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 (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 &&
178 evt.getKeyCode() <= KeyEvent.VK_NUMPAD9)
180 && Character.isDigit(evt.getKeyChar()))
181 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
184 switch (evt.getKeyCode())
187 case 27: // escape key
188 deselectAllSequenceMenuItem_actionPerformed(null);
192 case KeyEvent.VK_DOWN:
193 if (evt.isAltDown() || !viewport.cursorMode)
194 moveSelectedSequences(false);
195 if (viewport.cursorMode)
196 alignPanel.seqPanel.moveCursor(0, 1);
200 if (evt.isAltDown() || !viewport.cursorMode)
201 moveSelectedSequences(true);
202 if (viewport.cursorMode)
203 alignPanel.seqPanel.moveCursor(0, -1);
207 case KeyEvent.VK_LEFT:
208 if (evt.isAltDown() || !viewport.cursorMode)
209 slideSequences(false,
210 alignPanel.seqPanel.getKeyboardNo1());
212 alignPanel.seqPanel.moveCursor( -1, 0);
217 case KeyEvent.VK_RIGHT:
218 if (evt.isAltDown() || !viewport.cursorMode)
220 alignPanel.seqPanel.getKeyboardNo1());
222 alignPanel.seqPanel.moveCursor(1, 0);
225 case KeyEvent.VK_SPACE:
226 if (viewport.cursorMode)
228 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
234 case KeyEvent.VK_DELETE:
235 case KeyEvent.VK_BACK_SPACE:
236 if (!viewport.cursorMode)
238 cut_actionPerformed(null);
242 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
250 if (viewport.cursorMode)
252 alignPanel.seqPanel.setCursorRow();
256 if (viewport.cursorMode && !evt.isControlDown())
258 alignPanel.seqPanel.setCursorColumn();
262 if (viewport.cursorMode)
264 alignPanel.seqPanel.setCursorPosition();
268 case KeyEvent.VK_ENTER:
269 case KeyEvent.VK_COMMA:
270 if (viewport.cursorMode)
272 alignPanel.seqPanel.setCursorRowAndColumn();
277 if (viewport.cursorMode)
279 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
283 if (viewport.cursorMode)
285 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
290 viewport.cursorMode = !viewport.cursorMode;
291 statusBar.setText("Keyboard editing mode is " +
292 (viewport.cursorMode ? "on" : "off"));
293 if (viewport.cursorMode)
295 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
296 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
298 alignPanel.seqPanel.seqCanvas.repaint();
304 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
305 java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
306 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
308 javax.help.HelpBroker hb = hs.createHelpBroker();
309 hb.setCurrentID("home");
310 hb.setDisplayed(true);
314 ex.printStackTrace();
320 boolean toggleSeqs = !evt.isControlDown();
321 boolean toggleCols = !evt.isShiftDown();
323 boolean hide = false;
325 SequenceGroup sg = viewport.getSelectionGroup();
328 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
330 hideSelSequences_actionPerformed(null);
333 else if (! (toggleCols &&
334 viewport.colSel.getSelected().size() > 0))
336 showAllSeqs_actionPerformed(null);
342 if (viewport.colSel.getSelected().size() > 0)
344 hideSelColumns_actionPerformed(null);
347 viewport.selectionGroup = sg;
352 showAllColumns_actionPerformed(null);
357 case KeyEvent.VK_PAGE_UP:
358 if (viewport.wrapAlignment)
360 alignPanel.scrollUp(true);
364 alignPanel.setScrollValues(viewport.startRes,
366 - viewport.endSeq + viewport.startSeq);
369 case KeyEvent.VK_PAGE_DOWN:
370 if (viewport.wrapAlignment)
372 alignPanel.scrollUp(false);
376 alignPanel.setScrollValues(viewport.startRes,
378 + viewport.endSeq - viewport.startSeq);
384 public void keyReleased(KeyEvent evt)
386 switch(evt.getKeyCode())
388 case KeyEvent.VK_LEFT:
389 if (evt.isAltDown() || !viewport.cursorMode)
390 viewport.firePropertyChange("alignment", null,
391 viewport.getAlignment().getSequences());
394 case KeyEvent.VK_RIGHT:
395 if (evt.isAltDown() || !viewport.cursorMode)
396 viewport.firePropertyChange("alignment", null,
397 viewport.getAlignment().getSequences());
405 public void addAlignmentPanel(final AlignmentPanel ap,
408 ap.alignFrame = this;
410 alignPanels.addElement(ap);
412 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
414 int aSize = alignPanels.size();
416 tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
418 if (aSize == 1 && ap.av.viewName==null)
420 this.getContentPane().add(ap, BorderLayout.CENTER);
426 setInitialTabVisible();
429 expandViews.setEnabled(true);
430 gatherViews.setEnabled(true);
431 tabbedPane.addTab(ap.av.viewName, ap);
433 ap.setVisible(false);
440 ap.av.alignment.padGaps();
442 ap.av.updateConservation(ap);
443 ap.av.updateConsensus(ap);
447 public void setInitialTabVisible()
449 expandViews.setEnabled(true);
450 gatherViews.setEnabled(true);
451 tabbedPane.setVisible(true);
452 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
453 tabbedPane.addTab(first.av.viewName,first);
454 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
458 public AlignViewport getViewport()
463 /* Set up intrinsic listeners for dynamically generated GUI bits. */
464 private void addServiceListeners()
466 final java.beans.PropertyChangeListener thisListener;
467 // Do this once to get current state
468 BuildWebServiceMenu();
469 Desktop.discoverer.addPropertyChangeListener(
470 thisListener = new java.beans.PropertyChangeListener()
472 public void propertyChange(PropertyChangeEvent evt)
474 // System.out.println("Discoverer property change.");
475 if (evt.getPropertyName().equals("services"))
477 // System.out.println("Rebuilding web service menu");
478 BuildWebServiceMenu();
483 addInternalFrameListener(new javax.swing.event.
484 InternalFrameAdapter()
486 public void internalFrameClosed(
487 javax.swing.event.InternalFrameEvent evt)
489 // System.out.println("deregistering discoverer listener");
490 Desktop.discoverer.removePropertyChangeListener(thisListener);
491 closeMenuItem_actionPerformed(true);
497 public void setGUINucleotide(boolean nucleotide)
499 showTranslation.setVisible( nucleotide );
500 conservationMenuItem.setEnabled( !nucleotide );
501 modifyConservation.setEnabled( !nucleotide );
503 //Remember AlignFrame always starts as protein
506 calculateMenu.remove(calculateMenu.getItemCount()-2);
511 * Need to call this method when tabs are selected for multiple views,
512 * or when loading from Jalview2XML.java
513 * @param av AlignViewport
515 void setMenusFromViewport(AlignViewport av)
517 padGapsMenuitem.setSelected(av.padGaps);
518 colourTextMenuItem.setSelected(av.showColourText);
519 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
520 conservationMenuItem.setSelected(av.getConservationSelected());
521 seqLimits.setSelected(av.getShowJVSuffix());
522 idRightAlign.setSelected(av.rightAlignIds);
523 renderGapsMenuItem.setSelected(av.renderGaps);
524 wrapMenuItem.setSelected(av.wrapAlignment);
525 scaleAbove.setVisible(av.wrapAlignment);
526 scaleLeft.setVisible(av.wrapAlignment);
527 scaleRight.setVisible(av.wrapAlignment);
528 annotationPanelMenuItem.setState(av.showAnnotation);
529 viewBoxesMenuItem.setSelected(av.showBoxes);
530 viewTextMenuItem.setSelected(av.showText);
532 setColourSelected(ColourSchemeProperty.
533 getColourName(av.getGlobalColourScheme()));
535 showSeqFeatures.setSelected(av.showSequenceFeatures);
536 hiddenMarkers.setState(av.showHiddenMarkers);
537 applyToAllGroups.setState(av.colourAppliesToAllGroups);
543 Hashtable progressBars;
544 public void setProgressBar(String message, long id)
546 if(progressBars == null)
548 progressBars = new Hashtable();
551 JPanel progressPanel;
552 GridLayout layout = (GridLayout) statusPanel.getLayout();
553 if(progressBars.get( new Long(id) )!=null)
555 progressPanel = (JPanel)progressBars.get( new Long(id) );
556 statusPanel.remove(progressPanel);
557 progressBars.remove( progressPanel );
558 progressPanel = null;
561 statusBar.setText(message);
564 layout.setRows(layout.getRows() - 1);
568 progressPanel = new JPanel(new BorderLayout(10, 5));
570 JProgressBar progressBar = new JProgressBar();
571 progressBar.setIndeterminate(true);
573 progressPanel.add(new JLabel(message), BorderLayout.WEST);
574 progressPanel.add(progressBar, BorderLayout.CENTER);
576 layout.setRows(layout.getRows() + 1);
577 statusPanel.add(progressPanel);
579 progressBars.put(new Long(id), progressPanel);
589 Added so Castor Mapping file can obtain Jalview Version
591 public String getVersion()
593 return jalview.bin.Cache.getProperty("VERSION");
596 public FeatureRenderer getFeatureRenderer()
598 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
602 public void fetchSequence_actionPerformed(ActionEvent e)
604 new SequenceFetcher(this);
607 public void addFromFile_actionPerformed(ActionEvent e)
609 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
612 public void reload_actionPerformed(ActionEvent e)
616 if(currentFileFormat.equals("Jalview"))
618 JInternalFrame [] frames = Desktop.desktop.getAllFrames();
619 for(int i=0; i<frames.length; i++)
621 if (frames[i] instanceof AlignFrame
623 && ( (AlignFrame) frames[i]).fileName.equals(fileName))
627 frames[i].setSelected(true);
628 Desktop.instance.closeAssociatedWindows();
630 catch (java.beans.PropertyVetoException ex)
635 Desktop.instance.closeAssociatedWindows();
637 FileLoader loader = new FileLoader();
638 String protocol = fileName.startsWith("http:")? "URL":"File";
639 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
643 Rectangle bounds = this.getBounds();
645 FileLoader loader = new FileLoader();
646 String protocol = fileName.startsWith("http:") ? "URL" : "File";
647 AlignFrame newframe =
648 loader.LoadFileWaitTillLoaded(fileName, protocol, currentFileFormat);
650 newframe.setBounds(bounds);
652 this.closeMenuItem_actionPerformed(true);
658 public void addFromText_actionPerformed(ActionEvent e)
660 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
663 public void addFromURL_actionPerformed(ActionEvent e)
665 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
669 public void save_actionPerformed(ActionEvent e)
672 || currentFileFormat==null
673 || fileName.startsWith("http")
676 saveAs_actionPerformed(null);
680 saveAlignment(fileName, currentFileFormat);
687 * @param e DOCUMENT ME!
689 public void saveAs_actionPerformed(ActionEvent e)
691 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
692 getProperty( "LAST_DIRECTORY"),
694 { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" },
696 { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
701 chooser.setFileView(new JalviewFileView());
702 chooser.setDialogTitle("Save Alignment to file");
703 chooser.setToolTipText("Save");
705 int value = chooser.showSaveDialog(this);
707 if (value == JalviewFileChooser.APPROVE_OPTION)
709 currentFileFormat = chooser.getSelectedFormat();
710 if (currentFileFormat == null)
712 JOptionPane.showInternalMessageDialog(Desktop.desktop,
713 "You must select a file format before saving!",
714 "File format not specified",
715 JOptionPane.WARNING_MESSAGE);
716 value = chooser.showSaveDialog(this);
720 fileName = chooser.getSelectedFile().getPath();
722 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
725 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
727 saveAlignment(fileName, currentFileFormat);
731 public boolean saveAlignment(String file, String format)
733 boolean success = true;
735 if (format.equalsIgnoreCase("Jalview"))
737 String shortName = title;
739 if (shortName.indexOf(java.io.File.separatorChar) > -1)
741 shortName = shortName.substring(shortName.lastIndexOf(
742 java.io.File.separatorChar) + 1);
745 success = new Jalview2XML().SaveAlignment(this, file, shortName);
747 statusBar.setText("Successfully saved to file: "
749 +format +" format.");
755 String[] omitHidden = null;
757 if (viewport.hasHiddenColumns)
759 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
760 "The Alignment contains hidden columns."
761 + "\nDo you want to save only the visible alignment?",
762 "Save / Omit Hidden Columns",
763 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
765 if (reply == JOptionPane.YES_OPTION)
767 omitHidden = viewport.getViewAsString(false);
771 String output = new FormatAdapter().formatSequences(
773 viewport.alignment.getSequencesArray(),
784 java.io.PrintWriter out = new java.io.PrintWriter(
785 new java.io.FileWriter(file));
790 statusBar.setText("Successfully saved to file: "
792 + format + " format.");
797 ex.printStackTrace();
804 JOptionPane.showInternalMessageDialog(
805 this, "Couldn't save file: " + fileName,
807 JOptionPane.WARNING_MESSAGE);
816 * @param e DOCUMENT ME!
818 protected void outputText_actionPerformed(ActionEvent e)
820 String [] omitHidden = null;
822 if(viewport.hasHiddenColumns)
824 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
825 "The Alignment contains hidden columns."
826 +"\nDo you want to output only the visible alignment?",
827 "Save / Omit Hidden Columns",
828 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
830 if(reply==JOptionPane.YES_OPTION)
832 omitHidden = viewport.getViewAsString(false);
836 CutAndPasteTransfer cap = new CutAndPasteTransfer();
837 cap.setForInput(null);
838 Desktop.addInternalFrame(cap,
839 "Alignment output - " + e.getActionCommand(), 600,
843 cap.setText(new FormatAdapter().formatSequences(
844 e.getActionCommand(),
845 viewport.alignment.getSequencesArray(),
852 * @param e DOCUMENT ME!
854 protected void htmlMenuItem_actionPerformed(ActionEvent e)
856 new HTMLOutput(alignPanel,
857 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
858 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
861 public void createImageMap(File file, String image)
863 alignPanel.makePNGImageMap(file, image);
869 * @param e DOCUMENT ME!
871 public void createPNG(File f)
873 alignPanel.makePNG(f);
879 * @param e DOCUMENT ME!
881 public void createEPS(File f)
883 alignPanel.makeEPS(f);
887 public void pageSetup_actionPerformed(ActionEvent e)
889 PrinterJob printJob = PrinterJob.getPrinterJob();
890 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
896 * @param e DOCUMENT ME!
898 public void printMenuItem_actionPerformed(ActionEvent e)
900 //Putting in a thread avoids Swing painting problems
901 PrintThread thread = new PrintThread(alignPanel);
905 public void exportFeatures_actionPerformed(ActionEvent e)
907 new AnnotationExporter().exportFeatures(alignPanel);
911 public void exportAnnotations_actionPerformed(ActionEvent e)
913 new AnnotationExporter().exportAnnotations(
915 viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
916 viewport.alignment.getGroups()
921 public void associatedData_actionPerformed(ActionEvent e)
923 // Pick the tree file
924 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
927 chooser.setFileView(new JalviewFileView());
928 chooser.setDialogTitle("Load Jalview Annotations or Features File");
929 chooser.setToolTipText("Load Jalview Annotations / Features file");
931 int value = chooser.showOpenDialog(null);
933 if (value == JalviewFileChooser.APPROVE_OPTION)
935 String choice = chooser.getSelectedFile().getPath();
936 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
937 loadJalviewDataFile(choice);
946 * @param e DOCUMENT ME!
948 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
950 if(alignPanels!=null && alignPanels.size()<2)
957 if(alignPanels!=null)
961 for (int i = 0; i < alignPanels.size(); i++)
963 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
964 jalview.structure.StructureSelectionManager.getStructureSelectionManager()
965 .removeStructureViewerListener(ap.seqPanel, null);
966 PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
967 PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
968 PaintRefresher.RemoveComponent(ap);
969 ap.av.alignment = null;
974 int index = tabbedPane.getSelectedIndex();
976 alignPanels.removeElement(alignPanel);
977 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
978 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
979 PaintRefresher.RemoveComponent(alignPanel);
980 viewport.alignment = null;
984 tabbedPane.removeTabAt(index);
985 tabbedPane.validate();
987 if(index==tabbedPane.getTabCount())
992 this.tabSelectionChanged(index);
998 this.setClosed(true);
1001 catch (Exception ex)
1003 ex.printStackTrace();
1011 void updateEditMenuBar()
1014 if (viewport.historyList.size() > 0)
1016 undoMenuItem.setEnabled(true);
1017 CommandI command = (CommandI) viewport.historyList.peek();
1018 undoMenuItem.setText("Undo " + command.getDescription());
1022 undoMenuItem.setEnabled(false);
1023 undoMenuItem.setText("Undo");
1026 if (viewport.redoList.size() > 0)
1028 redoMenuItem.setEnabled(true);
1030 CommandI command = (CommandI) viewport.redoList.peek();
1031 redoMenuItem.setText("Redo " + command.getDescription());
1035 redoMenuItem.setEnabled(false);
1036 redoMenuItem.setText("Redo");
1041 public void addHistoryItem(CommandI command)
1043 if(command.getSize()>0)
1045 viewport.historyList.push(command);
1046 viewport.redoList.clear();
1047 updateEditMenuBar();
1048 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1057 * @param e DOCUMENT ME!
1059 protected void undoMenuItem_actionPerformed(ActionEvent e)
1061 CommandI command = (CommandI)viewport.historyList.pop();
1062 viewport.redoList.push(command);
1063 command.undoCommand();
1065 AlignViewport originalSource = getOriginatingSource(command);
1066 updateEditMenuBar();
1068 if(originalSource!=null)
1070 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1071 originalSource.firePropertyChange("alignment",
1073 originalSource.alignment.getSequences());
1080 * @param e DOCUMENT ME!
1082 protected void redoMenuItem_actionPerformed(ActionEvent e)
1084 if(viewport.redoList.size()<1)
1089 CommandI command = (CommandI) viewport.redoList.pop();
1090 viewport.historyList.push(command);
1091 command.doCommand();
1093 AlignViewport originalSource = getOriginatingSource(command);
1094 updateEditMenuBar();
1096 if(originalSource!=null)
1098 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1099 originalSource.firePropertyChange("alignment",
1101 originalSource.alignment.getSequences());
1105 AlignViewport getOriginatingSource(CommandI command)
1107 AlignViewport originalSource = null;
1108 //For sequence removal and addition, we need to fire
1109 //the property change event FROM the viewport where the
1110 //original alignment was altered
1112 if (command instanceof EditCommand)
1114 EditCommand editCommand = (EditCommand) command;
1115 al = editCommand.getAlignment();
1116 Vector comps = (Vector) PaintRefresher.components
1117 .get(viewport.getSequenceSetId());
1119 for (int i = 0; i < comps.size(); i++)
1121 if (comps.elementAt(i) instanceof AlignmentPanel)
1123 if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
1125 originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
1132 if (originalSource == null)
1134 //The original view is closed, we must validate
1135 //the current view against the closed view first
1138 PaintRefresher.validateSequences(al, viewport.alignment);
1141 originalSource = viewport;
1144 return originalSource;
1150 * @param up DOCUMENT ME!
1152 public void moveSelectedSequences(boolean up)
1154 SequenceGroup sg = viewport.getSelectionGroup();
1163 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1165 SequenceI seq = viewport.alignment.getSequenceAt(i);
1167 if (!sg.getSequences(null).contains(seq))
1172 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1174 if (sg.getSequences(null).contains(temp))
1179 viewport.alignment.getSequences().setElementAt(temp, i);
1180 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1185 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1187 SequenceI seq = viewport.alignment.getSequenceAt(i);
1189 if (!sg.getSequences(null).contains(seq))
1194 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1196 if (sg.getSequences(null).contains(temp))
1201 viewport.alignment.getSequences().setElementAt(temp, i);
1202 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1206 alignPanel.paintAlignment(true);
1212 synchronized void slideSequences(boolean right, int size)
1214 Vector sg = new Vector();
1215 if(viewport.cursorMode)
1217 sg.addElement(viewport.alignment.getSequenceAt(
1218 alignPanel.seqPanel.seqCanvas.cursorY));
1220 else if(viewport.getSelectionGroup()!=null
1221 && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight())
1223 sg = viewport.getSelectionGroup().getSequences(
1224 viewport.hiddenRepSequences);
1232 Vector invertGroup = new Vector();
1234 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1236 if(!sg.contains(viewport.alignment.getSequenceAt(i)))
1237 invertGroup.add(viewport.alignment.getSequenceAt(i));
1240 SequenceI[] seqs1 = new SequenceI[sg.size()];
1241 for (int i = 0; i < sg.size(); i++)
1242 seqs1[i] = (SequenceI) sg.elementAt(i);
1244 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1245 for (int i = 0; i < invertGroup.size(); i++)
1246 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1248 SlideSequencesCommand ssc;
1250 ssc = new SlideSequencesCommand("Slide Sequences",
1252 viewport.getGapCharacter()
1255 ssc = new SlideSequencesCommand("Slide Sequences",
1257 viewport.getGapCharacter()
1260 int groupAdjustment = 0;
1261 if (ssc.getGapsInsertedBegin() && right)
1263 if (viewport.cursorMode)
1264 alignPanel.seqPanel.moveCursor(size, 0);
1266 groupAdjustment = size;
1268 else if (!ssc.getGapsInsertedBegin() && !right)
1270 if (viewport.cursorMode)
1271 alignPanel.seqPanel.moveCursor( -size, 0);
1273 groupAdjustment = -size;
1276 if (groupAdjustment != 0)
1278 viewport.getSelectionGroup().setStartRes(
1279 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1280 viewport.getSelectionGroup().setEndRes(
1281 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1285 boolean appendHistoryItem = false;
1286 if(viewport.historyList!=null
1287 && viewport.historyList.size()>0
1288 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1290 appendHistoryItem = ssc.appendSlideCommand(
1291 (SlideSequencesCommand)viewport.historyList.peek())
1295 if(!appendHistoryItem)
1296 addHistoryItem(ssc);
1305 * @param e DOCUMENT ME!
1307 protected void copy_actionPerformed(ActionEvent e)
1310 if (viewport.getSelectionGroup() == null)
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 newap.av.gatherViewsHere = false;
1975 if (viewport.viewName == null)
1977 viewport.viewName = "Original";
1980 newap.av.historyList = viewport.historyList;
1981 newap.av.redoList = viewport.redoList;
1983 int index = Desktop.getViewCount(viewport.getSequenceSetId());
1984 String newViewName = "View " +index;
1986 Vector comps = (Vector) PaintRefresher.components.get(viewport.
1987 getSequenceSetId());
1988 Vector existingNames = new Vector();
1989 for(int i=0; i<comps.size(); i++)
1991 if(comps.elementAt(i) instanceof AlignmentPanel)
1993 AlignmentPanel ap = (AlignmentPanel)comps.elementAt(i);
1994 if(!existingNames.contains(ap.av.viewName))
1996 existingNames.addElement(ap.av.viewName);
2001 while(existingNames.contains(newViewName))
2003 newViewName = "View "+ (++index);
2006 newap.av.viewName = newViewName;
2008 addAlignmentPanel(newap, false);
2010 if(alignPanels.size()==2)
2012 viewport.gatherViewsHere = true;
2014 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2017 public void expandViews_actionPerformed(ActionEvent e)
2019 Desktop.instance.explodeViews(this);
2022 public void gatherViews_actionPerformed(ActionEvent e)
2024 Desktop.instance.gatherViews(this);
2032 * @param e DOCUMENT ME!
2034 public void font_actionPerformed(ActionEvent e)
2036 new FontChooser(alignPanel);
2043 * @param e DOCUMENT ME!
2045 protected void seqLimit_actionPerformed(ActionEvent e)
2047 viewport.setShowJVSuffix(seqLimits.isSelected());
2049 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
2050 alignPanel.paintAlignment(true);
2053 public void idRightAlign_actionPerformed(ActionEvent e)
2055 viewport.rightAlignIds = idRightAlign.isSelected();
2056 alignPanel.paintAlignment(true);
2064 * @param e DOCUMENT ME!
2066 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2068 viewport.setColourText(colourTextMenuItem.isSelected());
2069 alignPanel.paintAlignment(true);
2075 * @param e DOCUMENT ME!
2077 public void wrapMenuItem_actionPerformed(ActionEvent e)
2079 scaleAbove.setVisible(wrapMenuItem.isSelected());
2080 scaleLeft.setVisible(wrapMenuItem.isSelected());
2081 scaleRight.setVisible(wrapMenuItem.isSelected());
2082 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2083 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2086 public void showAllSeqs_actionPerformed(ActionEvent e)
2088 viewport.showAllHiddenSeqs();
2091 public void showAllColumns_actionPerformed(ActionEvent e)
2093 viewport.showAllHiddenColumns();
2097 public void hideSelSequences_actionPerformed(ActionEvent e)
2099 viewport.hideAllSelectedSeqs();
2100 alignPanel.paintAlignment(true);
2103 public void hideSelColumns_actionPerformed(ActionEvent e)
2105 viewport.hideSelectedColumns();
2106 alignPanel.paintAlignment(true);
2109 public void hiddenMarkers_actionPerformed(ActionEvent e)
2111 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2118 * @param e DOCUMENT ME!
2120 protected void scaleAbove_actionPerformed(ActionEvent e)
2122 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2123 alignPanel.paintAlignment(true);
2129 * @param e DOCUMENT ME!
2131 protected void scaleLeft_actionPerformed(ActionEvent e)
2133 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2134 alignPanel.paintAlignment(true);
2140 * @param e DOCUMENT ME!
2142 protected void scaleRight_actionPerformed(ActionEvent e)
2144 viewport.setScaleRightWrapped(scaleRight.isSelected());
2145 alignPanel.paintAlignment(true);
2151 * @param e DOCUMENT ME!
2153 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2155 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2156 alignPanel.paintAlignment(true);
2162 * @param e DOCUMENT ME!
2164 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2166 viewport.setShowText(viewTextMenuItem.isSelected());
2167 alignPanel.paintAlignment(true);
2173 * @param e DOCUMENT ME!
2175 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2177 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2178 alignPanel.paintAlignment(true);
2182 public FeatureSettings featureSettings;
2183 public void featureSettings_actionPerformed(ActionEvent e)
2185 if(featureSettings !=null )
2187 featureSettings.close();
2188 featureSettings = null;
2190 featureSettings = new FeatureSettings(this);
2196 * @param evt DOCUMENT ME!
2198 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2200 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2201 alignPanel.paintAlignment(true);
2202 if (alignPanel.getOverviewPanel() != null)
2204 alignPanel.getOverviewPanel().updateOverviewImage();
2211 * @param e DOCUMENT ME!
2213 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2215 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2216 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2222 * @param e DOCUMENT ME!
2224 public void overviewMenuItem_actionPerformed(ActionEvent e)
2226 if (alignPanel.overviewPanel != null)
2231 JInternalFrame frame = new JInternalFrame();
2232 OverviewPanel overview = new OverviewPanel(alignPanel);
2233 frame.setContentPane(overview);
2234 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2235 frame.getWidth(), frame.getHeight());
2237 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2238 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2240 public void internalFrameClosed(
2241 javax.swing.event.InternalFrameEvent evt)
2243 alignPanel.setOverviewPanel(null);
2248 alignPanel.setOverviewPanel(overview);
2251 public void textColour_actionPerformed(ActionEvent e)
2253 new TextColourChooser().chooseColour(alignPanel, null);
2259 * @param e DOCUMENT ME!
2261 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2269 * @param e DOCUMENT ME!
2271 public void clustalColour_actionPerformed(ActionEvent e)
2273 changeColour(new ClustalxColourScheme(
2274 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
2280 * @param e DOCUMENT ME!
2282 public void zappoColour_actionPerformed(ActionEvent e)
2284 changeColour(new ZappoColourScheme());
2290 * @param e DOCUMENT ME!
2292 public void taylorColour_actionPerformed(ActionEvent e)
2294 changeColour(new TaylorColourScheme());
2300 * @param e DOCUMENT ME!
2302 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2304 changeColour(new HydrophobicColourScheme());
2310 * @param e DOCUMENT ME!
2312 public void helixColour_actionPerformed(ActionEvent e)
2314 changeColour(new HelixColourScheme());
2320 * @param e DOCUMENT ME!
2322 public void strandColour_actionPerformed(ActionEvent e)
2324 changeColour(new StrandColourScheme());
2330 * @param e DOCUMENT ME!
2332 public void turnColour_actionPerformed(ActionEvent e)
2334 changeColour(new TurnColourScheme());
2340 * @param e DOCUMENT ME!
2342 public void buriedColour_actionPerformed(ActionEvent e)
2344 changeColour(new BuriedColourScheme());
2350 * @param e DOCUMENT ME!
2352 public void nucleotideColour_actionPerformed(ActionEvent e)
2354 changeColour(new NucleotideColourScheme());
2357 public void annotationColour_actionPerformed(ActionEvent e)
2359 new AnnotationColourChooser(viewport, alignPanel);
2366 * @param e DOCUMENT ME!
2368 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2370 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2376 * @param cs DOCUMENT ME!
2378 public void changeColour(ColourSchemeI cs)
2384 if (viewport.getAbovePIDThreshold())
2386 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2389 cs.setThreshold(threshold,
2390 viewport.getIgnoreGapsConsensus());
2392 viewport.setGlobalColourScheme(cs);
2396 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2399 if (viewport.getConservationSelected())
2402 Alignment al = (Alignment) viewport.alignment;
2403 Conservation c = new Conservation("All",
2404 ResidueProperties.propHash, 3,
2405 al.getSequences(), 0,
2409 c.verdict(false, viewport.ConsPercGaps);
2411 cs.setConservation(c);
2413 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
2418 cs.setConservation(null);
2421 cs.setConsensus(viewport.hconsensus);
2424 viewport.setGlobalColourScheme(cs);
2426 if (viewport.getColourAppliesToAllGroups())
2428 Vector groups = viewport.alignment.getGroups();
2430 for (int i = 0; i < groups.size(); i++)
2432 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2440 if (cs instanceof ClustalxColourScheme)
2442 sg.cs = new ClustalxColourScheme(
2443 sg.getSequences(viewport.hiddenRepSequences), sg.getWidth());
2445 else if (cs instanceof UserColourScheme)
2447 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
2453 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2455 catch (Exception ex)
2460 if (viewport.getAbovePIDThreshold()
2461 || cs instanceof PIDColourScheme
2462 || cs instanceof Blosum62ColourScheme)
2464 sg.cs.setThreshold(threshold,
2465 viewport.getIgnoreGapsConsensus());
2467 sg.cs.setConsensus(AAFrequency.calculate(
2468 sg.getSequences(viewport.hiddenRepSequences), sg.getStartRes(),
2473 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2477 if (viewport.getConservationSelected())
2479 Conservation c = new Conservation("Group",
2480 ResidueProperties.propHash, 3,
2481 sg.getSequences(viewport.
2482 hiddenRepSequences),
2486 c.verdict(false, viewport.ConsPercGaps);
2487 sg.cs.setConservation(c);
2491 sg.cs.setConservation(null);
2496 if (alignPanel.getOverviewPanel() != null)
2498 alignPanel.getOverviewPanel().updateOverviewImage();
2504 alignPanel.paintAlignment(true);
2510 * @param e DOCUMENT ME!
2512 protected void modifyPID_actionPerformed(ActionEvent e)
2514 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
2516 SliderPanel.setPIDSliderSource(alignPanel,
2517 viewport.getGlobalColourScheme(),
2519 SliderPanel.showPIDSlider();
2526 * @param e DOCUMENT ME!
2528 protected void modifyConservation_actionPerformed(ActionEvent e)
2530 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
2532 SliderPanel.setConservationSlider(alignPanel,
2533 viewport.globalColourScheme,
2535 SliderPanel.showConservationSlider();
2542 * @param e DOCUMENT ME!
2544 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2546 viewport.setConservationSelected(conservationMenuItem.isSelected());
2548 viewport.setAbovePIDThreshold(false);
2549 abovePIDThreshold.setSelected(false);
2551 changeColour(viewport.getGlobalColourScheme());
2553 modifyConservation_actionPerformed(null);
2559 * @param e DOCUMENT ME!
2561 public void abovePIDThreshold_actionPerformed(ActionEvent e)
2563 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
2565 conservationMenuItem.setSelected(false);
2566 viewport.setConservationSelected(false);
2568 changeColour(viewport.getGlobalColourScheme());
2570 modifyPID_actionPerformed(null);
2576 * @param e DOCUMENT ME!
2578 public void userDefinedColour_actionPerformed(ActionEvent e)
2580 if (e.getActionCommand().equals("User Defined..."))
2582 new UserDefinedColours(alignPanel, null);
2586 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
2587 getUserColourSchemes().get(e.getActionCommand());
2593 public void updateUserColourMenu()
2596 Component[] menuItems = colourMenu.getMenuComponents();
2597 int i, iSize = menuItems.length;
2598 for (i = 0; i < iSize; i++)
2600 if (menuItems[i].getName() != null &&
2601 menuItems[i].getName().equals("USER_DEFINED"))
2603 colourMenu.remove(menuItems[i]);
2607 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
2609 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
2610 getUserColourSchemes().keys();
2612 while (userColours.hasMoreElements())
2614 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
2616 nextElement().toString());
2617 radioItem.setName("USER_DEFINED");
2618 radioItem.addMouseListener(new MouseAdapter()
2620 public void mousePressed(MouseEvent evt)
2622 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
2624 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
2626 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
2628 "Remove from default list?",
2629 "Remove user defined colour",
2630 JOptionPane.YES_NO_OPTION);
2631 if(option == JOptionPane.YES_OPTION)
2633 jalview.gui.UserDefinedColours.removeColourFromDefaults(
2634 radioItem.getText());
2635 colourMenu.remove(radioItem);
2639 radioItem.addActionListener(new ActionListener()
2641 public void actionPerformed(ActionEvent evt)
2643 userDefinedColour_actionPerformed(evt);
2650 radioItem.addActionListener(new ActionListener()
2652 public void actionPerformed(ActionEvent evt)
2654 userDefinedColour_actionPerformed(evt);
2658 colourMenu.insert(radioItem, 15);
2659 colours.add(radioItem);
2667 * @param e DOCUMENT ME!
2669 public void PIDColour_actionPerformed(ActionEvent e)
2671 changeColour(new PIDColourScheme());
2677 * @param e DOCUMENT ME!
2679 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
2681 changeColour(new Blosum62ColourScheme());
2687 * @param e DOCUMENT ME!
2689 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2691 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2692 AlignmentSorter.sortByPID(viewport.getAlignment(),
2693 viewport.getAlignment().getSequenceAt(0));
2694 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2695 viewport.alignment));
2696 alignPanel.paintAlignment(true);
2702 * @param e DOCUMENT ME!
2704 public void sortIDMenuItem_actionPerformed(ActionEvent e)
2706 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2707 AlignmentSorter.sortByID(viewport.getAlignment());
2708 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
2709 alignPanel.paintAlignment(true);
2715 * @param e DOCUMENT ME!
2717 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
2719 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2720 AlignmentSorter.sortByGroup(viewport.getAlignment());
2721 addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
2723 alignPanel.paintAlignment(true);
2729 * @param e DOCUMENT ME!
2731 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2733 new RedundancyPanel(alignPanel, this);
2740 * @param e DOCUMENT ME!
2742 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2744 if ( (viewport.getSelectionGroup() == null) ||
2745 (viewport.getSelectionGroup().getSize() < 2))
2747 JOptionPane.showInternalMessageDialog(this,
2748 "You must select at least 2 sequences.",
2749 "Invalid Selection",
2750 JOptionPane.WARNING_MESSAGE);
2754 JInternalFrame frame = new JInternalFrame();
2755 frame.setContentPane(new PairwiseAlignPanel(viewport));
2756 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
2763 * @param e DOCUMENT ME!
2765 public void PCAMenuItem_actionPerformed(ActionEvent e)
2767 if ( ( (viewport.getSelectionGroup() != null) &&
2768 (viewport.getSelectionGroup().getSize() < 4) &&
2769 (viewport.getSelectionGroup().getSize() > 0)) ||
2770 (viewport.getAlignment().getHeight() < 4))
2772 JOptionPane.showInternalMessageDialog(this,
2773 "Principal component analysis must take\n" +
2774 "at least 4 input sequences.",
2775 "Sequence selection insufficient",
2776 JOptionPane.WARNING_MESSAGE);
2781 new PCAPanel(alignPanel);
2785 public void autoCalculate_actionPerformed(ActionEvent e)
2787 viewport.autoCalculateConsensus = autoCalculate.isSelected();
2788 if(viewport.autoCalculateConsensus)
2790 viewport.firePropertyChange("alignment",
2792 viewport.getAlignment().getSequences());
2800 * @param e DOCUMENT ME!
2802 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2804 NewTreePanel("AV", "PID", "Average distance tree using PID");
2810 * @param e DOCUMENT ME!
2812 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2814 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2820 * @param e DOCUMENT ME!
2822 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2824 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2830 * @param e DOCUMENT ME!
2832 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2834 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2840 * @param type DOCUMENT ME!
2841 * @param pwType DOCUMENT ME!
2842 * @param title DOCUMENT ME!
2844 void NewTreePanel(String type, String pwType, String title)
2848 if (viewport.getSelectionGroup() != null)
2850 if (viewport.getSelectionGroup().getSize() < 3)
2852 JOptionPane.showMessageDialog(Desktop.desktop,
2853 "You need to have more than two sequences selected to build a tree!",
2854 "Not enough sequences",
2855 JOptionPane.WARNING_MESSAGE);
2860 SequenceGroup sg = viewport.getSelectionGroup();
2862 /* Decide if the selection is a column region */
2863 while (s < sg.getSize())
2865 if ( ( (SequenceI) sg.getSequences(null).elementAt(s++)).getLength() <
2868 JOptionPane.showMessageDialog(Desktop.desktop,
2869 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
2870 "Try using the Pad function in the edit menu,\n" +
2871 "or one of the multiple sequence alignment web services.",
2872 "Sequences in selection are not aligned",
2873 JOptionPane.WARNING_MESSAGE);
2879 title = title + " on region";
2880 tp = new TreePanel(alignPanel, type, pwType);
2884 //are the sequences aligned?
2885 if (!viewport.alignment.isAligned())
2887 JOptionPane.showMessageDialog(Desktop.desktop,
2888 "The sequences must be aligned before creating a tree.\n" +
2889 "Try using the Pad function in the edit menu,\n" +
2890 "or one of the multiple sequence alignment web services.",
2891 "Sequences not aligned",
2892 JOptionPane.WARNING_MESSAGE);
2897 if(viewport.alignment.getHeight()<2)
2902 tp = new TreePanel(alignPanel, type, pwType);
2907 if(viewport.viewName!=null)
2909 title+= viewport.viewName+" of ";
2912 title += this.title;
2914 Desktop.addInternalFrame(tp, title, 600, 500);
2920 * @param title DOCUMENT ME!
2921 * @param order DOCUMENT ME!
2923 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
2925 final JMenuItem item = new JMenuItem("by " + title);
2927 item.addActionListener(new java.awt.event.ActionListener()
2929 public void actionPerformed(ActionEvent e)
2931 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2933 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
2934 AlignmentSorter.sortBy(viewport.getAlignment(), order);
2936 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
2937 viewport.alignment));
2939 alignPanel.paintAlignment(true);
2945 * Maintain the Order by->Displayed Tree menu.
2946 * Creates a new menu item for a TreePanel with an appropriate
2947 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
2948 * to remove the menu item when the treePanel is closed, and adjust
2949 * the tree leaf to sequence mapping when the alignment is modified.
2950 * @param treePanel Displayed tree window.
2951 * @param title SortBy menu item title.
2953 public void buildTreeMenu()
2955 sortByTreeMenu.removeAll();
2957 Vector comps = (Vector) PaintRefresher.components.get(viewport.
2958 getSequenceSetId());
2959 Vector treePanels = new Vector();
2960 int i, iSize = comps.size();
2961 for(i=0; i<iSize; i++)
2963 if(comps.elementAt(i) instanceof TreePanel)
2965 treePanels.add(comps.elementAt(i));
2969 iSize = treePanels.size();
2973 sortByTreeMenu.setVisible(false);
2977 sortByTreeMenu.setVisible(true);
2979 for(i=0; i<treePanels.size(); i++)
2981 TreePanel tp = (TreePanel)treePanels.elementAt(i);
2982 final JMenuItem item = new JMenuItem(tp.getTitle());
2983 final NJTree tree = ((TreePanel)treePanels.elementAt(i)).getTree();
2984 item.addActionListener(new java.awt.event.ActionListener()
2986 public void actionPerformed(ActionEvent e)
2988 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2989 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
2991 addHistoryItem(new OrderCommand("Tree Sort",
2993 viewport.alignment));
2995 alignPanel.paintAlignment(true);
2999 sortByTreeMenu.add(item);
3004 * Work out whether the whole set of sequences
3005 * or just the selected set will be submitted for multiple alignment.
3008 private jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3010 // Now, check we have enough sequences
3011 AlignmentView msa = null;
3013 if ( (viewport.getSelectionGroup() != null) &&
3014 (viewport.getSelectionGroup().getSize() > 1))
3016 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
3017 /*SequenceGroup seqs = viewport.getSelectionGroup();
3019 msa = new SequenceI[sz = seqs.getSize(false)];
3021 for (int i = 0; i < sz; i++)
3023 msa[i] = (SequenceI) seqs.getSequenceAt(i);
3025 msa = viewport.getAlignmentView(true);
3029 /*Vector seqs = viewport.getAlignment().getSequences();
3031 if (seqs.size() > 1)
3033 msa = new SequenceI[seqs.size()];
3035 for (int i = 0; i < seqs.size(); i++)
3037 msa[i] = (SequenceI) seqs.elementAt(i);
3040 msa = viewport.getAlignmentView(false);
3046 * Decides what is submitted to a secondary structure prediction service,
3047 * the currently selected sequence, or the currently selected alignment
3048 * (where the first sequence in the set is the one that the prediction
3051 AlignmentView gatherSeqOrMsaForSecStrPrediction()
3053 AlignmentView seqs = null;
3055 if ( (viewport.getSelectionGroup() != null) &&
3056 (viewport.getSelectionGroup().getSize() > 0))
3058 seqs = viewport.getAlignmentView(true);
3062 seqs = viewport.getAlignmentView(false);
3064 // limit sequences - JBPNote in future - could spawn multiple prediction jobs
3065 // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3066 if (!viewport.alignment.isAligned())
3068 seqs.setSequences(new SeqCigar[]
3069 {seqs.getSequences()[0]});
3076 * @param e DOCUMENT ME!
3078 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3080 // Pick the tree file
3081 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
3084 chooser.setFileView(new JalviewFileView());
3085 chooser.setDialogTitle("Select a newick-like tree file");
3086 chooser.setToolTipText("Load a tree file");
3088 int value = chooser.showOpenDialog(null);
3090 if (value == JalviewFileChooser.APPROVE_OPTION)
3092 String choice = chooser.getSelectedFile().getPath();
3093 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3097 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
3099 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3101 catch (Exception ex)
3103 JOptionPane.showMessageDialog(Desktop.desktop,
3104 "Problem reading tree file",
3106 JOptionPane.WARNING_MESSAGE);
3107 ex.printStackTrace();
3113 public TreePanel ShowNewickTree(NewickFile nf, String title)
3115 return ShowNewickTree(nf,title,600,500,4,5);
3118 public TreePanel ShowNewickTree(NewickFile nf, String title,
3119 AlignmentView input)
3121 return ShowNewickTree(nf,title, input, 600,500,4,5);
3124 public TreePanel ShowNewickTree(NewickFile nf, String title, int w, int h,
3127 return ShowNewickTree(nf, title, null, w, h, x, y);
3130 * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
3132 * @param nf the tree
3133 * @param title tree viewer title
3134 * @param input Associated alignment input data (or null)
3139 * @return TreePanel handle
3141 public TreePanel ShowNewickTree(NewickFile nf, String title,
3142 AlignmentView input, int w, int h, int x,
3145 TreePanel tp = null;
3151 if (nf.getTree() != null)
3153 tp = new TreePanel(alignPanel,
3162 tp.setLocation(x,y);
3166 Desktop.addInternalFrame(tp, title, w, h);
3169 catch (Exception ex)
3171 ex.printStackTrace();
3179 * Generates menu items and listener event actions for web service clients
3182 public void BuildWebServiceMenu()
3184 if ( (Discoverer.services != null)
3185 && (Discoverer.services.size() > 0))
3187 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
3188 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
3189 Vector wsmenu = new Vector();
3190 final AlignFrame af = this;
3193 // Add any Multiple Sequence Alignment Services
3194 final JMenu msawsmenu = new JMenu("Alignment");
3195 for (int i = 0, j = msaws.size(); i < j; i++)
3197 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
3199 final JMenuItem method = new JMenuItem(sh.getName());
3200 method.addActionListener(new ActionListener()
3202 public void actionPerformed(ActionEvent e)
3204 AlignmentView msa = gatherSequencesForAlignment();
3205 new jalview.ws.MsaWSClient(sh, title, msa,
3207 viewport.getAlignment().getDataset(),
3213 msawsmenu.add(method);
3214 // Deal with services that we know accept partial alignments.
3215 if (sh.getName().indexOf("lustal") > -1)
3217 // We know that ClustalWS can accept partial alignments for refinement.
3218 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
3219 methodR.addActionListener(new ActionListener()
3221 public void actionPerformed(ActionEvent e)
3223 AlignmentView msa = gatherSequencesForAlignment();
3224 new jalview.ws.MsaWSClient(sh, title, msa,
3226 viewport.getAlignment().getDataset(),
3232 msawsmenu.add(methodR);
3236 wsmenu.add(msawsmenu);
3238 if (secstrpr != null)
3240 // Add any secondary structure prediction services
3241 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
3242 for (int i = 0, j = secstrpr.size(); i < j; i++)
3244 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
3246 final JMenuItem method = new JMenuItem(sh.getName());
3247 method.addActionListener(new ActionListener()
3249 public void actionPerformed(ActionEvent e)
3251 AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
3252 if (msa.getSequences().length == 1)
3254 // Single Sequence prediction
3255 new jalview.ws.JPredClient(sh, title, false, msa, af, true);
3259 if (msa.getSequences().length > 1)
3261 // Sequence profile based prediction
3262 new jalview.ws.JPredClient(sh,
3263 title, true, msa, af, true);
3268 secstrmenu.add(method);
3270 wsmenu.add(secstrmenu);
3272 this.webService.removeAll();
3273 for (int i = 0, j = wsmenu.size(); i < j; i++)
3275 webService.add( (JMenu) wsmenu.get(i));
3280 this.webService.removeAll();
3281 this.webService.add(this.webServiceNoServices);
3283 // TODO: add in rediscovery function
3284 // TODO: reduce code redundancy.
3285 // TODO: group services by location as well as function.
3288 /* public void vamsasStore_actionPerformed(ActionEvent e)
3290 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
3291 getProperty("LAST_DIRECTORY"));
3293 chooser.setFileView(new JalviewFileView());
3294 chooser.setDialogTitle("Export to Vamsas file");
3295 chooser.setToolTipText("Export");
3297 int value = chooser.showSaveDialog(this);
3299 if (value == JalviewFileChooser.APPROVE_OPTION)
3301 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
3302 //vs.store(chooser.getSelectedFile().getAbsolutePath() );
3303 vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
3310 public void showTranslation_actionPerformed(ActionEvent e)
3312 ///////////////////////////////
3313 // Collect Data to be translated/transferred
3315 SequenceI [] selection = viewport.getSelectionAsNewSequence();
3316 String [] seqstring = viewport.getViewAsString(true);
3317 AlignmentI al = null;
3319 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring, viewport.getViewAsVisibleContigs(true),
3320 viewport.getGapCharacter(), viewport.alignment.getAlignmentAnnotation(),
3321 viewport.alignment.getWidth());
3322 } catch (Exception ex) {
3324 jalview.bin.Cache.log.debug("Exception during translation.",ex);
3328 JOptionPane.showMessageDialog(Desktop.desktop,
3329 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
3330 "Translation Failed",
3331 JOptionPane.WARNING_MESSAGE);
3333 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
3334 Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
3343 * @param String DOCUMENT ME!
3345 public boolean parseFeaturesFile(String file, String type)
3347 boolean featuresFile = false;
3350 featuresFile = new FeaturesFile(file,
3351 type).parse(viewport.alignment.getDataset(),
3352 alignPanel.seqPanel.seqCanvas.
3353 getFeatureRenderer().featureColours,
3358 ex.printStackTrace();
3363 viewport.showSequenceFeatures = true;
3364 showSeqFeatures.setSelected(true);
3365 alignPanel.paintAlignment(true);
3368 return featuresFile;
3371 public void dragEnter(DropTargetDragEvent evt)
3374 public void dragExit(DropTargetEvent evt)
3377 public void dragOver(DropTargetDragEvent evt)
3380 public void dropActionChanged(DropTargetDragEvent evt)
3383 public void drop(DropTargetDropEvent evt)
3385 Transferable t = evt.getTransferable();
3386 java.util.List files = null;
3390 DataFlavor uriListFlavor = new DataFlavor(
3391 "text/uri-list;class=java.lang.String");
3392 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
3394 //Works on Windows and MacOSX
3395 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3396 files = (java.util.List) t.getTransferData(DataFlavor.
3397 javaFileListFlavor);
3399 else if (t.isDataFlavorSupported(uriListFlavor))
3401 // This is used by Unix drag system
3402 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3403 String data = (String) t.getTransferData(uriListFlavor);
3404 files = new java.util.ArrayList(1);
3405 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
3408 st.hasMoreTokens(); )
3410 String s = st.nextToken();
3411 if (s.startsWith("#"))
3413 // the line is a comment (as per the RFC 2483)
3417 java.net.URI uri = new java.net.URI(s);
3418 java.io.File file = new java.io.File(uri);
3425 e.printStackTrace();
3432 for (int i = 0; i < files.size(); i++)
3434 loadJalviewDataFile(files.get(i).toString());
3437 catch (Exception ex)
3439 ex.printStackTrace();
3444 // This method will attempt to load a "dropped" file first by testing
3445 // whether its and Annotation file, then features file. If both are
3446 // false then the user may have dropped an alignment file onto this
3448 public void loadJalviewDataFile(String file)
3452 String protocol = "File";
3454 if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
3459 boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
3460 alignment, file, protocol);
3464 boolean isGroupsFile = parseFeaturesFile(file,protocol);
3467 String format = new IdentifyFile().Identify(file, protocol);
3469 if(format.equalsIgnoreCase("JnetFile"))
3471 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
3473 new JnetAnnotationMaker().add_annotation(predictions,
3474 viewport.getAlignment(),
3476 alignPanel.adjustAnnotationHeight();
3477 alignPanel.paintAlignment(true);
3481 new FileLoader().LoadFile(viewport, file, protocol, format);
3488 alignPanel.adjustAnnotationHeight();
3492 catch (Exception ex)
3494 ex.printStackTrace();
3498 public void tabSelectionChanged(int index)
3502 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
3503 viewport = alignPanel.av;
3504 setMenusFromViewport(viewport);
3508 public void tabbedPane_mousePressed(MouseEvent e)
3510 if(SwingUtilities.isRightMouseButton(e))
3512 String reply = JOptionPane.showInternalInputDialog(this,
3515 JOptionPane.QUESTION_MESSAGE);
3519 viewport.viewName = reply;
3520 tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
3526 public AlignViewport getCurrentView()
3536 public PrintThread(AlignmentPanel ap)
3540 static PageFormat pf;
3543 PrinterJob printJob = PrinterJob.getPrinterJob();
3547 printJob.setPrintable(ap, pf);
3551 printJob.setPrintable(ap);
3554 if (printJob.printDialog())
3560 catch (Exception PrintException)
3562 PrintException.printStackTrace();