2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Softwarechang
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
26 import java.awt.datatransfer.*;
27 import java.awt.dnd.*;
28 import java.awt.event.*;
29 import java.awt.print.*;
31 import javax.swing.event.MenuEvent;
33 import jalview.analysis.*;
34 import jalview.commands.*;
35 import jalview.datamodel.*;
37 import jalview.jbgui.*;
38 import jalview.schemes.*;
47 public class AlignFrame
48 extends GAlignFrame implements DropTargetListener
51 public static final int DEFAULT_WIDTH = 700;
54 public static final int DEFAULT_HEIGHT = 500;
55 public AlignmentPanel alignPanel;
57 AlignViewport viewport;
59 Vector alignPanels = new Vector();
63 String currentFileFormat = null;
65 String fileName = null;
69 * Creates a new AlignFrame object.
71 * @param al DOCUMENT ME!
73 public AlignFrame(AlignmentI al, int width, int height)
75 this(al, null, width, height);
80 * new alignment window with hidden columns
81 * @param al AlignmentI
82 * @param hiddenColumns ColumnSelection or null
84 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
85 int width, int height)
87 this.setSize(width, height);
88 viewport = new AlignViewport(al, hiddenColumns);
90 alignPanel = new AlignmentPanel(this, viewport);
92 if(al.getDataset()==null)
97 addAlignmentPanel(alignPanel, true);
102 * Make a new AlignFrame from exisiting alignmentPanels
103 * @param ap AlignmentPanel
104 * @param av AlignViewport
106 public AlignFrame(AlignmentPanel ap)
110 addAlignmentPanel(ap, false);
116 if (viewport.conservation == null)
118 BLOSUM62Colour.setEnabled(false);
119 conservationMenuItem.setEnabled(false);
120 modifyConservation.setEnabled(false);
121 // PIDColour.setEnabled(false);
122 // abovePIDThreshold.setEnabled(false);
123 // modifyPID.setEnabled(false);
126 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
128 if (sortby.equals("Id"))
130 sortIDMenuItem_actionPerformed(null);
132 else if (sortby.equals("Pairwise Identity"))
134 sortPairwiseMenuItem_actionPerformed(null);
137 if (Desktop.desktop != null)
139 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
140 addServiceListeners();
141 setGUINucleotide(viewport.alignment.isNucleotide());
144 setMenusFromViewport(viewport);
145 buildSortByAnnotationScoresMenu();
146 if (viewport.wrapAlignment)
148 wrapMenuItem_actionPerformed(null);
151 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW",false))
153 this.overviewMenuItem_actionPerformed(null);
160 public void setFileName(String file, String format)
163 currentFileFormat = format;
164 reload.setEnabled(true);
167 void addKeyListener()
169 addKeyListener(new KeyAdapter()
171 public void keyPressed(KeyEvent evt)
173 if (viewport.cursorMode &&
174 ( (evt.getKeyCode() >= KeyEvent.VK_0 &&
175 evt.getKeyCode() <= KeyEvent.VK_9)
177 (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 &&
178 evt.getKeyCode() <= KeyEvent.VK_NUMPAD9)
180 && Character.isDigit(evt.getKeyChar()))
181 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
183 switch (evt.getKeyCode())
186 case 27: // escape key
187 deselectAllSequenceMenuItem_actionPerformed(null);
191 case KeyEvent.VK_DOWN:
192 if (evt.isAltDown() || !viewport.cursorMode)
193 moveSelectedSequences(false);
194 if (viewport.cursorMode)
195 alignPanel.seqPanel.moveCursor(0, 1);
199 if (evt.isAltDown() || !viewport.cursorMode)
200 moveSelectedSequences(true);
201 if (viewport.cursorMode)
202 alignPanel.seqPanel.moveCursor(0, -1);
206 case KeyEvent.VK_LEFT:
207 if (evt.isAltDown() || !viewport.cursorMode)
208 slideSequences(false,
209 alignPanel.seqPanel.getKeyboardNo1());
211 alignPanel.seqPanel.moveCursor( -1, 0);
216 case KeyEvent.VK_RIGHT:
217 if (evt.isAltDown() || !viewport.cursorMode)
219 alignPanel.seqPanel.getKeyboardNo1());
221 alignPanel.seqPanel.moveCursor(1, 0);
224 case KeyEvent.VK_SPACE:
225 if (viewport.cursorMode)
227 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
233 case KeyEvent.VK_DELETE:
234 case KeyEvent.VK_BACK_SPACE:
235 if (!viewport.cursorMode)
237 cut_actionPerformed(null);
241 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
249 if (viewport.cursorMode)
251 alignPanel.seqPanel.setCursorRow();
255 if (viewport.cursorMode && !evt.isControlDown())
257 alignPanel.seqPanel.setCursorColumn();
261 if (viewport.cursorMode)
263 alignPanel.seqPanel.setCursorPosition();
267 case KeyEvent.VK_ENTER:
268 case KeyEvent.VK_COMMA:
269 if (viewport.cursorMode)
271 alignPanel.seqPanel.setCursorRowAndColumn();
276 if (viewport.cursorMode)
278 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
282 if (viewport.cursorMode)
284 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
289 viewport.cursorMode = !viewport.cursorMode;
290 statusBar.setText("Keyboard editing mode is " +
291 (viewport.cursorMode ? "on" : "off"));
292 if (viewport.cursorMode)
294 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
295 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
297 alignPanel.seqPanel.seqCanvas.repaint();
303 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
304 java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
305 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
307 javax.help.HelpBroker hb = hs.createHelpBroker();
308 hb.setCurrentID("home");
309 hb.setDisplayed(true);
313 ex.printStackTrace();
319 boolean toggleSeqs = !evt.isControlDown();
320 boolean toggleCols = !evt.isShiftDown();
322 boolean hide = false;
324 SequenceGroup sg = viewport.getSelectionGroup();
327 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
329 hideSelSequences_actionPerformed(null);
332 else if (! (toggleCols &&
333 viewport.colSel.getSelected().size() > 0))
335 showAllSeqs_actionPerformed(null);
341 if (viewport.colSel.getSelected().size() > 0)
343 hideSelColumns_actionPerformed(null);
346 viewport.selectionGroup = sg;
351 showAllColumns_actionPerformed(null);
356 case KeyEvent.VK_PAGE_UP:
357 if (viewport.wrapAlignment)
359 alignPanel.scrollUp(true);
363 alignPanel.setScrollValues(viewport.startRes,
365 - viewport.endSeq + viewport.startSeq);
368 case KeyEvent.VK_PAGE_DOWN:
369 if (viewport.wrapAlignment)
371 alignPanel.scrollUp(false);
375 alignPanel.setScrollValues(viewport.startRes,
377 + viewport.endSeq - viewport.startSeq);
383 public void keyReleased(KeyEvent evt)
385 switch(evt.getKeyCode())
387 case KeyEvent.VK_LEFT:
388 if (evt.isAltDown() || !viewport.cursorMode)
389 viewport.firePropertyChange("alignment", null,
390 viewport.getAlignment().getSequences());
393 case KeyEvent.VK_RIGHT:
394 if (evt.isAltDown() || !viewport.cursorMode)
395 viewport.firePropertyChange("alignment", null,
396 viewport.getAlignment().getSequences());
404 public void addAlignmentPanel(final AlignmentPanel ap,
407 ap.alignFrame = this;
409 alignPanels.addElement(ap);
411 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
413 int aSize = alignPanels.size();
415 tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
417 if (aSize == 1 && ap.av.viewName==null)
419 this.getContentPane().add(ap, BorderLayout.CENTER);
425 setInitialTabVisible();
428 expandViews.setEnabled(true);
429 gatherViews.setEnabled(true);
430 tabbedPane.addTab(ap.av.viewName, ap);
432 ap.setVisible(false);
439 ap.av.alignment.padGaps();
441 ap.av.updateConservation(ap);
442 ap.av.updateConsensus(ap);
446 public void setInitialTabVisible()
448 expandViews.setEnabled(true);
449 gatherViews.setEnabled(true);
450 tabbedPane.setVisible(true);
451 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
452 tabbedPane.addTab(first.av.viewName,first);
453 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
457 public AlignViewport getViewport()
462 /* Set up intrinsic listeners for dynamically generated GUI bits. */
463 private void addServiceListeners()
465 final java.beans.PropertyChangeListener thisListener;
466 // Do this once to get current state
467 BuildWebServiceMenu();
468 Desktop.discoverer.addPropertyChangeListener(
469 thisListener = new java.beans.PropertyChangeListener()
471 public void propertyChange(PropertyChangeEvent evt)
473 // System.out.println("Discoverer property change.");
474 if (evt.getPropertyName().equals("services"))
476 // System.out.println("Rebuilding web service menu");
477 BuildWebServiceMenu();
482 addInternalFrameListener(new javax.swing.event.
483 InternalFrameAdapter()
485 public void internalFrameClosed(
486 javax.swing.event.InternalFrameEvent evt)
488 // System.out.println("deregistering discoverer listener");
489 Desktop.discoverer.removePropertyChangeListener(thisListener);
490 closeMenuItem_actionPerformed(true);
496 public void setGUINucleotide(boolean nucleotide)
498 showTranslation.setVisible( nucleotide );
499 conservationMenuItem.setEnabled( !nucleotide );
500 modifyConservation.setEnabled( !nucleotide );
502 //Remember AlignFrame always starts as protein
505 calculateMenu.remove(calculateMenu.getItemCount()-2);
510 * Need to call this method when tabs are selected for multiple views,
511 * or when loading from Jalview2XML.java
512 * @param av AlignViewport
514 void setMenusFromViewport(AlignViewport av)
516 padGapsMenuitem.setSelected(av.padGaps);
517 colourTextMenuItem.setSelected(av.showColourText);
518 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
519 conservationMenuItem.setSelected(av.getConservationSelected());
520 seqLimits.setSelected(av.getShowJVSuffix());
521 idRightAlign.setSelected(av.rightAlignIds);
522 renderGapsMenuItem.setSelected(av.renderGaps);
523 wrapMenuItem.setSelected(av.wrapAlignment);
524 scaleAbove.setVisible(av.wrapAlignment);
525 scaleLeft.setVisible(av.wrapAlignment);
526 scaleRight.setVisible(av.wrapAlignment);
527 annotationPanelMenuItem.setState(av.showAnnotation);
528 viewBoxesMenuItem.setSelected(av.showBoxes);
529 viewTextMenuItem.setSelected(av.showText);
531 setColourSelected(ColourSchemeProperty.
532 getColourName(av.getGlobalColourScheme()));
534 showSeqFeatures.setSelected(av.showSequenceFeatures);
535 hiddenMarkers.setState(av.showHiddenMarkers);
536 applyToAllGroups.setState(av.colourAppliesToAllGroups);
542 Hashtable progressBars;
543 public void setProgressBar(String message, long id)
545 if(progressBars == null)
547 progressBars = new Hashtable();
550 JPanel progressPanel;
551 GridLayout layout = (GridLayout) statusPanel.getLayout();
552 if(progressBars.get( new Long(id) )!=null)
554 progressPanel = (JPanel)progressBars.get( new Long(id) );
555 statusPanel.remove(progressPanel);
556 progressBars.remove( progressPanel );
557 progressPanel = null;
560 statusBar.setText(message);
563 layout.setRows(layout.getRows() - 1);
567 progressPanel = new JPanel(new BorderLayout(10, 5));
569 JProgressBar progressBar = new JProgressBar();
570 progressBar.setIndeterminate(true);
572 progressPanel.add(new JLabel(message), BorderLayout.WEST);
573 progressPanel.add(progressBar, BorderLayout.CENTER);
575 layout.setRows(layout.getRows() + 1);
576 statusPanel.add(progressPanel);
578 progressBars.put(new Long(id), progressPanel);
588 Added so Castor Mapping file can obtain Jalview Version
590 public String getVersion()
592 return jalview.bin.Cache.getProperty("VERSION");
595 public FeatureRenderer getFeatureRenderer()
597 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
601 public void fetchSequence_actionPerformed(ActionEvent e)
603 new SequenceFetcher(this);
606 public void addFromFile_actionPerformed(ActionEvent e)
608 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
611 public void reload_actionPerformed(ActionEvent e)
615 if(currentFileFormat.equals("Jalview"))
617 JInternalFrame [] frames = Desktop.desktop.getAllFrames();
618 for(int i=0; i<frames.length; i++)
620 if (frames[i] instanceof AlignFrame
622 && ( (AlignFrame) frames[i]).fileName.equals(fileName))
626 frames[i].setSelected(true);
627 Desktop.instance.closeAssociatedWindows();
629 catch (java.beans.PropertyVetoException ex)
634 Desktop.instance.closeAssociatedWindows();
636 FileLoader loader = new FileLoader();
637 String protocol = fileName.startsWith("http:")? "URL":"File";
638 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
642 Rectangle bounds = this.getBounds();
644 FileLoader loader = new FileLoader();
645 String protocol = fileName.startsWith("http:") ? "URL" : "File";
646 AlignFrame newframe =
647 loader.LoadFileWaitTillLoaded(fileName, protocol, currentFileFormat);
649 newframe.setBounds(bounds);
651 this.closeMenuItem_actionPerformed(true);
657 public void addFromText_actionPerformed(ActionEvent e)
659 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
662 public void addFromURL_actionPerformed(ActionEvent e)
664 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
668 public void save_actionPerformed(ActionEvent e)
671 || currentFileFormat==null
672 || fileName.startsWith("http")
675 saveAs_actionPerformed(null);
679 saveAlignment(fileName, currentFileFormat);
686 * @param e DOCUMENT ME!
688 public void saveAs_actionPerformed(ActionEvent e)
690 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
691 getProperty( "LAST_DIRECTORY"),
693 { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" },
695 { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
700 chooser.setFileView(new JalviewFileView());
701 chooser.setDialogTitle("Save Alignment to file");
702 chooser.setToolTipText("Save");
704 int value = chooser.showSaveDialog(this);
706 if (value == JalviewFileChooser.APPROVE_OPTION)
708 currentFileFormat = chooser.getSelectedFormat();
709 if (currentFileFormat == null)
711 JOptionPane.showInternalMessageDialog(Desktop.desktop,
712 "You must select a file format before saving!",
713 "File format not specified",
714 JOptionPane.WARNING_MESSAGE);
715 value = chooser.showSaveDialog(this);
719 fileName = chooser.getSelectedFile().getPath();
721 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
724 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
726 saveAlignment(fileName, currentFileFormat);
730 public boolean saveAlignment(String file, String format)
732 boolean success = true;
734 if (format.equalsIgnoreCase("Jalview"))
736 String shortName = title;
738 if (shortName.indexOf(java.io.File.separatorChar) > -1)
740 shortName = shortName.substring(shortName.lastIndexOf(
741 java.io.File.separatorChar) + 1);
744 success = new Jalview2XML().SaveAlignment(this, file, shortName);
746 statusBar.setText("Successfully saved to file: "
748 +format +" format.");
754 String[] omitHidden = null;
756 if (viewport.hasHiddenColumns)
758 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
759 "The Alignment contains hidden columns."
760 + "\nDo you want to save only the visible alignment?",
761 "Save / Omit Hidden Columns",
762 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
764 if (reply == JOptionPane.YES_OPTION)
766 omitHidden = viewport.getViewAsString(false);
770 String output = new FormatAdapter().formatSequences(
772 viewport.alignment.getSequencesArray(),
783 java.io.PrintWriter out = new java.io.PrintWriter(
784 new java.io.FileWriter(file));
789 statusBar.setText("Successfully saved to file: "
791 + format + " format.");
796 ex.printStackTrace();
803 JOptionPane.showInternalMessageDialog(
804 this, "Couldn't save file: " + fileName,
806 JOptionPane.WARNING_MESSAGE);
815 * @param e DOCUMENT ME!
817 protected void outputText_actionPerformed(ActionEvent e)
819 String [] omitHidden = null;
821 if(viewport.hasHiddenColumns)
823 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
824 "The Alignment contains hidden columns."
825 +"\nDo you want to output only the visible alignment?",
826 "Save / Omit Hidden Columns",
827 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
829 if(reply==JOptionPane.YES_OPTION)
831 omitHidden = viewport.getViewAsString(false);
835 CutAndPasteTransfer cap = new CutAndPasteTransfer();
836 cap.setForInput(null);
837 Desktop.addInternalFrame(cap,
838 "Alignment output - " + e.getActionCommand(), 600,
842 cap.setText(new FormatAdapter().formatSequences(
843 e.getActionCommand(),
844 viewport.alignment.getSequencesArray(),
851 * @param e DOCUMENT ME!
853 protected void htmlMenuItem_actionPerformed(ActionEvent e)
855 new HTMLOutput(alignPanel,
856 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
857 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
860 public void createImageMap(File file, String image)
862 alignPanel.makePNGImageMap(file, image);
868 * @param e DOCUMENT ME!
870 public void createPNG(File f)
872 alignPanel.makePNG(f);
878 * @param e DOCUMENT ME!
880 public void createEPS(File f)
882 alignPanel.makeEPS(f);
886 public void pageSetup_actionPerformed(ActionEvent e)
888 PrinterJob printJob = PrinterJob.getPrinterJob();
889 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
895 * @param e DOCUMENT ME!
897 public void printMenuItem_actionPerformed(ActionEvent e)
899 //Putting in a thread avoids Swing painting problems
900 PrintThread thread = new PrintThread(alignPanel);
904 public void exportFeatures_actionPerformed(ActionEvent e)
906 new AnnotationExporter().exportFeatures(alignPanel);
910 public void exportAnnotations_actionPerformed(ActionEvent e)
912 new AnnotationExporter().exportAnnotations(
914 viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
915 viewport.alignment.getGroups(),
916 ((Alignment)viewport.alignment).alignmentProperties
921 public void associatedData_actionPerformed(ActionEvent e)
923 // Pick the tree file
924 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
927 chooser.setFileView(new JalviewFileView());
928 chooser.setDialogTitle("Load Jalview Annotations or Features File");
929 chooser.setToolTipText("Load Jalview Annotations / Features file");
931 int value = chooser.showOpenDialog(null);
933 if (value == JalviewFileChooser.APPROVE_OPTION)
935 String choice = chooser.getSelectedFile().getPath();
936 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
937 loadJalviewDataFile(choice);
946 * @param e DOCUMENT ME!
948 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
950 if(alignPanels!=null && alignPanels.size()<2)
957 if(alignPanels!=null)
961 for (int i = 0; i < alignPanels.size(); i++)
963 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
964 jalview.structure.StructureSelectionManager.getStructureSelectionManager()
965 .removeStructureViewerListener(ap.seqPanel, null);
966 PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
967 PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
968 PaintRefresher.RemoveComponent(ap);
969 ap.av.alignment = null;
974 int index = tabbedPane.getSelectedIndex();
976 alignPanels.removeElement(alignPanel);
977 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
978 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
979 PaintRefresher.RemoveComponent(alignPanel);
980 viewport.alignment = null;
984 tabbedPane.removeTabAt(index);
985 tabbedPane.validate();
987 if(index==tabbedPane.getTabCount())
992 this.tabSelectionChanged(index);
998 this.setClosed(true);
1001 catch (Exception ex)
1003 ex.printStackTrace();
1011 void updateEditMenuBar()
1014 if (viewport.historyList.size() > 0)
1016 undoMenuItem.setEnabled(true);
1017 CommandI command = (CommandI) viewport.historyList.peek();
1018 undoMenuItem.setText("Undo " + command.getDescription());
1022 undoMenuItem.setEnabled(false);
1023 undoMenuItem.setText("Undo");
1026 if (viewport.redoList.size() > 0)
1028 redoMenuItem.setEnabled(true);
1030 CommandI command = (CommandI) viewport.redoList.peek();
1031 redoMenuItem.setText("Redo " + command.getDescription());
1035 redoMenuItem.setEnabled(false);
1036 redoMenuItem.setText("Redo");
1041 public void addHistoryItem(CommandI command)
1043 if(command.getSize()>0)
1045 viewport.historyList.push(command);
1046 viewport.redoList.clear();
1047 updateEditMenuBar();
1048 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1054 * @return alignment objects for all views
1056 AlignmentI[] getViewAlignments()
1058 if (alignPanels!=null)
1060 Enumeration e = alignPanels.elements();
1061 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1062 for (int i=0; e.hasMoreElements(); i++)
1064 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1070 return new AlignmentI[] { viewport.alignment };
1077 * @param e DOCUMENT ME!
1079 protected void undoMenuItem_actionPerformed(ActionEvent e)
1081 if (viewport.historyList.empty())
1083 CommandI command = (CommandI)viewport.historyList.pop();
1084 viewport.redoList.push(command);
1085 command.undoCommand(getViewAlignments());
1087 AlignViewport originalSource = getOriginatingSource(command);
1088 updateEditMenuBar();
1090 if(originalSource!=null)
1092 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1093 originalSource.firePropertyChange("alignment",
1095 originalSource.alignment.getSequences());
1102 * @param e DOCUMENT ME!
1104 protected void redoMenuItem_actionPerformed(ActionEvent e)
1106 if(viewport.redoList.size()<1)
1111 CommandI command = (CommandI) viewport.redoList.pop();
1112 viewport.historyList.push(command);
1113 command.doCommand(getViewAlignments());
1115 AlignViewport originalSource = getOriginatingSource(command);
1116 updateEditMenuBar();
1118 if(originalSource!=null)
1120 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1121 originalSource.firePropertyChange("alignment",
1123 originalSource.alignment.getSequences());
1127 AlignViewport getOriginatingSource(CommandI command)
1129 AlignViewport originalSource = null;
1130 //For sequence removal and addition, we need to fire
1131 //the property change event FROM the viewport where the
1132 //original alignment was altered
1134 if (command instanceof EditCommand)
1136 EditCommand editCommand = (EditCommand) command;
1137 al = editCommand.getAlignment();
1138 Vector comps = (Vector) PaintRefresher.components
1139 .get(viewport.getSequenceSetId());
1141 for (int i = 0; i < comps.size(); i++)
1143 if (comps.elementAt(i) instanceof AlignmentPanel)
1145 if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
1147 originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
1154 if (originalSource == null)
1156 //The original view is closed, we must validate
1157 //the current view against the closed view first
1160 PaintRefresher.validateSequences(al, viewport.alignment);
1163 originalSource = viewport;
1166 return originalSource;
1172 * @param up DOCUMENT ME!
1174 public void moveSelectedSequences(boolean up)
1176 SequenceGroup sg = viewport.getSelectionGroup();
1185 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1187 SequenceI seq = viewport.alignment.getSequenceAt(i);
1189 if (!sg.getSequences(null).contains(seq))
1194 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1196 if (sg.getSequences(null).contains(temp))
1201 viewport.alignment.getSequences().setElementAt(temp, i);
1202 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1207 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1209 SequenceI seq = viewport.alignment.getSequenceAt(i);
1211 if (!sg.getSequences(null).contains(seq))
1216 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1218 if (sg.getSequences(null).contains(temp))
1223 viewport.alignment.getSequences().setElementAt(temp, i);
1224 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1228 alignPanel.paintAlignment(true);
1234 synchronized void slideSequences(boolean right, int size)
1236 Vector sg = new Vector();
1237 if(viewport.cursorMode)
1239 sg.addElement(viewport.alignment.getSequenceAt(
1240 alignPanel.seqPanel.seqCanvas.cursorY));
1242 else if(viewport.getSelectionGroup()!=null
1243 && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight())
1245 sg = viewport.getSelectionGroup().getSequences(
1246 viewport.hiddenRepSequences);
1254 Vector invertGroup = new Vector();
1256 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1258 if(!sg.contains(viewport.alignment.getSequenceAt(i)))
1259 invertGroup.add(viewport.alignment.getSequenceAt(i));
1262 SequenceI[] seqs1 = new SequenceI[sg.size()];
1263 for (int i = 0; i < sg.size(); i++)
1264 seqs1[i] = (SequenceI) sg.elementAt(i);
1266 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1267 for (int i = 0; i < invertGroup.size(); i++)
1268 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1270 SlideSequencesCommand ssc;
1272 ssc = new SlideSequencesCommand("Slide Sequences",
1274 viewport.getGapCharacter()
1277 ssc = new SlideSequencesCommand("Slide Sequences",
1279 viewport.getGapCharacter()
1282 int groupAdjustment = 0;
1283 if (ssc.getGapsInsertedBegin() && right)
1285 if (viewport.cursorMode)
1286 alignPanel.seqPanel.moveCursor(size, 0);
1288 groupAdjustment = size;
1290 else if (!ssc.getGapsInsertedBegin() && !right)
1292 if (viewport.cursorMode)
1293 alignPanel.seqPanel.moveCursor( -size, 0);
1295 groupAdjustment = -size;
1298 if (groupAdjustment != 0)
1300 viewport.getSelectionGroup().setStartRes(
1301 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1302 viewport.getSelectionGroup().setEndRes(
1303 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1307 boolean appendHistoryItem = false;
1308 if(viewport.historyList!=null
1309 && viewport.historyList.size()>0
1310 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1312 appendHistoryItem = ssc.appendSlideCommand(
1313 (SlideSequencesCommand)viewport.historyList.peek())
1317 if(!appendHistoryItem)
1318 addHistoryItem(ssc);
1327 * @param e DOCUMENT ME!
1329 protected void copy_actionPerformed(ActionEvent e)
1332 if (viewport.getSelectionGroup() == null)
1336 // TODO: preserve the ordering of displayed alignment annotation in any internal paste (particularly sequence associated annotation)
1337 SequenceI [] seqs = viewport.getSelectionAsNewSequence();
1338 String[] omitHidden = null;
1340 if (viewport.hasHiddenColumns)
1342 omitHidden = viewport.getViewAsString(true);
1345 String output = new FormatAdapter().formatSequences(
1350 StringSelection ss = new StringSelection(output);
1354 jalview.gui.Desktop.internalCopy = true;
1355 //Its really worth setting the clipboard contents
1356 //to empty before setting the large StringSelection!!
1357 Toolkit.getDefaultToolkit().getSystemClipboard()
1358 .setContents(new StringSelection(""), null);
1360 Toolkit.getDefaultToolkit().getSystemClipboard()
1361 .setContents(ss, Desktop.instance);
1363 catch (OutOfMemoryError er)
1365 er.printStackTrace();
1366 javax.swing.SwingUtilities.invokeLater(new Runnable()
1370 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1371 "Out of memory copying region!!"
1373 "\nSee help files for increasing Java Virtual Machine memory."
1375 javax.swing.JOptionPane.WARNING_MESSAGE);
1382 Vector hiddenColumns = null;
1383 if(viewport.hasHiddenColumns)
1385 hiddenColumns =new Vector();
1386 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1387 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
1390 int[] region = (int[])
1391 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
1393 hiddenColumns.addElement(new int[]
1394 {region[0] - hiddenOffset,
1395 region[1]-hiddenOffset});
1399 Desktop.jalviewClipboard = new Object[]
1402 viewport.alignment.getDataset(),
1404 statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
1410 * @param e DOCUMENT ME!
1412 protected void pasteNew_actionPerformed(ActionEvent e)
1420 * @param e DOCUMENT ME!
1422 protected void pasteThis_actionPerformed(ActionEvent e)
1430 * @param newAlignment DOCUMENT ME!
1432 void paste(boolean newAlignment)
1434 boolean externalPaste=true;
1437 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1438 Transferable contents = c.getContents(this);
1440 if (contents == null)
1448 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1449 if (str.length() < 1)
1454 format = new IdentifyFile().Identify(str, "Paste");
1457 catch (OutOfMemoryError er)
1459 er.printStackTrace();
1460 javax.swing.SwingUtilities.invokeLater(new Runnable()
1464 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1465 "Out of memory pasting sequences!!"
1467 "\nSee help files for increasing Java Virtual Machine memory."
1469 javax.swing.JOptionPane.WARNING_MESSAGE);
1476 SequenceI[] sequences;
1477 boolean annotationAdded = false;
1478 AlignmentI alignment = null;
1480 if(Desktop.jalviewClipboard!=null)
1482 // The clipboard was filled from within Jalview, we must use the sequences
1483 // And dataset from the copied alignment
1484 SequenceI[] newseq = (SequenceI[])Desktop.jalviewClipboard[0];
1485 // be doubly sure that we create *new* sequence objects.
1486 sequences = new SequenceI[newseq.length];
1487 for (int i=0;i<newseq.length;i++) {
1488 sequences[i] = new Sequence(newseq[i]);
1490 alignment = new Alignment(sequences);
1491 externalPaste = false;
1495 // parse the clipboard as an alignment.
1496 alignment = new FormatAdapter().readFile(str, "Paste", format);
1497 sequences = alignment.getSequencesArray();
1505 if (Desktop.jalviewClipboard != null)
1507 // dataset is inherited
1508 alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
1512 // new dataset is constructed
1513 alignment.setDataset(null);
1515 alwidth = alignment.getWidth()+1;
1519 AlignmentI pastedal = alignment; // preserve pasted alignment object
1520 // Add pasted sequences and dataset into existing alignment.
1521 alignment = viewport.getAlignment();
1522 alwidth = alignment.getWidth()+1;
1523 // decide if we need to import sequences from an existing dataset
1524 boolean importDs = Desktop.jalviewClipboard != null
1525 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1526 // importDs==true instructs us to copy over new dataset sequences from
1527 // an existing alignment
1528 Vector newDs = (importDs) ? new Vector() : null; // used to create
1529 // minimum dataset set
1531 for (int i = 0; i < sequences.length; i++)
1535 newDs.addElement(null);
1537 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1539 if (importDs && ds != null)
1541 if (!newDs.contains(ds))
1543 newDs.setElementAt(ds, i);
1544 ds = new Sequence(ds);
1545 // update with new dataset sequence
1546 sequences[i].setDatasetSequence(ds);
1550 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1555 // copy and derive new dataset sequence
1556 sequences[i] = sequences[i].deriveSequence();
1557 alignment.getDataset().addSequence(sequences[i].getDatasetSequence());
1558 // TODO: avoid creation of duplicate dataset sequences with a
1559 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1561 alignment.addSequence(sequences[i]); // merges dataset
1565 newDs.clear(); // tidy up
1567 if (pastedal.getAlignmentAnnotation()!=null) {
1568 // Add any annotation attached to alignment.
1569 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1570 for (int i=0; i<alann.length; i++)
1572 annotationAdded=true;
1573 if (alann[i].sequenceRef==null && !alann[i].autoCalculated) {
1574 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1575 newann.padAnnotation(alwidth);
1576 alignment.addAnnotation(newann);
1581 if (!newAlignment) {
1585 addHistoryItem(new EditCommand(
1590 alignment.getWidth(),
1594 // Add any annotations attached to sequences
1595 for (int i = 0; i < sequences.length; i++)
1597 if (sequences[i].getAnnotation() != null)
1599 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1601 annotationAdded=true;
1602 sequences[i].getAnnotation()[a].adjustForAlignment();
1603 sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1604 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation was duplicated earlier
1605 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1609 if (!newAlignment) {
1611 // propagate alignment changed.
1612 viewport.setEndSeq(alignment.getHeight());
1613 if (annotationAdded)
1615 // Duplicate sequence annotation in all views.
1616 AlignmentI[] alview = this.getViewAlignments();
1617 for (int i = 0; i < sequences.length; i++)
1619 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1622 for (int avnum=0;avnum<alview.length; avnum++)
1624 if (alview[avnum]!=alignment)
1626 // duplicate in a view other than the one with input focus
1627 int avwidth = alview[avnum].getWidth()+1;
1628 // this relies on sann being preserved after we
1629 // modify the sequence's annotation array for each duplication
1630 for (int a=0; a<sann.length; a++)
1632 AlignmentAnnotation newann = new AlignmentAnnotation(sann[a]);
1633 sequences[i].addAlignmentAnnotation(newann);
1634 newann.padAnnotation(avwidth);
1635 alview[avnum].addAnnotation(newann); // annotation was duplicated earlier
1636 alview[avnum].setAnnotationIndex(newann, a);
1641 buildSortByAnnotationScoresMenu();
1643 viewport.firePropertyChange("alignment", null, alignment.getSequences());
1646 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
1647 String newtitle = new String("Copied sequences");
1649 if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
1651 Vector hc = (Vector)Desktop.jalviewClipboard[2];
1652 for(int i=0; i<hc.size(); i++)
1654 int [] region = (int[]) hc.elementAt(i);
1655 af.viewport.hideColumns(region[0], region[1]);
1660 //>>>This is a fix for the moment, until a better solution is found!!<<<
1661 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
1662 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1664 // TODO: maintain provenance of an alignment, rather than just make the title a concatenation of operations.
1665 if (!externalPaste) {
1666 if (title.startsWith("Copied sequences"))
1672 newtitle = newtitle.concat("- from " + title);
1675 newtitle = new String("Pasted sequences");
1678 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1685 catch (Exception ex)
1687 ex.printStackTrace();
1688 System.out.println("Exception whilst pasting: "+ex);
1689 // could be anything being pasted in here
1698 * @param e DOCUMENT ME!
1700 protected void cut_actionPerformed(ActionEvent e)
1702 copy_actionPerformed(null);
1703 delete_actionPerformed(null);
1709 * @param e DOCUMENT ME!
1711 protected void delete_actionPerformed(ActionEvent evt)
1714 SequenceGroup sg = viewport.getSelectionGroup();
1720 Vector seqs = new Vector();
1722 for (int i = 0; i < sg.getSize(); i++)
1724 seq = sg.getSequenceAt(i);
1725 seqs.addElement(seq);
1729 // If the cut affects all sequences, remove highlighted columns
1730 if (sg.getSize() == viewport.alignment.getHeight())
1732 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1733 sg.getEndRes() + 1);
1737 SequenceI [] cut = new SequenceI[seqs.size()];
1738 for(int i=0; i<seqs.size(); i++)
1740 cut[i] = (SequenceI)seqs.elementAt(i);
1747 addHistoryItem(new EditCommand("Cut Sequences",
1751 sg.getEndRes()-sg.getStartRes()+1,
1752 viewport.alignment));
1755 viewport.setSelectionGroup(null);
1756 viewport.alignment.deleteGroup(sg);
1758 viewport.firePropertyChange("alignment", null,
1759 viewport.getAlignment().getSequences());
1761 if (viewport.getAlignment().getHeight() < 1)
1765 this.setClosed(true);
1767 catch (Exception ex)
1776 * @param e DOCUMENT ME!
1778 protected void deleteGroups_actionPerformed(ActionEvent e)
1780 viewport.alignment.deleteAllGroups();
1781 viewport.sequenceColours = null;
1782 viewport.setSelectionGroup(null);
1783 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1784 alignPanel.paintAlignment(true);
1790 * @param e DOCUMENT ME!
1792 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1794 SequenceGroup sg = new SequenceGroup();
1796 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1799 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1802 sg.setEndRes(viewport.alignment.getWidth() - 1);
1803 viewport.setSelectionGroup(sg);
1804 alignPanel.paintAlignment(true);
1805 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1811 * @param e DOCUMENT ME!
1813 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1815 if(viewport.cursorMode)
1817 alignPanel.seqPanel.keyboardNo1 = null;
1818 alignPanel.seqPanel.keyboardNo2 = null;
1820 viewport.setSelectionGroup(null);
1821 viewport.getColumnSelection().clear();
1822 viewport.setSelectionGroup(null);
1823 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1824 alignPanel.idPanel.idCanvas.searchResults = null;
1825 alignPanel.paintAlignment(true);
1826 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1832 * @param e DOCUMENT ME!
1834 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1836 SequenceGroup sg = viewport.getSelectionGroup();
1840 selectAllSequenceMenuItem_actionPerformed(null);
1845 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1848 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1851 alignPanel.paintAlignment(true);
1853 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1856 public void invertColSel_actionPerformed(ActionEvent e)
1858 viewport.invertColumnSelection();
1859 alignPanel.paintAlignment(true);
1866 * @param e DOCUMENT ME!
1868 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1870 trimAlignment(true);
1876 * @param e DOCUMENT ME!
1878 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
1880 trimAlignment(false);
1883 void trimAlignment(boolean trimLeft)
1885 ColumnSelection colSel = viewport.getColumnSelection();
1888 if (colSel.size() > 0)
1892 column = colSel.getMin();
1896 column = colSel.getMax();
1900 if(viewport.getSelectionGroup()!=null)
1902 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
1903 hiddenRepSequences);
1907 seqs = viewport.alignment.getSequencesArray();
1911 TrimRegionCommand trimRegion;
1914 trimRegion = new TrimRegionCommand("Remove Left",
1915 TrimRegionCommand.TRIM_LEFT,
1920 viewport.selectionGroup);
1921 viewport.setStartRes(0);
1925 trimRegion = new TrimRegionCommand("Remove Right",
1926 TrimRegionCommand.TRIM_RIGHT,
1931 viewport.selectionGroup);
1934 statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
1937 addHistoryItem(trimRegion);
1939 Vector groups = viewport.alignment.getGroups();
1941 for (int i = 0; i < groups.size(); i++)
1943 SequenceGroup sg = (SequenceGroup) groups.get(i);
1945 if ( (trimLeft && !sg.adjustForRemoveLeft(column))
1946 || (!trimLeft && !sg.adjustForRemoveRight(column)))
1948 viewport.alignment.deleteGroup(sg);
1952 viewport.firePropertyChange("alignment", null,
1953 viewport.getAlignment().getSequences());
1960 * @param e DOCUMENT ME!
1962 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1964 int start = 0, end = viewport.alignment.getWidth()-1;
1967 if (viewport.getSelectionGroup() != null)
1969 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
1970 hiddenRepSequences);
1971 start = viewport.getSelectionGroup().getStartRes();
1972 end = viewport.getSelectionGroup().getEndRes();
1976 seqs = viewport.alignment.getSequencesArray();
1980 RemoveGapColCommand removeGapCols =
1981 new RemoveGapColCommand("Remove Gapped Columns",
1984 viewport.alignment);
1986 addHistoryItem(removeGapCols);
1988 statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
1990 //This is to maintain viewport position on first residue
1992 SequenceI seq = viewport.alignment.getSequenceAt(0);
1993 int startRes = seq.findPosition(viewport.startRes);
1994 // ShiftList shifts;
1995 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
1996 // edit.alColumnChanges=shifts.getInverse();
1997 // if (viewport.hasHiddenColumns)
1998 // viewport.getColumnSelection().compensateForEdits(shifts);
1999 viewport.setStartRes(seq.findIndex(startRes)-1);
2000 viewport.firePropertyChange("alignment", null,
2001 viewport.getAlignment().getSequences());
2008 * @param e DOCUMENT ME!
2010 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2012 int start = 0, end = viewport.alignment.getWidth()-1;
2015 if (viewport.getSelectionGroup() != null)
2017 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
2018 hiddenRepSequences);
2019 start = viewport.getSelectionGroup().getStartRes();
2020 end = viewport.getSelectionGroup().getEndRes();
2024 seqs = viewport.alignment.getSequencesArray();
2027 //This is to maintain viewport position on first residue
2029 SequenceI seq = viewport.alignment.getSequenceAt(0);
2030 int startRes = seq.findPosition(viewport.startRes);
2032 addHistoryItem(new RemoveGapsCommand("Remove Gaps",
2035 viewport.alignment));
2037 viewport.setStartRes(seq.findIndex(startRes)-1);
2039 viewport.firePropertyChange("alignment", null,
2040 viewport.getAlignment().getSequences());
2047 * @param e DOCUMENT ME!
2049 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2051 viewport.padGaps = padGapsMenuitem.isSelected();
2053 viewport.firePropertyChange("alignment",
2055 viewport.getAlignment().getSequences());
2061 * @param e DOCUMENT ME!
2063 public void findMenuItem_actionPerformed(ActionEvent e)
2068 public void newView_actionPerformed(ActionEvent e)
2070 AlignmentPanel newap =
2071 new Jalview2XML().copyAlignPanel(alignPanel, true);
2073 newap.av.gatherViewsHere = false;
2075 if (viewport.viewName == null)
2077 viewport.viewName = "Original";
2080 newap.av.historyList = viewport.historyList;
2081 newap.av.redoList = viewport.redoList;
2083 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2084 String newViewName = "View " +index;
2086 Vector comps = (Vector) PaintRefresher.components.get(viewport.
2087 getSequenceSetId());
2088 Vector existingNames = new Vector();
2089 for(int i=0; i<comps.size(); i++)
2091 if(comps.elementAt(i) instanceof AlignmentPanel)
2093 AlignmentPanel ap = (AlignmentPanel)comps.elementAt(i);
2094 if(!existingNames.contains(ap.av.viewName))
2096 existingNames.addElement(ap.av.viewName);
2101 while(existingNames.contains(newViewName))
2103 newViewName = "View "+ (++index);
2106 newap.av.viewName = newViewName;
2108 addAlignmentPanel(newap, false);
2110 if(alignPanels.size()==2)
2112 viewport.gatherViewsHere = true;
2114 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2117 public void expandViews_actionPerformed(ActionEvent e)
2119 Desktop.instance.explodeViews(this);
2122 public void gatherViews_actionPerformed(ActionEvent e)
2124 Desktop.instance.gatherViews(this);
2132 * @param e DOCUMENT ME!
2134 public void font_actionPerformed(ActionEvent e)
2136 new FontChooser(alignPanel);
2143 * @param e DOCUMENT ME!
2145 protected void seqLimit_actionPerformed(ActionEvent e)
2147 viewport.setShowJVSuffix(seqLimits.isSelected());
2149 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
2150 alignPanel.paintAlignment(true);
2153 public void idRightAlign_actionPerformed(ActionEvent e)
2155 viewport.rightAlignIds = idRightAlign.isSelected();
2156 alignPanel.paintAlignment(true);
2164 * @param e DOCUMENT ME!
2166 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2168 viewport.setColourText(colourTextMenuItem.isSelected());
2169 alignPanel.paintAlignment(true);
2175 * @param e DOCUMENT ME!
2177 public void wrapMenuItem_actionPerformed(ActionEvent e)
2179 scaleAbove.setVisible(wrapMenuItem.isSelected());
2180 scaleLeft.setVisible(wrapMenuItem.isSelected());
2181 scaleRight.setVisible(wrapMenuItem.isSelected());
2182 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2183 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2186 public void showAllSeqs_actionPerformed(ActionEvent e)
2188 viewport.showAllHiddenSeqs();
2191 public void showAllColumns_actionPerformed(ActionEvent e)
2193 viewport.showAllHiddenColumns();
2197 public void hideSelSequences_actionPerformed(ActionEvent e)
2199 viewport.hideAllSelectedSeqs();
2200 alignPanel.paintAlignment(true);
2203 public void hideSelColumns_actionPerformed(ActionEvent e)
2205 viewport.hideSelectedColumns();
2206 alignPanel.paintAlignment(true);
2209 public void hiddenMarkers_actionPerformed(ActionEvent e)
2211 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2218 * @param e DOCUMENT ME!
2220 protected void scaleAbove_actionPerformed(ActionEvent e)
2222 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2223 alignPanel.paintAlignment(true);
2229 * @param e DOCUMENT ME!
2231 protected void scaleLeft_actionPerformed(ActionEvent e)
2233 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2234 alignPanel.paintAlignment(true);
2240 * @param e DOCUMENT ME!
2242 protected void scaleRight_actionPerformed(ActionEvent e)
2244 viewport.setScaleRightWrapped(scaleRight.isSelected());
2245 alignPanel.paintAlignment(true);
2251 * @param e DOCUMENT ME!
2253 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2255 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2256 alignPanel.paintAlignment(true);
2262 * @param e DOCUMENT ME!
2264 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2266 viewport.setShowText(viewTextMenuItem.isSelected());
2267 alignPanel.paintAlignment(true);
2273 * @param e DOCUMENT ME!
2275 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2277 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2278 alignPanel.paintAlignment(true);
2282 public FeatureSettings featureSettings;
2283 public void featureSettings_actionPerformed(ActionEvent e)
2285 if(featureSettings !=null )
2287 featureSettings.close();
2288 featureSettings = null;
2290 featureSettings = new FeatureSettings(this);
2296 * @param evt DOCUMENT ME!
2298 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2300 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2301 alignPanel.paintAlignment(true);
2302 if (alignPanel.getOverviewPanel() != null)
2304 alignPanel.getOverviewPanel().updateOverviewImage();
2311 * @param e DOCUMENT ME!
2313 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2315 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2316 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2319 public void alignmentProperties()
2321 JEditorPane editPane = new JEditorPane("text/html","");
2322 editPane.setEditable(false);
2323 StringBuffer contents = new StringBuffer("<html>");
2326 int min=Integer.MAX_VALUE, max=0;
2327 for(int i=0; i<viewport.alignment.getHeight(); i++)
2329 int size = viewport.alignment.getSequenceAt(i).getEnd()
2330 -viewport.alignment.getSequenceAt(i).getStart();
2337 avg = avg/(float)viewport.alignment.getHeight();
2339 contents.append("<br>Sequences: "+ viewport.alignment.getHeight());
2340 contents.append("<br>Minimum Sequence Length: "+min);
2341 contents.append("<br>Maximum Sequence Length: "+max);
2342 contents.append("<br>Average Length: "+(int)avg);
2344 if (((Alignment)viewport.alignment).getProperties() != null)
2346 Hashtable props = ((Alignment)viewport.alignment).getProperties();
2347 Enumeration en = props.keys();
2348 contents.append("<br><br><table border=\"1\">");
2349 while(en.hasMoreElements())
2351 String key = en.nextElement().toString();
2352 StringBuffer val = new StringBuffer();
2353 String vals = props.get(key).toString();
2356 npos = vals.indexOf("\n",pos);
2359 val.append(vals.substring(pos));
2361 val.append(vals.substring(pos, npos));
2366 contents.append("<tr><td>"+key+"</td><td>"+val+"</td></tr>");
2368 contents.append("</table>");
2370 editPane.setText(contents.toString()+"</html>");
2371 JInternalFrame frame = new JInternalFrame();
2372 frame.getContentPane().add(new JScrollPane(editPane));
2374 Desktop.instance.addInternalFrame(frame,"Alignment Properties: "+getTitle(),500,400);
2381 * @param e DOCUMENT ME!
2383 public void overviewMenuItem_actionPerformed(ActionEvent e)
2385 if (alignPanel.overviewPanel != null)
2390 JInternalFrame frame = new JInternalFrame();
2391 OverviewPanel overview = new OverviewPanel(alignPanel);
2392 frame.setContentPane(overview);
2393 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2394 frame.getWidth(), frame.getHeight());
2396 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2397 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2399 public void internalFrameClosed(
2400 javax.swing.event.InternalFrameEvent evt)
2402 alignPanel.setOverviewPanel(null);
2407 alignPanel.setOverviewPanel(overview);
2410 public void textColour_actionPerformed(ActionEvent e)
2412 new TextColourChooser().chooseColour(alignPanel, null);
2418 * @param e DOCUMENT ME!
2420 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2428 * @param e DOCUMENT ME!
2430 public void clustalColour_actionPerformed(ActionEvent e)
2432 changeColour(new ClustalxColourScheme(
2433 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
2439 * @param e DOCUMENT ME!
2441 public void zappoColour_actionPerformed(ActionEvent e)
2443 changeColour(new ZappoColourScheme());
2449 * @param e DOCUMENT ME!
2451 public void taylorColour_actionPerformed(ActionEvent e)
2453 changeColour(new TaylorColourScheme());
2459 * @param e DOCUMENT ME!
2461 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2463 changeColour(new HydrophobicColourScheme());
2469 * @param e DOCUMENT ME!
2471 public void helixColour_actionPerformed(ActionEvent e)
2473 changeColour(new HelixColourScheme());
2479 * @param e DOCUMENT ME!
2481 public void strandColour_actionPerformed(ActionEvent e)
2483 changeColour(new StrandColourScheme());
2489 * @param e DOCUMENT ME!
2491 public void turnColour_actionPerformed(ActionEvent e)
2493 changeColour(new TurnColourScheme());
2499 * @param e DOCUMENT ME!
2501 public void buriedColour_actionPerformed(ActionEvent e)
2503 changeColour(new BuriedColourScheme());
2509 * @param e DOCUMENT ME!
2511 public void nucleotideColour_actionPerformed(ActionEvent e)
2513 changeColour(new NucleotideColourScheme());
2516 public void annotationColour_actionPerformed(ActionEvent e)
2518 new AnnotationColourChooser(viewport, alignPanel);
2525 * @param e DOCUMENT ME!
2527 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2529 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2535 * @param cs DOCUMENT ME!
2537 public void changeColour(ColourSchemeI cs)
2543 if (viewport.getAbovePIDThreshold())
2545 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2548 cs.setThreshold(threshold,
2549 viewport.getIgnoreGapsConsensus());
2551 viewport.setGlobalColourScheme(cs);
2555 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2558 if (viewport.getConservationSelected())
2561 Alignment al = (Alignment) viewport.alignment;
2562 Conservation c = new Conservation("All",
2563 ResidueProperties.propHash, 3,
2564 al.getSequences(), 0,
2568 c.verdict(false, viewport.ConsPercGaps);
2570 cs.setConservation(c);
2572 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
2577 cs.setConservation(null);
2580 cs.setConsensus(viewport.hconsensus);
2583 viewport.setGlobalColourScheme(cs);
2585 if (viewport.getColourAppliesToAllGroups())
2587 Vector groups = viewport.alignment.getGroups();
2589 for (int i = 0; i < groups.size(); i++)
2591 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2599 if (cs instanceof ClustalxColourScheme)
2601 sg.cs = new ClustalxColourScheme(
2602 sg.getSequences(viewport.hiddenRepSequences), sg.getWidth());
2604 else if (cs instanceof UserColourScheme)
2606 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
2612 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2614 catch (Exception ex)
2619 if (viewport.getAbovePIDThreshold()
2620 || cs instanceof PIDColourScheme
2621 || cs instanceof Blosum62ColourScheme)
2623 sg.cs.setThreshold(threshold,
2624 viewport.getIgnoreGapsConsensus());
2626 sg.cs.setConsensus(AAFrequency.calculate(
2627 sg.getSequences(viewport.hiddenRepSequences), sg.getStartRes(),
2632 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2636 if (viewport.getConservationSelected())
2638 Conservation c = new Conservation("Group",
2639 ResidueProperties.propHash, 3,
2640 sg.getSequences(viewport.
2641 hiddenRepSequences),
2645 c.verdict(false, viewport.ConsPercGaps);
2646 sg.cs.setConservation(c);
2650 sg.cs.setConservation(null);
2655 if (alignPanel.getOverviewPanel() != null)
2657 alignPanel.getOverviewPanel().updateOverviewImage();
2663 alignPanel.paintAlignment(true);
2669 * @param e DOCUMENT ME!
2671 protected void modifyPID_actionPerformed(ActionEvent e)
2673 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
2675 SliderPanel.setPIDSliderSource(alignPanel,
2676 viewport.getGlobalColourScheme(),
2678 SliderPanel.showPIDSlider();
2685 * @param e DOCUMENT ME!
2687 protected void modifyConservation_actionPerformed(ActionEvent e)
2689 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
2691 SliderPanel.setConservationSlider(alignPanel,
2692 viewport.globalColourScheme,
2694 SliderPanel.showConservationSlider();
2701 * @param e DOCUMENT ME!
2703 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2705 viewport.setConservationSelected(conservationMenuItem.isSelected());
2707 viewport.setAbovePIDThreshold(false);
2708 abovePIDThreshold.setSelected(false);
2710 changeColour(viewport.getGlobalColourScheme());
2712 modifyConservation_actionPerformed(null);
2718 * @param e DOCUMENT ME!
2720 public void abovePIDThreshold_actionPerformed(ActionEvent e)
2722 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
2724 conservationMenuItem.setSelected(false);
2725 viewport.setConservationSelected(false);
2727 changeColour(viewport.getGlobalColourScheme());
2729 modifyPID_actionPerformed(null);
2735 * @param e DOCUMENT ME!
2737 public void userDefinedColour_actionPerformed(ActionEvent e)
2739 if (e.getActionCommand().equals("User Defined..."))
2741 new UserDefinedColours(alignPanel, null);
2745 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
2746 getUserColourSchemes().get(e.getActionCommand());
2752 public void updateUserColourMenu()
2755 Component[] menuItems = colourMenu.getMenuComponents();
2756 int i, iSize = menuItems.length;
2757 for (i = 0; i < iSize; i++)
2759 if (menuItems[i].getName() != null &&
2760 menuItems[i].getName().equals("USER_DEFINED"))
2762 colourMenu.remove(menuItems[i]);
2766 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
2768 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
2769 getUserColourSchemes().keys();
2771 while (userColours.hasMoreElements())
2773 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
2775 nextElement().toString());
2776 radioItem.setName("USER_DEFINED");
2777 radioItem.addMouseListener(new MouseAdapter()
2779 public void mousePressed(MouseEvent evt)
2781 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
2783 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
2785 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
2787 "Remove from default list?",
2788 "Remove user defined colour",
2789 JOptionPane.YES_NO_OPTION);
2790 if(option == JOptionPane.YES_OPTION)
2792 jalview.gui.UserDefinedColours.removeColourFromDefaults(
2793 radioItem.getText());
2794 colourMenu.remove(radioItem);
2798 radioItem.addActionListener(new ActionListener()
2800 public void actionPerformed(ActionEvent evt)
2802 userDefinedColour_actionPerformed(evt);
2809 radioItem.addActionListener(new ActionListener()
2811 public void actionPerformed(ActionEvent evt)
2813 userDefinedColour_actionPerformed(evt);
2817 colourMenu.insert(radioItem, 15);
2818 colours.add(radioItem);
2826 * @param e DOCUMENT ME!
2828 public void PIDColour_actionPerformed(ActionEvent e)
2830 changeColour(new PIDColourScheme());
2836 * @param e DOCUMENT ME!
2838 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
2840 changeColour(new Blosum62ColourScheme());
2846 * @param e DOCUMENT ME!
2848 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2850 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2851 AlignmentSorter.sortByPID(viewport.getAlignment(),
2852 viewport.getAlignment().getSequenceAt(0));
2853 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2854 viewport.alignment));
2855 alignPanel.paintAlignment(true);
2861 * @param e DOCUMENT ME!
2863 public void sortIDMenuItem_actionPerformed(ActionEvent e)
2865 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2866 AlignmentSorter.sortByID(viewport.getAlignment());
2867 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
2868 alignPanel.paintAlignment(true);
2874 * @param e DOCUMENT ME!
2876 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
2878 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2879 AlignmentSorter.sortByGroup(viewport.getAlignment());
2880 addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
2882 alignPanel.paintAlignment(true);
2887 * @param e DOCUMENT ME!
2889 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2891 new RedundancyPanel(alignPanel, this);
2898 * @param e DOCUMENT ME!
2900 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2902 if ( (viewport.getSelectionGroup() == null) ||
2903 (viewport.getSelectionGroup().getSize() < 2))
2905 JOptionPane.showInternalMessageDialog(this,
2906 "You must select at least 2 sequences.",
2907 "Invalid Selection",
2908 JOptionPane.WARNING_MESSAGE);
2912 JInternalFrame frame = new JInternalFrame();
2913 frame.setContentPane(new PairwiseAlignPanel(viewport));
2914 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
2921 * @param e DOCUMENT ME!
2923 public void PCAMenuItem_actionPerformed(ActionEvent e)
2925 if ( ( (viewport.getSelectionGroup() != null) &&
2926 (viewport.getSelectionGroup().getSize() < 4) &&
2927 (viewport.getSelectionGroup().getSize() > 0)) ||
2928 (viewport.getAlignment().getHeight() < 4))
2930 JOptionPane.showInternalMessageDialog(this,
2931 "Principal component analysis must take\n" +
2932 "at least 4 input sequences.",
2933 "Sequence selection insufficient",
2934 JOptionPane.WARNING_MESSAGE);
2939 new PCAPanel(alignPanel);
2943 public void autoCalculate_actionPerformed(ActionEvent e)
2945 viewport.autoCalculateConsensus = autoCalculate.isSelected();
2946 if(viewport.autoCalculateConsensus)
2948 viewport.firePropertyChange("alignment",
2950 viewport.getAlignment().getSequences());
2958 * @param e DOCUMENT ME!
2960 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2962 NewTreePanel("AV", "PID", "Average distance tree using PID");
2968 * @param e DOCUMENT ME!
2970 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2972 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2978 * @param e DOCUMENT ME!
2980 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2982 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2988 * @param e DOCUMENT ME!
2990 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2992 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2998 * @param type DOCUMENT ME!
2999 * @param pwType DOCUMENT ME!
3000 * @param title DOCUMENT ME!
3002 void NewTreePanel(String type, String pwType, String title)
3006 if (viewport.getSelectionGroup() != null)
3008 if (viewport.getSelectionGroup().getSize() < 3)
3010 JOptionPane.showMessageDialog(Desktop.desktop,
3011 "You need to have more than two sequences selected to build a tree!",
3012 "Not enough sequences",
3013 JOptionPane.WARNING_MESSAGE);
3018 SequenceGroup sg = viewport.getSelectionGroup();
3020 /* Decide if the selection is a column region */
3021 while (s < sg.getSize())
3023 if ( ( (SequenceI) sg.getSequences(null).elementAt(s++)).getLength() <
3026 JOptionPane.showMessageDialog(Desktop.desktop,
3027 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
3028 "Try using the Pad function in the edit menu,\n" +
3029 "or one of the multiple sequence alignment web services.",
3030 "Sequences in selection are not aligned",
3031 JOptionPane.WARNING_MESSAGE);
3037 title = title + " on region";
3038 tp = new TreePanel(alignPanel, type, pwType);
3042 //are the sequences aligned?
3043 if (!viewport.alignment.isAligned())
3045 JOptionPane.showMessageDialog(Desktop.desktop,
3046 "The sequences must be aligned before creating a tree.\n" +
3047 "Try using the Pad function in the edit menu,\n" +
3048 "or one of the multiple sequence alignment web services.",
3049 "Sequences not aligned",
3050 JOptionPane.WARNING_MESSAGE);
3055 if(viewport.alignment.getHeight()<2)
3060 tp = new TreePanel(alignPanel, type, pwType);
3065 if(viewport.viewName!=null)
3067 title+= viewport.viewName+" of ";
3070 title += this.title;
3072 Desktop.addInternalFrame(tp, title, 600, 500);
3078 * @param title DOCUMENT ME!
3079 * @param order DOCUMENT ME!
3081 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
3083 final JMenuItem item = new JMenuItem("by " + title);
3085 item.addActionListener(new java.awt.event.ActionListener()
3087 public void actionPerformed(ActionEvent e)
3089 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
3091 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
3092 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3094 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3095 viewport.alignment));
3097 alignPanel.paintAlignment(true);
3102 * Add a new sort by annotation score menu item
3103 * @param sort the menu to add the option to
3104 * @param scoreLabel the label used to retrieve scores for each sequence on the alignment
3106 public void addSortByAnnotScoreMenuItem(JMenu sort, final String scoreLabel)
3108 final JMenuItem item = new JMenuItem(scoreLabel);
3110 item.addActionListener(new java.awt.event.ActionListener()
3112 public void actionPerformed(ActionEvent e)
3114 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
3115 AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport.getAlignment());
3116 addHistoryItem(new OrderCommand("Sort by "+scoreLabel, oldOrder, viewport.alignment));
3117 alignPanel.paintAlignment(true);
3122 * last hash for alignment's annotation array - used to minimise cost of rebuild.
3124 protected int _annotationScoreVectorHash;
3126 * search the alignment and rebuild the sort by annotation score submenu
3127 * the last alignment annotation vector hash is stored to minimize
3128 * cost of rebuilding in subsequence calls.
3131 public void buildSortByAnnotationScoresMenu()
3133 if(viewport.alignment.getAlignmentAnnotation()==null)
3138 if (viewport.alignment.getAlignmentAnnotation().hashCode()!=_annotationScoreVectorHash)
3140 sortByAnnotScore.removeAll();
3141 // almost certainly a quicker way to do this - but we keep it simple
3142 Hashtable scoreSorts=new Hashtable();
3143 AlignmentAnnotation aann[];
3144 Enumeration sq = viewport.alignment.getSequences().elements();
3145 while (sq.hasMoreElements())
3147 aann = ((SequenceI) sq.nextElement()).getAnnotation();
3148 for (int i=0;aann!=null && i<aann.length; i++)
3150 if (aann[i].hasScore() && aann[i].sequenceRef!=null)
3152 scoreSorts.put(aann[i].label, aann[i].label);
3156 Enumeration labels = scoreSorts.keys();
3157 while (labels.hasMoreElements())
3159 addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels.nextElement());
3161 sortByAnnotScore.setVisible(scoreSorts.size()>0);
3164 _annotationScoreVectorHash =
3165 viewport.alignment.getAlignmentAnnotation().hashCode();
3170 * Maintain the Order by->Displayed Tree menu.
3171 * Creates a new menu item for a TreePanel with an appropriate
3172 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
3173 * to remove the menu item when the treePanel is closed, and adjust
3174 * the tree leaf to sequence mapping when the alignment is modified.
3175 * @param treePanel Displayed tree window.
3176 * @param title SortBy menu item title.
3178 public void buildTreeMenu()
3180 sortByTreeMenu.removeAll();
3182 Vector comps = (Vector) PaintRefresher.components.get(viewport.
3183 getSequenceSetId());
3184 Vector treePanels = new Vector();
3185 int i, iSize = comps.size();
3186 for(i=0; i<iSize; i++)
3188 if(comps.elementAt(i) instanceof TreePanel)
3190 treePanels.add(comps.elementAt(i));
3194 iSize = treePanels.size();
3198 sortByTreeMenu.setVisible(false);
3202 sortByTreeMenu.setVisible(true);
3204 for(i=0; i<treePanels.size(); i++)
3206 TreePanel tp = (TreePanel)treePanels.elementAt(i);
3207 final JMenuItem item = new JMenuItem(tp.getTitle());
3208 final NJTree tree = ((TreePanel)treePanels.elementAt(i)).getTree();
3209 item.addActionListener(new java.awt.event.ActionListener()
3211 public void actionPerformed(ActionEvent e)
3213 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3214 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
3216 addHistoryItem(new OrderCommand("Tree Sort",
3218 viewport.alignment));
3220 alignPanel.paintAlignment(true);
3224 sortByTreeMenu.add(item);
3229 * Work out whether the whole set of sequences
3230 * or just the selected set will be submitted for multiple alignment.
3233 private jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3235 // Now, check we have enough sequences
3236 AlignmentView msa = null;
3238 if ( (viewport.getSelectionGroup() != null) &&
3239 (viewport.getSelectionGroup().getSize() > 1))
3241 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
3242 /*SequenceGroup seqs = viewport.getSelectionGroup();
3244 msa = new SequenceI[sz = seqs.getSize(false)];
3246 for (int i = 0; i < sz; i++)
3248 msa[i] = (SequenceI) seqs.getSequenceAt(i);
3250 msa = viewport.getAlignmentView(true);
3254 /*Vector seqs = viewport.getAlignment().getSequences();
3256 if (seqs.size() > 1)
3258 msa = new SequenceI[seqs.size()];
3260 for (int i = 0; i < seqs.size(); i++)
3262 msa[i] = (SequenceI) seqs.elementAt(i);
3265 msa = viewport.getAlignmentView(false);
3271 * Decides what is submitted to a secondary structure prediction service,
3272 * the currently selected sequence, or the currently selected alignment
3273 * (where the first sequence in the set is the one that the prediction
3276 AlignmentView gatherSeqOrMsaForSecStrPrediction()
3278 AlignmentView seqs = null;
3280 if ( (viewport.getSelectionGroup() != null) &&
3281 (viewport.getSelectionGroup().getSize() > 0))
3283 seqs = viewport.getAlignmentView(true);
3287 seqs = viewport.getAlignmentView(false);
3289 // limit sequences - JBPNote in future - could spawn multiple prediction jobs
3290 // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3291 if (!viewport.alignment.isAligned())
3293 seqs.setSequences(new SeqCigar[]
3294 {seqs.getSequences()[0]});
3301 * @param e DOCUMENT ME!
3303 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3305 // Pick the tree file
3306 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
3309 chooser.setFileView(new JalviewFileView());
3310 chooser.setDialogTitle("Select a newick-like tree file");
3311 chooser.setToolTipText("Load a tree file");
3313 int value = chooser.showOpenDialog(null);
3315 if (value == JalviewFileChooser.APPROVE_OPTION)
3317 String choice = chooser.getSelectedFile().getPath();
3318 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3322 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
3324 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3326 catch (Exception ex)
3328 JOptionPane.showMessageDialog(Desktop.desktop,
3329 "Problem reading tree file",
3331 JOptionPane.WARNING_MESSAGE);
3332 ex.printStackTrace();
3338 public TreePanel ShowNewickTree(NewickFile nf, String title)
3340 return ShowNewickTree(nf,title,600,500,4,5);
3343 public TreePanel ShowNewickTree(NewickFile nf, String title,
3344 AlignmentView input)
3346 return ShowNewickTree(nf,title, input, 600,500,4,5);
3349 public TreePanel ShowNewickTree(NewickFile nf, String title, int w, int h,
3352 return ShowNewickTree(nf, title, null, w, h, x, y);
3355 * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
3357 * @param nf the tree
3358 * @param title tree viewer title
3359 * @param input Associated alignment input data (or null)
3364 * @return TreePanel handle
3366 public TreePanel ShowNewickTree(NewickFile nf, String title,
3367 AlignmentView input, int w, int h, int x,
3370 TreePanel tp = null;
3376 if (nf.getTree() != null)
3378 tp = new TreePanel(alignPanel,
3387 tp.setLocation(x,y);
3391 Desktop.addInternalFrame(tp, title, w, h);
3394 catch (Exception ex)
3396 ex.printStackTrace();
3404 * Generates menu items and listener event actions for web service clients
3407 public void BuildWebServiceMenu()
3409 if ( (Discoverer.services != null)
3410 && (Discoverer.services.size() > 0))
3412 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
3413 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
3414 Vector wsmenu = new Vector();
3415 final AlignFrame af = this;
3418 // Add any Multiple Sequence Alignment Services
3419 final JMenu msawsmenu = new JMenu("Alignment");
3420 for (int i = 0, j = msaws.size(); i < j; i++)
3422 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
3424 final JMenuItem method = new JMenuItem(sh.getName());
3425 method.addActionListener(new ActionListener()
3427 public void actionPerformed(ActionEvent e)
3429 AlignmentView msa = gatherSequencesForAlignment();
3430 new jalview.ws.MsaWSClient(sh, title, msa,
3432 viewport.getAlignment().getDataset(),
3438 msawsmenu.add(method);
3439 // Deal with services that we know accept partial alignments.
3440 if (sh.getName().indexOf("lustal") > -1)
3442 // We know that ClustalWS can accept partial alignments for refinement.
3443 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
3444 methodR.addActionListener(new ActionListener()
3446 public void actionPerformed(ActionEvent e)
3448 AlignmentView msa = gatherSequencesForAlignment();
3449 new jalview.ws.MsaWSClient(sh, title, msa,
3451 viewport.getAlignment().getDataset(),
3457 msawsmenu.add(methodR);
3461 wsmenu.add(msawsmenu);
3463 if (secstrpr != null)
3465 // Add any secondary structure prediction services
3466 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
3467 for (int i = 0, j = secstrpr.size(); i < j; i++)
3469 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
3471 final JMenuItem method = new JMenuItem(sh.getName());
3472 method.addActionListener(new ActionListener()
3474 public void actionPerformed(ActionEvent e)
3476 AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
3477 if (msa.getSequences().length == 1)
3479 // Single Sequence prediction
3480 new jalview.ws.JPredClient(sh, title, false, msa, af, true);
3484 if (msa.getSequences().length > 1)
3486 // Sequence profile based prediction
3487 new jalview.ws.JPredClient(sh,
3488 title, true, msa, af, true);
3493 secstrmenu.add(method);
3495 wsmenu.add(secstrmenu);
3497 resetWebServiceMenu();
3498 for (int i = 0, j = wsmenu.size(); i < j; i++)
3500 webService.add( (JMenu) wsmenu.get(i));
3505 resetWebServiceMenu();
3506 this.webService.add(this.webServiceNoServices);
3508 // TODO: add in rediscovery function
3509 // TODO: reduce code redundancy.
3510 // TODO: group services by location as well as function.
3515 * empty the web service menu and add any ad-hoc functions
3516 * not dynamically discovered.
3519 private void resetWebServiceMenu()
3521 webService.removeAll();
3522 // Temporary hack - DBRef Fetcher always top level ws entry.
3523 JMenuItem rfetch = new JMenuItem("Fetch DB References");
3524 rfetch.setToolTipText("Retrieve and parse uniprot records for the alignment or the currently selected sequences");
3525 webService.add(rfetch);
3526 rfetch.addActionListener(new ActionListener() {
3528 public void actionPerformed(ActionEvent e)
3530 new jalview.io.DBRefFetcher(
3531 alignPanel.av.getSequenceSelection(),
3532 alignPanel.alignFrame).fetchDBRefs(false);
3538 /* public void vamsasStore_actionPerformed(ActionEvent e)
3540 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
3541 getProperty("LAST_DIRECTORY"));
3543 chooser.setFileView(new JalviewFileView());
3544 chooser.setDialogTitle("Export to Vamsas file");
3545 chooser.setToolTipText("Export");
3547 int value = chooser.showSaveDialog(this);
3549 if (value == JalviewFileChooser.APPROVE_OPTION)
3551 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
3552 //vs.store(chooser.getSelectedFile().getAbsolutePath() );
3553 vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
3559 public void showTranslation_actionPerformed(ActionEvent e)
3561 ///////////////////////////////
3562 // Collect Data to be translated/transferred
3564 SequenceI [] selection = viewport.getSequenceSelection();
3565 String [] seqstring = viewport.getViewAsString(true);
3566 AlignmentI al = null;
3568 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring, viewport.getViewAsVisibleContigs(true),
3569 viewport.getGapCharacter(), viewport.alignment.getAlignmentAnnotation(),
3570 viewport.alignment.getWidth());
3571 } catch (Exception ex) {
3573 jalview.bin.Cache.log.debug("Exception during translation.",ex);
3577 JOptionPane.showMessageDialog(Desktop.desktop,
3578 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
3579 "Translation Failed",
3580 JOptionPane.WARNING_MESSAGE);
3582 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
3583 Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
3592 * @param String DOCUMENT ME!
3594 public boolean parseFeaturesFile(String file, String type)
3596 boolean featuresFile = false;
3599 featuresFile = new FeaturesFile(file,
3600 type).parse(viewport.alignment.getDataset(),
3601 alignPanel.seqPanel.seqCanvas.
3602 getFeatureRenderer().featureColours,
3607 ex.printStackTrace();
3612 viewport.showSequenceFeatures = true;
3613 showSeqFeatures.setSelected(true);
3614 alignPanel.paintAlignment(true);
3617 return featuresFile;
3620 public void dragEnter(DropTargetDragEvent evt)
3623 public void dragExit(DropTargetEvent evt)
3626 public void dragOver(DropTargetDragEvent evt)
3629 public void dropActionChanged(DropTargetDragEvent evt)
3632 public void drop(DropTargetDropEvent evt)
3634 Transferable t = evt.getTransferable();
3635 java.util.List files = null;
3639 DataFlavor uriListFlavor = new DataFlavor(
3640 "text/uri-list;class=java.lang.String");
3641 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
3643 //Works on Windows and MacOSX
3644 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3645 files = (java.util.List) t.getTransferData(DataFlavor.
3646 javaFileListFlavor);
3648 else if (t.isDataFlavorSupported(uriListFlavor))
3650 // This is used by Unix drag system
3651 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3652 String data = (String) t.getTransferData(uriListFlavor);
3653 files = new java.util.ArrayList(1);
3654 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
3657 st.hasMoreTokens(); )
3659 String s = st.nextToken();
3660 if (s.startsWith("#"))
3662 // the line is a comment (as per the RFC 2483)
3666 java.net.URI uri = new java.net.URI(s);
3667 java.io.File file = new java.io.File(uri);
3674 e.printStackTrace();
3681 for (int i = 0; i < files.size(); i++)
3683 loadJalviewDataFile(files.get(i).toString());
3686 catch (Exception ex)
3688 ex.printStackTrace();
3693 // This method will attempt to load a "dropped" file first by testing
3694 // whether its and Annotation file, then features file. If both are
3695 // false then the user may have dropped an alignment file onto this
3697 public void loadJalviewDataFile(String file)
3701 String protocol = "File";
3703 if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
3708 boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
3709 alignment, file, protocol);
3713 boolean isGroupsFile = parseFeaturesFile(file,protocol);
3716 String format = new IdentifyFile().Identify(file, protocol);
3718 if(format.equalsIgnoreCase("JnetFile"))
3720 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
3722 new JnetAnnotationMaker().add_annotation(predictions,
3723 viewport.getAlignment(),
3725 alignPanel.adjustAnnotationHeight();
3726 alignPanel.paintAlignment(true);
3730 new FileLoader().LoadFile(viewport, file, protocol, format);
3737 alignPanel.adjustAnnotationHeight();
3738 buildSortByAnnotationScoresMenu();
3742 catch (Exception ex)
3744 ex.printStackTrace();
3748 public void tabSelectionChanged(int index)
3752 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
3753 viewport = alignPanel.av;
3754 setMenusFromViewport(viewport);
3758 public void tabbedPane_mousePressed(MouseEvent e)
3760 if(SwingUtilities.isRightMouseButton(e))
3762 String reply = JOptionPane.showInternalInputDialog(this,
3765 JOptionPane.QUESTION_MESSAGE);
3769 viewport.viewName = reply;
3770 tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
3776 public AlignViewport getCurrentView()
3783 * Open the dialog for regex description parsing.
3785 protected void extractScores_actionPerformed(ActionEvent e)
3787 ParseProperties pp = new jalview.analysis.ParseProperties(viewport.alignment);
3788 if (pp.getScoresFromDescription("col", "score column ", "\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)")>0)
3790 buildSortByAnnotationScoresMenu();
3799 public PrintThread(AlignmentPanel ap)
3803 static PageFormat pf;
3806 PrinterJob printJob = PrinterJob.getPrinterJob();
3810 printJob.setPrintable(ap, pf);
3814 printJob.setPrintable(ap);
3817 if (printJob.printDialog())
3823 catch (Exception PrintException)
3825 PrintException.printStackTrace();