 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2234 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2236 public void internalFrameClosed(
2237 javax.swing.event.InternalFrameEvent evt)
2239 alignPanel.setOverviewPanel(null);
2244 alignPanel.setOverviewPanel(overview);
2247 public void textColour_actionPerformed(ActionEvent e)
2249 new TextColourChooser().chooseColour(alignPanel, null);
2255 * @param e DOCUMENT ME!
2257 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2265 * @param e DOCUMENT ME!
2267 public void clustalColour_actionPerformed(ActionEvent e)
2269 changeColour(new ClustalxColourScheme(
2270 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
2276 * @param e DOCUMENT ME!
2278 public void zappoColour_actionPerformed(ActionEvent e)
2280 changeColour(new ZappoColourScheme());
2286 * @param e DOCUMENT ME!
2288 public void taylorColour_actionPerformed(ActionEvent e)
2290 changeColour(new TaylorColourScheme());
2296 * @param e DOCUMENT ME!
2298 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2300 changeColour(new HydrophobicColourScheme());
2306 * @param e DOCUMENT ME!
2308 public void helixColour_actionPerformed(ActionEvent e)
2310 changeColour(new HelixColourScheme());
2316 * @param e DOCUMENT ME!
2318 public void strandColour_actionPerformed(ActionEvent e)
2320 changeColour(new StrandColourScheme());
2326 * @param e DOCUMENT ME!
2328 public void turnColour_actionPerformed(ActionEvent e)
2330 changeColour(new TurnColourScheme());
2336 * @param e DOCUMENT ME!
2338 public void buriedColour_actionPerformed(ActionEvent e)
2340 changeColour(new BuriedColourScheme());
2346 * @param e DOCUMENT ME!
2348 public void nucleotideColour_actionPerformed(ActionEvent e)
2350 changeColour(new NucleotideColourScheme());
2353 public void annotationColour_actionPerformed(ActionEvent e)
2355 new AnnotationColourChooser(viewport, alignPanel);
2362 * @param e DOCUMENT ME!
2364 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2366 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2372 * @param cs DOCUMENT ME!
2374 public void changeColour(ColourSchemeI cs)
2380 if (viewport.getAbovePIDThreshold())
2382 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2385 cs.setThreshold(threshold,
2386 viewport.getIgnoreGapsConsensus());
2388 viewport.setGlobalColourScheme(cs);
2392 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2395 if (viewport.getConservationSelected())
2398 Alignment al = (Alignment) viewport.alignment;
2399 Conservation c = new Conservation("All",
2400 ResidueProperties.propHash, 3,
2401 al.getSequences(), 0,
2405 c.verdict(false, viewport.ConsPercGaps);
2407 cs.setConservation(c);
2409 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
2414 cs.setConservation(null);
2417 cs.setConsensus(viewport.hconsensus);
2420 viewport.setGlobalColourScheme(cs);
2422 if (viewport.getColourAppliesToAllGroups())
2424 Vector groups = viewport.alignment.getGroups();
2426 for (int i = 0; i < groups.size(); i++)
2428 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2436 if (cs instanceof ClustalxColourScheme)
2438 sg.cs = new ClustalxColourScheme(
2439 sg.getSequences(viewport.hiddenRepSequences), sg.getWidth());
2441 else if (cs instanceof UserColourScheme)
2443 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
2449 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2451 catch (Exception ex)
2456 if (viewport.getAbovePIDThreshold()
2457 || cs instanceof PIDColourScheme
2458 || cs instanceof Blosum62ColourScheme)
2460 sg.cs.setThreshold(threshold,
2461 viewport.getIgnoreGapsConsensus());
2463 sg.cs.setConsensus(AAFrequency.calculate(
2464 sg.getSequences(viewport.hiddenRepSequences), sg.getStartRes(),
2469 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2473 if (viewport.getConservationSelected())
2475 Conservation c = new Conservation("Group",
2476 ResidueProperties.propHash, 3,
2477 sg.getSequences(viewport.
2478 hiddenRepSequences),
2482 c.verdict(false, viewport.ConsPercGaps);
2483 sg.cs.setConservation(c);
2487 sg.cs.setConservation(null);
2492 if (alignPanel.getOverviewPanel() != null)
2494 alignPanel.getOverviewPanel().updateOverviewImage();
2500 alignPanel.paintAlignment(true);
2506 * @param e DOCUMENT ME!
2508 protected void modifyPID_actionPerformed(ActionEvent e)
2510 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
2512 SliderPanel.setPIDSliderSource(alignPanel,
2513 viewport.getGlobalColourScheme(),
2515 SliderPanel.showPIDSlider();
2522 * @param e DOCUMENT ME!
2524 protected void modifyConservation_actionPerformed(ActionEvent e)
2526 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
2528 SliderPanel.setConservationSlider(alignPanel,
2529 viewport.globalColourScheme,
2531 SliderPanel.showConservationSlider();
2538 * @param e DOCUMENT ME!
2540 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2542 viewport.setConservationSelected(conservationMenuItem.isSelected());
2544 viewport.setAbovePIDThreshold(false);
2545 abovePIDThreshold.setSelected(false);
2547 changeColour(viewport.getGlobalColourScheme());
2549 modifyConservation_actionPerformed(null);
2555 * @param e DOCUMENT ME!
2557 public void abovePIDThreshold_actionPerformed(ActionEvent e)
2559 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
2561 conservationMenuItem.setSelected(false);
2562 viewport.setConservationSelected(false);
2564 changeColour(viewport.getGlobalColourScheme());
2566 modifyPID_actionPerformed(null);
2572 * @param e DOCUMENT ME!
2574 public void userDefinedColour_actionPerformed(ActionEvent e)
2576 if (e.getActionCommand().equals("User Defined..."))
2578 new UserDefinedColours(alignPanel, null);
2582 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
2583 getUserColourSchemes().get(e.getActionCommand());
2589 public void updateUserColourMenu()
2592 Component[] menuItems = colourMenu.getMenuComponents();
2593 int i, iSize = menuItems.length;
2594 for (i = 0; i < iSize; i++)
2596 if (menuItems[i].getName() != null &&
2597 menuItems[i].getName().equals("USER_DEFINED"))
2599 colourMenu.remove(menuItems[i]);
2603 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
2605 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
2606 getUserColourSchemes().keys();
2608 while (userColours.hasMoreElements())
2610 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
2612 nextElement().toString());
2613 radioItem.setName("USER_DEFINED");
2614 radioItem.addMouseListener(new MouseAdapter()
2616 public void mousePressed(MouseEvent evt)
2618 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
2620 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
2622 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
2624 "Remove from default list?",
2625 "Remove user defined colour",
2626 JOptionPane.YES_NO_OPTION);
2627 if(option == JOptionPane.YES_OPTION)
2629 jalview.gui.UserDefinedColours.removeColourFromDefaults(
2630 radioItem.getText());
2631 colourMenu.remove(radioItem);
2635 radioItem.addActionListener(new ActionListener()
2637 public void actionPerformed(ActionEvent evt)
2639 userDefinedColour_actionPerformed(evt);
2646 radioItem.addActionListener(new ActionListener()
2648 public void actionPerformed(ActionEvent evt)
2650 userDefinedColour_actionPerformed(evt);
2654 colourMenu.insert(radioItem, 15);
2655 colours.add(radioItem);
2663 * @param e DOCUMENT ME!
2665 public void PIDColour_actionPerformed(ActionEvent e)
2667 changeColour(new PIDColourScheme());
2673 * @param e DOCUMENT ME!
2675 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
2677 changeColour(new Blosum62ColourScheme());
2683 * @param e DOCUMENT ME!
2685 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2687 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2688 AlignmentSorter.sortByPID(viewport.getAlignment(),
2689 viewport.getAlignment().getSequenceAt(0));
2690 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2691 viewport.alignment));
2692 alignPanel.paintAlignment(true);
2698 * @param e DOCUMENT ME!
2700 public void sortIDMenuItem_actionPerformed(ActionEvent e)
2702 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2703 AlignmentSorter.sortByID(viewport.getAlignment());
2704 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
2705 alignPanel.paintAlignment(true);
2711 * @param e DOCUMENT ME!
2713 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
2715 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2716 AlignmentSorter.sortByGroup(viewport.getAlignment());
2717 addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
2719 alignPanel.paintAlignment(true);
2725 * @param e DOCUMENT ME!
2727 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2729 new RedundancyPanel(alignPanel, this);
2736 * @param e DOCUMENT ME!
2738 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2740 if ( (viewport.getSelectionGroup() == null) ||
2741 (viewport.getSelectionGroup().getSize() < 2))
2743 JOptionPane.showInternalMessageDialog(this,
2744 "You must select at least 2 sequences.",
2745 "Invalid Selection",
2746 JOptionPane.WARNING_MESSAGE);
2750 JInternalFrame frame = new JInternalFrame();
2751 frame.setContentPane(new PairwiseAlignPanel(viewport));
2752 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
2759 * @param e DOCUMENT ME!
2761 public void PCAMenuItem_actionPerformed(ActionEvent e)
2763 if ( ( (viewport.getSelectionGroup() != null) &&
2764 (viewport.getSelectionGroup().getSize() < 4) &&
2765 (viewport.getSelectionGroup().getSize() > 0)) ||
2766 (viewport.getAlignment().getHeight() < 4))
2768 JOptionPane.showInternalMessageDialog(this,
2769 "Principal component analysis must take\n" +
2770 "at least 4 input sequences.",
2771 "Sequence selection insufficient",
2772 JOptionPane.WARNING_MESSAGE);
2777 new PCAPanel(alignPanel);
2781 public void autoCalculate_actionPerformed(ActionEvent e)
2783 viewport.autoCalculateConsensus = autoCalculate.isSelected();
2784 if(viewport.autoCalculateConsensus)
2786 viewport.firePropertyChange("alignment",
2788 viewport.getAlignment().getSequences());
2796 * @param e DOCUMENT ME!
2798 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2800 NewTreePanel("AV", "PID", "Average distance tree using PID");
2806 * @param e DOCUMENT ME!
2808 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2810 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2816 * @param e DOCUMENT ME!
2818 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2820 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2826 * @param e DOCUMENT ME!
2828 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2830 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2836 * @param type DOCUMENT ME!
2837 * @param pwType DOCUMENT ME!
2838 * @param title DOCUMENT ME!
2840 void NewTreePanel(String type, String pwType, String title)
2844 if (viewport.getSelectionGroup() != null)
2846 if (viewport.getSelectionGroup().getSize() < 3)
2848 JOptionPane.showMessageDialog(Desktop.desktop,
2849 "You need to have more than two sequences selected to build a tree!",
2850 "Not enough sequences",
2851 JOptionPane.WARNING_MESSAGE);
2856 SequenceGroup sg = viewport.getSelectionGroup();
2858 /* Decide if the selection is a column region */
2859 while (s < sg.getSize())
2861 if ( ( (SequenceI) sg.getSequences(null).elementAt(s++)).getLength() <
2864 JOptionPane.showMessageDialog(Desktop.desktop,
2865 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
2866 "Try using the Pad function in the edit menu,\n" +
2867 "or one of the multiple sequence alignment web services.",
2868 "Sequences in selection are not aligned",
2869 JOptionPane.WARNING_MESSAGE);
2875 title = title + " on region";
2876 tp = new TreePanel(alignPanel, type, pwType);
2880 //are the sequences aligned?
2881 if (!viewport.alignment.isAligned())
2883 JOptionPane.showMessageDialog(Desktop.desktop,
2884 "The sequences must be aligned before creating a tree.\n" +
2885 "Try using the Pad function in the edit menu,\n" +
2886 "or one of the multiple sequence alignment web services.",
2887 "Sequences not aligned",
2888 JOptionPane.WARNING_MESSAGE);
2893 if(viewport.alignment.getHeight()<2)
2898 tp = new TreePanel(alignPanel, type, pwType);
2903 if(viewport.viewName!=null)
2905 title+= viewport.viewName+" of ";
2908 title += this.title;
2910 Desktop.addInternalFrame(tp, title, 600, 500);
2916 * @param title DOCUMENT ME!
2917 * @param order DOCUMENT ME!
2919 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
2921 final JMenuItem item = new JMenuItem("by " + title);
2923 item.addActionListener(new java.awt.event.ActionListener()
2925 public void actionPerformed(ActionEvent e)
2927 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2929 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
2930 AlignmentSorter.sortBy(viewport.getAlignment(), order);
2932 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
2933 viewport.alignment));
2935 alignPanel.paintAlignment(true);
2941 * Maintain the Order by->Displayed Tree menu.
2942 * Creates a new menu item for a TreePanel with an appropriate
2943 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
2944 * to remove the menu item when the treePanel is closed, and adjust
2945 * the tree leaf to sequence mapping when the alignment is modified.
2946 * @param treePanel Displayed tree window.
2947 * @param title SortBy menu item title.
2949 public void buildTreeMenu()
2951 sortByTreeMenu.removeAll();
2953 Vector comps = (Vector) PaintRefresher.components.get(viewport.
2954 getSequenceSetId());
2955 Vector treePanels = new Vector();
2956 int i, iSize = comps.size();
2957 for(i=0; i<iSize; i++)
2959 if(comps.elementAt(i) instanceof TreePanel)
2961 treePanels.add(comps.elementAt(i));
2965 iSize = treePanels.size();
2969 sortByTreeMenu.setVisible(false);
2973 sortByTreeMenu.setVisible(true);
2975 for(i=0; i<treePanels.size(); i++)
2977 TreePanel tp = (TreePanel)treePanels.elementAt(i);
2978 final JMenuItem item = new JMenuItem(tp.getTitle());
2979 final NJTree tree = ((TreePanel)treePanels.elementAt(i)).getTree();
2980 item.addActionListener(new java.awt.event.ActionListener()
2982 public void actionPerformed(ActionEvent e)
2984 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2985 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
2987 addHistoryItem(new OrderCommand("Tree Sort",
2989 viewport.alignment));
2991 alignPanel.paintAlignment(true);
2995 sortByTreeMenu.add(item);
3000 * Work out whether the whole set of sequences
3001 * or just the selected set will be submitted for multiple alignment.
3004 private jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3006 // Now, check we have enough sequences
3007 AlignmentView msa = null;
3009 if ( (viewport.getSelectionGroup() != null) &&
3010 (viewport.getSelectionGroup().getSize() > 1))
3012 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
3013 /*SequenceGroup seqs = viewport.getSelectionGroup();
3015 msa = new SequenceI[sz = seqs.getSize(false)];
3017 for (int i = 0; i < sz; i++)
3019 msa[i] = (SequenceI) seqs.getSequenceAt(i);
3021 msa = viewport.getAlignmentView(true);
3025 /*Vector seqs = viewport.getAlignment().getSequences();
3027 if (seqs.size() > 1)
3029 msa = new SequenceI[seqs.size()];
3031 for (int i = 0; i < seqs.size(); i++)
3033 msa[i] = (SequenceI) seqs.elementAt(i);
3036 msa = viewport.getAlignmentView(false);
3042 * Decides what is submitted to a secondary structure prediction service,
3043 * the currently selected sequence, or the currently selected alignment
3044 * (where the first sequence in the set is the one that the prediction
3047 AlignmentView gatherSeqOrMsaForSecStrPrediction()
3049 AlignmentView seqs = null;
3051 if ( (viewport.getSelectionGroup() != null) &&
3052 (viewport.getSelectionGroup().getSize() > 0))
3054 seqs = viewport.getAlignmentView(true);
3058 seqs = viewport.getAlignmentView(false);
3060 // limit sequences - JBPNote in future - could spawn multiple prediction jobs
3061 // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3062 if (!viewport.alignment.isAligned())
3064 seqs.setSequences(new SeqCigar[]
3065 {seqs.getSequences()[0]});
3072 * @param e DOCUMENT ME!
3074 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3076 // Pick the tree file
3077 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
3080 chooser.setFileView(new JalviewFileView());
3081 chooser.setDialogTitle("Select a newick-like tree file");
3082 chooser.setToolTipText("Load a tree file");
3084 int value = chooser.showOpenDialog(null);
3086 if (value == JalviewFileChooser.APPROVE_OPTION)
3088 String choice = chooser.getSelectedFile().getPath();
3089 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3093 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
3095 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3097 catch (Exception ex)
3099 JOptionPane.showMessageDialog(Desktop.desktop,
3100 "Problem reading tree file",
3102 JOptionPane.WARNING_MESSAGE);
3103 ex.printStackTrace();
3109 public TreePanel ShowNewickTree(NewickFile nf, String title)
3111 return ShowNewickTree(nf,title,600,500,4,5);
3114 public TreePanel ShowNewickTree(NewickFile nf, String title,
3115 AlignmentView input)
3117 return ShowNewickTree(nf,title, input, 600,500,4,5);
3120 public TreePanel ShowNewickTree(NewickFile nf, String title, int w, int h,
3123 return ShowNewickTree(nf, title, null, w, h, x, y);
3126 * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
3128 * @param nf the tree
3129 * @param title tree viewer title
3130 * @param input Associated alignment input data (or null)
3135 * @return TreePanel handle
3137 public TreePanel ShowNewickTree(NewickFile nf, String title,
3138 AlignmentView input, int w, int h, int x,
3141 TreePanel tp = null;
3147 if (nf.getTree() != null)
3149 tp = new TreePanel(alignPanel,
3158 tp.setLocation(x,y);
3162 Desktop.addInternalFrame(tp, title, w, h);
3165 catch (Exception ex)
3167 ex.printStackTrace();
3175 * Generates menu items and listener event actions for web service clients
3178 public void BuildWebServiceMenu()
3180 if ( (Discoverer.services != null)
3181 && (Discoverer.services.size() > 0))
3183 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
3184 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
3185 Vector wsmenu = new Vector();
3186 final AlignFrame af = this;
3189 // Add any Multiple Sequence Alignment Services
3190 final JMenu msawsmenu = new JMenu("Alignment");
3191 for (int i = 0, j = msaws.size(); i < j; i++)
3193 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
3195 final JMenuItem method = new JMenuItem(sh.getName());
3196 method.addActionListener(new ActionListener()
3198 public void actionPerformed(ActionEvent e)
3200 AlignmentView msa = gatherSequencesForAlignment();
3201 new jalview.ws.MsaWSClient(sh, title, msa,
3203 viewport.getAlignment().getDataset(),
3209 msawsmenu.add(method);
3210 // Deal with services that we know accept partial alignments.
3211 if (sh.getName().indexOf("lustal") > -1)
3213 // We know that ClustalWS can accept partial alignments for refinement.
3214 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
3215 methodR.addActionListener(new ActionListener()
3217 public void actionPerformed(ActionEvent e)
3219 AlignmentView msa = gatherSequencesForAlignment();
3220 new jalview.ws.MsaWSClient(sh, title, msa,
3222 viewport.getAlignment().getDataset(),
3228 msawsmenu.add(methodR);
3232 wsmenu.add(msawsmenu);
3234 if (secstrpr != null)
3236 // Add any secondary structure prediction services
3237 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
3238 for (int i = 0, j = secstrpr.size(); i < j; i++)
3240 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
3242 final JMenuItem method = new JMenuItem(sh.getName());
3243 method.addActionListener(new ActionListener()
3245 public void actionPerformed(ActionEvent e)
3247 AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
3248 if (msa.getSequences().length == 1)
3250 // Single Sequence prediction
3251 new jalview.ws.JPredClient(sh, title, false, msa, af, true);
3255 if (msa.getSequences().length > 1)
3257 // Sequence profile based prediction
3258 new jalview.ws.JPredClient(sh,
3259 title, true, msa, af, true);
3264 secstrmenu.add(method);
3266 wsmenu.add(secstrmenu);
3268 this.webService.removeAll();
3269 for (int i = 0, j = wsmenu.size(); i < j; i++)
3271 webService.add( (JMenu) wsmenu.get(i));
3276 this.webService.removeAll();
3277 this.webService.add(this.webServiceNoServices);
3279 // TODO: add in rediscovery function
3280 // TODO: reduce code redundancy.
3281 // TODO: group services by location as well as function.
3284 /* public void vamsasStore_actionPerformed(ActionEvent e)
3286 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
3287 getProperty("LAST_DIRECTORY"));
3289 chooser.setFileView(new JalviewFileView());
3290 chooser.setDialogTitle("Export to Vamsas file");
3291 chooser.setToolTipText("Export");
3293 int value = chooser.showSaveDialog(this);
3295 if (value == JalviewFileChooser.APPROVE_OPTION)
3297 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
3298 //vs.store(chooser.getSelectedFile().getAbsolutePath() );
3299 vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
3306 public void showTranslation_actionPerformed(ActionEvent e)
3308 ///////////////////////////////
3309 // Collect Data to be translated/transferred
3311 SequenceI [] selection = viewport.getSelectionAsNewSequence();
3312 String [] seqstring = viewport.getViewAsString(true);
3313 AlignmentI al = null;
3315 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring, viewport.getViewAsVisibleContigs(true),
3316 viewport.getGapCharacter(), viewport.alignment.getAlignmentAnnotation(),
3317 viewport.alignment.getWidth());
3318 } catch (Exception ex) {
3320 jalview.bin.Cache.log.debug("Exception during translation.",ex);
3324 JOptionPane.showMessageDialog(Desktop.desktop,
3325 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
3326 "Translation Failed",
3327 JOptionPane.WARNING_MESSAGE);
3329 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
3330 Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
3339 * @param String DOCUMENT ME!
3341 public boolean parseFeaturesFile(String file, String type)
3343 boolean featuresFile = false;
3346 featuresFile = new FeaturesFile(file,
3347 type).parse(viewport.alignment.getDataset(),
3348 alignPanel.seqPanel.seqCanvas.
3349 getFeatureRenderer().featureColours,
3354 ex.printStackTrace();
3359 viewport.showSequenceFeatures = true;
3360 showSeqFeatures.setSelected(true);
3361 alignPanel.paintAlignment(true);
3364 return featuresFile;
3367 public void dragEnter(DropTargetDragEvent evt)
3370 public void dragExit(DropTargetEvent evt)
3373 public void dragOver(DropTargetDragEvent evt)
3376 public void dropActionChanged(DropTargetDragEvent evt)
3379 public void drop(DropTargetDropEvent evt)
3381 Transferable t = evt.getTransferable();
3382 java.util.List files = null;
3386 DataFlavor uriListFlavor = new DataFlavor(
3387 "text/uri-list;class=java.lang.String");
3388 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
3390 //Works on Windows and MacOSX
3391 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3392 files = (java.util.List) t.getTransferData(DataFlavor.
3393 javaFileListFlavor);
3395 else if (t.isDataFlavorSupported(uriListFlavor))
3397 // This is used by Unix drag system
3398 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3399 String data = (String) t.getTransferData(uriListFlavor);
3400 files = new java.util.ArrayList(1);
3401 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
3404 st.hasMoreTokens(); )
3406 String s = st.nextToken();
3407 if (s.startsWith("#"))
3409 // the line is a comment (as per the RFC 2483)
3413 java.net.URI uri = new java.net.URI(s);
3414 java.io.File file = new java.io.File(uri);
3421 e.printStackTrace();
3428 for (int i = 0; i < files.size(); i++)
3430 loadJalviewDataFile(files.get(i).toString());
3433 catch (Exception ex)
3435 ex.printStackTrace();
3440 // This method will attempt to load a "dropped" file first by testing
3441 // whether its and Annotation file, then features file. If both are
3442 // false then the user may have dropped an alignment file onto this
3444 public void loadJalviewDataFile(String file)
3448 String protocol = "File";
3450 if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
3455 boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
3456 alignment, file, protocol);
3460 boolean isGroupsFile = parseFeaturesFile(file,protocol);
3463 String format = new IdentifyFile().Identify(file, protocol);
3465 if(format.equalsIgnoreCase("JnetFile"))
3467 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
3469 new JnetAnnotationMaker().add_annotation(predictions,
3470 viewport.getAlignment(),
3472 alignPanel.adjustAnnotationHeight();
3473 alignPanel.paintAlignment(true);
3477 new FileLoader().LoadFile(viewport, file, protocol, format);
3484 alignPanel.adjustAnnotationHeight();
3488 catch (Exception ex)
3490 ex.printStackTrace();
3494 public void tabSelectionChanged(int index)
3498 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
3499 viewport = alignPanel.av;
3500 setMenusFromViewport(viewport);
3504 public void tabbedPane_mousePressed(MouseEvent e)
3506 if(SwingUtilities.isRightMouseButton(e))
3508 String reply = JOptionPane.showInternalInputDialog(this,
3511 JOptionPane.QUESTION_MESSAGE);
3515 viewport.viewName = reply;
3516 tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
3522 public AlignViewport getCurrentView()
3532 public PrintThread(AlignmentPanel ap)
3536 static PageFormat pf;
3539 PrinterJob printJob = PrinterJob.getPrinterJob();
3543 printJob.setPrintable(ap, pf);
3547 printJob.setPrintable(ap);
3550 if (printJob.printDialog())
3556 catch (Exception PrintException)
3558 PrintException.printStackTrace();