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);
507 setShowProductsEnabled();
513 * Need to call this method when tabs are selected for multiple views,
514 * or when loading from Jalview2XML.java
515 * @param av AlignViewport
517 void setMenusFromViewport(AlignViewport av)
519 padGapsMenuitem.setSelected(av.padGaps);
520 colourTextMenuItem.setSelected(av.showColourText);
521 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
522 conservationMenuItem.setSelected(av.getConservationSelected());
523 seqLimits.setSelected(av.getShowJVSuffix());
524 idRightAlign.setSelected(av.rightAlignIds);
525 renderGapsMenuItem.setSelected(av.renderGaps);
526 wrapMenuItem.setSelected(av.wrapAlignment);
527 scaleAbove.setVisible(av.wrapAlignment);
528 scaleLeft.setVisible(av.wrapAlignment);
529 scaleRight.setVisible(av.wrapAlignment);
530 annotationPanelMenuItem.setState(av.showAnnotation);
531 viewBoxesMenuItem.setSelected(av.showBoxes);
532 viewTextMenuItem.setSelected(av.showText);
534 setColourSelected(ColourSchemeProperty.
535 getColourName(av.getGlobalColourScheme()));
537 showSeqFeatures.setSelected(av.showSequenceFeatures);
538 hiddenMarkers.setState(av.showHiddenMarkers);
539 applyToAllGroups.setState(av.colourAppliesToAllGroups);
545 Hashtable progressBars;
546 public void setProgressBar(String message, long id)
548 if(progressBars == null)
550 progressBars = new Hashtable();
553 JPanel progressPanel;
554 GridLayout layout = (GridLayout) statusPanel.getLayout();
555 if(progressBars.get( new Long(id) )!=null)
557 progressPanel = (JPanel)progressBars.get( new Long(id) );
558 statusPanel.remove(progressPanel);
559 progressBars.remove( progressPanel );
560 progressPanel = null;
563 statusBar.setText(message);
566 layout.setRows(layout.getRows() - 1);
570 progressPanel = new JPanel(new BorderLayout(10, 5));
572 JProgressBar progressBar = new JProgressBar();
573 progressBar.setIndeterminate(true);
575 progressPanel.add(new JLabel(message), BorderLayout.WEST);
576 progressPanel.add(progressBar, BorderLayout.CENTER);
578 layout.setRows(layout.getRows() + 1);
579 statusPanel.add(progressPanel);
581 progressBars.put(new Long(id), progressPanel);
591 Added so Castor Mapping file can obtain Jalview Version
593 public String getVersion()
595 return jalview.bin.Cache.getProperty("VERSION");
598 public FeatureRenderer getFeatureRenderer()
600 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
604 public void fetchSequence_actionPerformed(ActionEvent e)
606 new SequenceFetcher(this);
609 public void addFromFile_actionPerformed(ActionEvent e)
611 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
614 public void reload_actionPerformed(ActionEvent e)
618 if(currentFileFormat.equals("Jalview"))
620 JInternalFrame [] frames = Desktop.desktop.getAllFrames();
621 for(int i=0; i<frames.length; i++)
623 if (frames[i] instanceof AlignFrame
625 && ( (AlignFrame) frames[i]).fileName.equals(fileName))
629 frames[i].setSelected(true);
630 Desktop.instance.closeAssociatedWindows();
632 catch (java.beans.PropertyVetoException ex)
637 Desktop.instance.closeAssociatedWindows();
639 FileLoader loader = new FileLoader();
640 String protocol = fileName.startsWith("http:")? "URL":"File";
641 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
645 Rectangle bounds = this.getBounds();
647 FileLoader loader = new FileLoader();
648 String protocol = fileName.startsWith("http:") ? "URL" : "File";
649 AlignFrame newframe =
650 loader.LoadFileWaitTillLoaded(fileName, protocol, currentFileFormat);
652 newframe.setBounds(bounds);
654 this.closeMenuItem_actionPerformed(true);
660 public void addFromText_actionPerformed(ActionEvent e)
662 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
665 public void addFromURL_actionPerformed(ActionEvent e)
667 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
671 public void save_actionPerformed(ActionEvent e)
674 || currentFileFormat==null
675 || fileName.startsWith("http")
678 saveAs_actionPerformed(null);
682 saveAlignment(fileName, currentFileFormat);
689 * @param e DOCUMENT ME!
691 public void saveAs_actionPerformed(ActionEvent e)
693 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
694 getProperty( "LAST_DIRECTORY"),
696 { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" },
698 { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
703 chooser.setFileView(new JalviewFileView());
704 chooser.setDialogTitle("Save Alignment to file");
705 chooser.setToolTipText("Save");
707 int value = chooser.showSaveDialog(this);
709 if (value == JalviewFileChooser.APPROVE_OPTION)
711 currentFileFormat = chooser.getSelectedFormat();
712 if (currentFileFormat == null)
714 JOptionPane.showInternalMessageDialog(Desktop.desktop,
715 "You must select a file format before saving!",
716 "File format not specified",
717 JOptionPane.WARNING_MESSAGE);
718 value = chooser.showSaveDialog(this);
722 fileName = chooser.getSelectedFile().getPath();
724 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
727 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
729 saveAlignment(fileName, currentFileFormat);
733 public boolean saveAlignment(String file, String format)
735 boolean success = true;
737 if (format.equalsIgnoreCase("Jalview"))
739 String shortName = title;
741 if (shortName.indexOf(java.io.File.separatorChar) > -1)
743 shortName = shortName.substring(shortName.lastIndexOf(
744 java.io.File.separatorChar) + 1);
747 success = new Jalview2XML().SaveAlignment(this, file, shortName);
749 statusBar.setText("Successfully saved to file: "
751 +format +" format.");
757 String[] omitHidden = null;
759 if (viewport.hasHiddenColumns)
761 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
762 "The Alignment contains hidden columns."
763 + "\nDo you want to save only the visible alignment?",
764 "Save / Omit Hidden Columns",
765 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
767 if (reply == JOptionPane.YES_OPTION)
769 omitHidden = viewport.getViewAsString(false);
773 String output = new FormatAdapter().formatSequences(
775 viewport.alignment.getSequencesArray(),
786 java.io.PrintWriter out = new java.io.PrintWriter(
787 new java.io.FileWriter(file));
792 statusBar.setText("Successfully saved to file: "
794 + format + " format.");
799 ex.printStackTrace();
806 JOptionPane.showInternalMessageDialog(
807 this, "Couldn't save file: " + fileName,
809 JOptionPane.WARNING_MESSAGE);
818 * @param e DOCUMENT ME!
820 protected void outputText_actionPerformed(ActionEvent e)
822 String [] omitHidden = null;
824 if(viewport.hasHiddenColumns)
826 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
827 "The Alignment contains hidden columns."
828 +"\nDo you want to output only the visible alignment?",
829 "Save / Omit Hidden Columns",
830 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
832 if(reply==JOptionPane.YES_OPTION)
834 omitHidden = viewport.getViewAsString(false);
838 CutAndPasteTransfer cap = new CutAndPasteTransfer();
839 cap.setForInput(null);
840 Desktop.addInternalFrame(cap,
841 "Alignment output - " + e.getActionCommand(), 600,
845 cap.setText(new FormatAdapter().formatSequences(
846 e.getActionCommand(),
847 viewport.alignment.getSequencesArray(),
854 * @param e DOCUMENT ME!
856 protected void htmlMenuItem_actionPerformed(ActionEvent e)
858 new HTMLOutput(alignPanel,
859 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
860 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
863 public void createImageMap(File file, String image)
865 alignPanel.makePNGImageMap(file, image);
871 * @param e DOCUMENT ME!
873 public void createPNG(File f)
875 alignPanel.makePNG(f);
881 * @param e DOCUMENT ME!
883 public void createEPS(File f)
885 alignPanel.makeEPS(f);
889 public void pageSetup_actionPerformed(ActionEvent e)
891 PrinterJob printJob = PrinterJob.getPrinterJob();
892 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
898 * @param e DOCUMENT ME!
900 public void printMenuItem_actionPerformed(ActionEvent e)
902 //Putting in a thread avoids Swing painting problems
903 PrintThread thread = new PrintThread(alignPanel);
907 public void exportFeatures_actionPerformed(ActionEvent e)
909 new AnnotationExporter().exportFeatures(alignPanel);
913 public void exportAnnotations_actionPerformed(ActionEvent e)
915 new AnnotationExporter().exportAnnotations(
917 viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
918 viewport.alignment.getGroups(),
919 ((Alignment)viewport.alignment).alignmentProperties
924 public void associatedData_actionPerformed(ActionEvent e)
926 // Pick the tree file
927 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
930 chooser.setFileView(new JalviewFileView());
931 chooser.setDialogTitle("Load Jalview Annotations or Features File");
932 chooser.setToolTipText("Load Jalview Annotations / Features file");
934 int value = chooser.showOpenDialog(null);
936 if (value == JalviewFileChooser.APPROVE_OPTION)
938 String choice = chooser.getSelectedFile().getPath();
939 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
940 loadJalviewDataFile(choice);
949 * @param e DOCUMENT ME!
951 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
953 if(alignPanels!=null && alignPanels.size()<2)
960 if(alignPanels!=null)
964 for (int i = 0; i < alignPanels.size(); i++)
966 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
967 jalview.structure.StructureSelectionManager.getStructureSelectionManager()
968 .removeStructureViewerListener(ap.seqPanel, null);
969 PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
970 PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
971 PaintRefresher.RemoveComponent(ap);
972 ap.av.alignment = null;
977 int index = tabbedPane.getSelectedIndex();
979 alignPanels.removeElement(alignPanel);
980 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
981 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
982 PaintRefresher.RemoveComponent(alignPanel);
983 viewport.alignment = null;
987 tabbedPane.removeTabAt(index);
988 tabbedPane.validate();
990 if(index==tabbedPane.getTabCount())
995 this.tabSelectionChanged(index);
1001 this.setClosed(true);
1004 catch (Exception ex)
1006 ex.printStackTrace();
1014 void updateEditMenuBar()
1017 if (viewport.historyList.size() > 0)
1019 undoMenuItem.setEnabled(true);
1020 CommandI command = (CommandI) viewport.historyList.peek();
1021 undoMenuItem.setText("Undo " + command.getDescription());
1025 undoMenuItem.setEnabled(false);
1026 undoMenuItem.setText("Undo");
1029 if (viewport.redoList.size() > 0)
1031 redoMenuItem.setEnabled(true);
1033 CommandI command = (CommandI) viewport.redoList.peek();
1034 redoMenuItem.setText("Redo " + command.getDescription());
1038 redoMenuItem.setEnabled(false);
1039 redoMenuItem.setText("Redo");
1044 public void addHistoryItem(CommandI command)
1046 if(command.getSize()>0)
1048 viewport.historyList.push(command);
1049 viewport.redoList.clear();
1050 updateEditMenuBar();
1051 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1057 * @return alignment objects for all views
1059 AlignmentI[] getViewAlignments()
1061 if (alignPanels!=null)
1063 Enumeration e = alignPanels.elements();
1064 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1065 for (int i=0; e.hasMoreElements(); i++)
1067 als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1073 return new AlignmentI[] { viewport.alignment };
1080 * @param e DOCUMENT ME!
1082 protected void undoMenuItem_actionPerformed(ActionEvent e)
1084 if (viewport.historyList.empty())
1086 CommandI command = (CommandI)viewport.historyList.pop();
1087 viewport.redoList.push(command);
1088 command.undoCommand(getViewAlignments());
1090 AlignViewport originalSource = getOriginatingSource(command);
1091 updateEditMenuBar();
1093 if(originalSource!=null)
1095 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1096 originalSource.firePropertyChange("alignment",
1098 originalSource.alignment.getSequences());
1105 * @param e DOCUMENT ME!
1107 protected void redoMenuItem_actionPerformed(ActionEvent e)
1109 if(viewport.redoList.size()<1)
1114 CommandI command = (CommandI) viewport.redoList.pop();
1115 viewport.historyList.push(command);
1116 command.doCommand(getViewAlignments());
1118 AlignViewport originalSource = getOriginatingSource(command);
1119 updateEditMenuBar();
1121 if(originalSource!=null)
1123 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1124 originalSource.firePropertyChange("alignment",
1126 originalSource.alignment.getSequences());
1130 AlignViewport getOriginatingSource(CommandI command)
1132 AlignViewport originalSource = null;
1133 //For sequence removal and addition, we need to fire
1134 //the property change event FROM the viewport where the
1135 //original alignment was altered
1137 if (command instanceof EditCommand)
1139 EditCommand editCommand = (EditCommand) command;
1140 al = editCommand.getAlignment();
1141 Vector comps = (Vector) PaintRefresher.components
1142 .get(viewport.getSequenceSetId());
1144 for (int i = 0; i < comps.size(); i++)
1146 if (comps.elementAt(i) instanceof AlignmentPanel)
1148 if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
1150 originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
1157 if (originalSource == null)
1159 //The original view is closed, we must validate
1160 //the current view against the closed view first
1163 PaintRefresher.validateSequences(al, viewport.alignment);
1166 originalSource = viewport;
1169 return originalSource;
1175 * @param up DOCUMENT ME!
1177 public void moveSelectedSequences(boolean up)
1179 SequenceGroup sg = viewport.getSelectionGroup();
1188 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1190 SequenceI seq = viewport.alignment.getSequenceAt(i);
1192 if (!sg.getSequences(null).contains(seq))
1197 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1199 if (sg.getSequences(null).contains(temp))
1204 viewport.alignment.getSequences().setElementAt(temp, i);
1205 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1210 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1212 SequenceI seq = viewport.alignment.getSequenceAt(i);
1214 if (!sg.getSequences(null).contains(seq))
1219 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1221 if (sg.getSequences(null).contains(temp))
1226 viewport.alignment.getSequences().setElementAt(temp, i);
1227 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1231 alignPanel.paintAlignment(true);
1237 synchronized void slideSequences(boolean right, int size)
1239 Vector sg = new Vector();
1240 if(viewport.cursorMode)
1242 sg.addElement(viewport.alignment.getSequenceAt(
1243 alignPanel.seqPanel.seqCanvas.cursorY));
1245 else if(viewport.getSelectionGroup()!=null
1246 && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight())
1248 sg = viewport.getSelectionGroup().getSequences(
1249 viewport.hiddenRepSequences);
1257 Vector invertGroup = new Vector();
1259 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1261 if(!sg.contains(viewport.alignment.getSequenceAt(i)))
1262 invertGroup.add(viewport.alignment.getSequenceAt(i));
1265 SequenceI[] seqs1 = new SequenceI[sg.size()];
1266 for (int i = 0; i < sg.size(); i++)
1267 seqs1[i] = (SequenceI) sg.elementAt(i);
1269 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1270 for (int i = 0; i < invertGroup.size(); i++)
1271 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1273 SlideSequencesCommand ssc;
1275 ssc = new SlideSequencesCommand("Slide Sequences",
1277 viewport.getGapCharacter()
1280 ssc = new SlideSequencesCommand("Slide Sequences",
1282 viewport.getGapCharacter()
1285 int groupAdjustment = 0;
1286 if (ssc.getGapsInsertedBegin() && right)
1288 if (viewport.cursorMode)
1289 alignPanel.seqPanel.moveCursor(size, 0);
1291 groupAdjustment = size;
1293 else if (!ssc.getGapsInsertedBegin() && !right)
1295 if (viewport.cursorMode)
1296 alignPanel.seqPanel.moveCursor( -size, 0);
1298 groupAdjustment = -size;
1301 if (groupAdjustment != 0)
1303 viewport.getSelectionGroup().setStartRes(
1304 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1305 viewport.getSelectionGroup().setEndRes(
1306 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1310 boolean appendHistoryItem = false;
1311 if(viewport.historyList!=null
1312 && viewport.historyList.size()>0
1313 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1315 appendHistoryItem = ssc.appendSlideCommand(
1316 (SlideSequencesCommand)viewport.historyList.peek())
1320 if(!appendHistoryItem)
1321 addHistoryItem(ssc);
1330 * @param e DOCUMENT ME!
1332 protected void copy_actionPerformed(ActionEvent e)
1335 if (viewport.getSelectionGroup() == null)
1339 // TODO: preserve the ordering of displayed alignment annotation in any internal paste (particularly sequence associated annotation)
1340 SequenceI [] seqs = viewport.getSelectionAsNewSequence();
1341 String[] omitHidden = null;
1343 if (viewport.hasHiddenColumns)
1345 omitHidden = viewport.getViewAsString(true);
1348 String output = new FormatAdapter().formatSequences(
1353 StringSelection ss = new StringSelection(output);
1357 jalview.gui.Desktop.internalCopy = true;
1358 //Its really worth setting the clipboard contents
1359 //to empty before setting the large StringSelection!!
1360 Toolkit.getDefaultToolkit().getSystemClipboard()
1361 .setContents(new StringSelection(""), null);
1363 Toolkit.getDefaultToolkit().getSystemClipboard()
1364 .setContents(ss, Desktop.instance);
1366 catch (OutOfMemoryError er)
1368 er.printStackTrace();
1369 javax.swing.SwingUtilities.invokeLater(new Runnable()
1373 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1374 "Out of memory copying region!!"
1376 "\nSee help files for increasing Java Virtual Machine memory."
1378 javax.swing.JOptionPane.WARNING_MESSAGE);
1385 Vector hiddenColumns = null;
1386 if(viewport.hasHiddenColumns)
1388 hiddenColumns =new Vector();
1389 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1390 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
1393 int[] region = (int[])
1394 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
1396 hiddenColumns.addElement(new int[]
1397 {region[0] - hiddenOffset,
1398 region[1]-hiddenOffset});
1402 Desktop.jalviewClipboard = new Object[]
1405 viewport.alignment.getDataset(),
1407 statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
1413 * @param e DOCUMENT ME!
1415 protected void pasteNew_actionPerformed(ActionEvent e)
1423 * @param e DOCUMENT ME!
1425 protected void pasteThis_actionPerformed(ActionEvent e)
1433 * @param newAlignment DOCUMENT ME!
1435 void paste(boolean newAlignment)
1437 boolean externalPaste=true;
1440 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1441 Transferable contents = c.getContents(this);
1443 if (contents == null)
1451 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1452 if (str.length() < 1)
1457 format = new IdentifyFile().Identify(str, "Paste");
1460 catch (OutOfMemoryError er)
1462 er.printStackTrace();
1463 javax.swing.SwingUtilities.invokeLater(new Runnable()
1467 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1468 "Out of memory pasting sequences!!"
1470 "\nSee help files for increasing Java Virtual Machine memory."
1472 javax.swing.JOptionPane.WARNING_MESSAGE);
1479 SequenceI[] sequences;
1480 boolean annotationAdded = false;
1481 AlignmentI alignment = null;
1483 if(Desktop.jalviewClipboard!=null)
1485 // The clipboard was filled from within Jalview, we must use the sequences
1486 // And dataset from the copied alignment
1487 SequenceI[] newseq = (SequenceI[])Desktop.jalviewClipboard[0];
1488 // be doubly sure that we create *new* sequence objects.
1489 sequences = new SequenceI[newseq.length];
1490 for (int i=0;i<newseq.length;i++) {
1491 sequences[i] = new Sequence(newseq[i]);
1493 alignment = new Alignment(sequences);
1494 externalPaste = false;
1498 // parse the clipboard as an alignment.
1499 alignment = new FormatAdapter().readFile(str, "Paste", format);
1500 sequences = alignment.getSequencesArray();
1508 if (Desktop.jalviewClipboard != null)
1510 // dataset is inherited
1511 alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
1515 // new dataset is constructed
1516 alignment.setDataset(null);
1518 alwidth = alignment.getWidth()+1;
1522 AlignmentI pastedal = alignment; // preserve pasted alignment object
1523 // Add pasted sequences and dataset into existing alignment.
1524 alignment = viewport.getAlignment();
1525 alwidth = alignment.getWidth()+1;
1526 // decide if we need to import sequences from an existing dataset
1527 boolean importDs = Desktop.jalviewClipboard != null
1528 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1529 // importDs==true instructs us to copy over new dataset sequences from
1530 // an existing alignment
1531 Vector newDs = (importDs) ? new Vector() : null; // used to create
1532 // minimum dataset set
1534 for (int i = 0; i < sequences.length; i++)
1538 newDs.addElement(null);
1540 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1542 if (importDs && ds != null)
1544 if (!newDs.contains(ds))
1546 newDs.setElementAt(ds, i);
1547 ds = new Sequence(ds);
1548 // update with new dataset sequence
1549 sequences[i].setDatasetSequence(ds);
1553 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1558 // copy and derive new dataset sequence
1559 sequences[i] = sequences[i].deriveSequence();
1560 alignment.getDataset().addSequence(sequences[i].getDatasetSequence());
1561 // TODO: avoid creation of duplicate dataset sequences with a
1562 // 'contains' method using SequenceI.equals()/SequenceI.contains()
1564 alignment.addSequence(sequences[i]); // merges dataset
1568 newDs.clear(); // tidy up
1570 if (pastedal.getAlignmentAnnotation()!=null) {
1571 // Add any annotation attached to alignment.
1572 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1573 for (int i=0; i<alann.length; i++)
1575 annotationAdded=true;
1576 if (alann[i].sequenceRef==null && !alann[i].autoCalculated) {
1577 AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1578 newann.padAnnotation(alwidth);
1579 alignment.addAnnotation(newann);
1584 if (!newAlignment) {
1588 addHistoryItem(new EditCommand(
1593 alignment.getWidth(),
1597 // Add any annotations attached to sequences
1598 for (int i = 0; i < sequences.length; i++)
1600 if (sequences[i].getAnnotation() != null)
1602 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1604 annotationAdded=true;
1605 sequences[i].getAnnotation()[a].adjustForAlignment();
1606 sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1607 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation was duplicated earlier
1608 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1612 if (!newAlignment) {
1614 // propagate alignment changed.
1615 viewport.setEndSeq(alignment.getHeight());
1616 if (annotationAdded)
1618 // Duplicate sequence annotation in all views.
1619 AlignmentI[] alview = this.getViewAlignments();
1620 for (int i = 0; i < sequences.length; i++)
1622 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1625 for (int avnum=0;avnum<alview.length; avnum++)
1627 if (alview[avnum]!=alignment)
1629 // duplicate in a view other than the one with input focus
1630 int avwidth = alview[avnum].getWidth()+1;
1631 // this relies on sann being preserved after we
1632 // modify the sequence's annotation array for each duplication
1633 for (int a=0; a<sann.length; a++)
1635 AlignmentAnnotation newann = new AlignmentAnnotation(sann[a]);
1636 sequences[i].addAlignmentAnnotation(newann);
1637 newann.padAnnotation(avwidth);
1638 alview[avnum].addAnnotation(newann); // annotation was duplicated earlier
1639 alview[avnum].setAnnotationIndex(newann, a);
1644 buildSortByAnnotationScoresMenu();
1646 viewport.firePropertyChange("alignment", null, alignment.getSequences());
1649 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
1650 String newtitle = new String("Copied sequences");
1652 if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
1654 Vector hc = (Vector)Desktop.jalviewClipboard[2];
1655 for(int i=0; i<hc.size(); i++)
1657 int [] region = (int[]) hc.elementAt(i);
1658 af.viewport.hideColumns(region[0], region[1]);
1663 //>>>This is a fix for the moment, until a better solution is found!!<<<
1664 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
1665 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1667 // TODO: maintain provenance of an alignment, rather than just make the title a concatenation of operations.
1668 if (!externalPaste) {
1669 if (title.startsWith("Copied sequences"))
1675 newtitle = newtitle.concat("- from " + title);
1678 newtitle = new String("Pasted sequences");
1681 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1688 catch (Exception ex)
1690 ex.printStackTrace();
1691 System.out.println("Exception whilst pasting: "+ex);
1692 // could be anything being pasted in here
1701 * @param e DOCUMENT ME!
1703 protected void cut_actionPerformed(ActionEvent e)
1705 copy_actionPerformed(null);
1706 delete_actionPerformed(null);
1712 * @param e DOCUMENT ME!
1714 protected void delete_actionPerformed(ActionEvent evt)
1717 SequenceGroup sg = viewport.getSelectionGroup();
1723 Vector seqs = new Vector();
1725 for (int i = 0; i < sg.getSize(); i++)
1727 seq = sg.getSequenceAt(i);
1728 seqs.addElement(seq);
1732 // If the cut affects all sequences, remove highlighted columns
1733 if (sg.getSize() == viewport.alignment.getHeight())
1735 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1736 sg.getEndRes() + 1);
1740 SequenceI [] cut = new SequenceI[seqs.size()];
1741 for(int i=0; i<seqs.size(); i++)
1743 cut[i] = (SequenceI)seqs.elementAt(i);
1750 addHistoryItem(new EditCommand("Cut Sequences",
1754 sg.getEndRes()-sg.getStartRes()+1,
1755 viewport.alignment));
1758 viewport.setSelectionGroup(null);
1759 viewport.alignment.deleteGroup(sg);
1761 viewport.firePropertyChange("alignment", null,
1762 viewport.getAlignment().getSequences());
1764 if (viewport.getAlignment().getHeight() < 1)
1768 this.setClosed(true);
1770 catch (Exception ex)
1779 * @param e DOCUMENT ME!
1781 protected void deleteGroups_actionPerformed(ActionEvent e)
1783 viewport.alignment.deleteAllGroups();
1784 viewport.sequenceColours = null;
1785 viewport.setSelectionGroup(null);
1786 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1787 alignPanel.paintAlignment(true);
1793 * @param e DOCUMENT ME!
1795 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1797 SequenceGroup sg = new SequenceGroup();
1799 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1802 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1805 sg.setEndRes(viewport.alignment.getWidth() - 1);
1806 viewport.setSelectionGroup(sg);
1807 alignPanel.paintAlignment(true);
1808 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1814 * @param e DOCUMENT ME!
1816 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1818 if(viewport.cursorMode)
1820 alignPanel.seqPanel.keyboardNo1 = null;
1821 alignPanel.seqPanel.keyboardNo2 = null;
1823 viewport.setSelectionGroup(null);
1824 viewport.getColumnSelection().clear();
1825 viewport.setSelectionGroup(null);
1826 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1827 alignPanel.idPanel.idCanvas.searchResults = null;
1828 alignPanel.paintAlignment(true);
1829 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1835 * @param e DOCUMENT ME!
1837 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1839 SequenceGroup sg = viewport.getSelectionGroup();
1843 selectAllSequenceMenuItem_actionPerformed(null);
1848 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1851 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1854 alignPanel.paintAlignment(true);
1856 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1859 public void invertColSel_actionPerformed(ActionEvent e)
1861 viewport.invertColumnSelection();
1862 alignPanel.paintAlignment(true);
1869 * @param e DOCUMENT ME!
1871 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1873 trimAlignment(true);
1879 * @param e DOCUMENT ME!
1881 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
1883 trimAlignment(false);
1886 void trimAlignment(boolean trimLeft)
1888 ColumnSelection colSel = viewport.getColumnSelection();
1891 if (colSel.size() > 0)
1895 column = colSel.getMin();
1899 column = colSel.getMax();
1903 if(viewport.getSelectionGroup()!=null)
1905 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
1906 hiddenRepSequences);
1910 seqs = viewport.alignment.getSequencesArray();
1914 TrimRegionCommand trimRegion;
1917 trimRegion = new TrimRegionCommand("Remove Left",
1918 TrimRegionCommand.TRIM_LEFT,
1923 viewport.selectionGroup);
1924 viewport.setStartRes(0);
1928 trimRegion = new TrimRegionCommand("Remove Right",
1929 TrimRegionCommand.TRIM_RIGHT,
1934 viewport.selectionGroup);
1937 statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
1940 addHistoryItem(trimRegion);
1942 Vector groups = viewport.alignment.getGroups();
1944 for (int i = 0; i < groups.size(); i++)
1946 SequenceGroup sg = (SequenceGroup) groups.get(i);
1948 if ( (trimLeft && !sg.adjustForRemoveLeft(column))
1949 || (!trimLeft && !sg.adjustForRemoveRight(column)))
1951 viewport.alignment.deleteGroup(sg);
1955 viewport.firePropertyChange("alignment", null,
1956 viewport.getAlignment().getSequences());
1963 * @param e DOCUMENT ME!
1965 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1967 int start = 0, end = viewport.alignment.getWidth()-1;
1970 if (viewport.getSelectionGroup() != null)
1972 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
1973 hiddenRepSequences);
1974 start = viewport.getSelectionGroup().getStartRes();
1975 end = viewport.getSelectionGroup().getEndRes();
1979 seqs = viewport.alignment.getSequencesArray();
1983 RemoveGapColCommand removeGapCols =
1984 new RemoveGapColCommand("Remove Gapped Columns",
1987 viewport.alignment);
1989 addHistoryItem(removeGapCols);
1991 statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
1993 //This is to maintain viewport position on first residue
1995 SequenceI seq = viewport.alignment.getSequenceAt(0);
1996 int startRes = seq.findPosition(viewport.startRes);
1997 // ShiftList shifts;
1998 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
1999 // edit.alColumnChanges=shifts.getInverse();
2000 // if (viewport.hasHiddenColumns)
2001 // viewport.getColumnSelection().compensateForEdits(shifts);
2002 viewport.setStartRes(seq.findIndex(startRes)-1);
2003 viewport.firePropertyChange("alignment", null,
2004 viewport.getAlignment().getSequences());
2011 * @param e DOCUMENT ME!
2013 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2015 int start = 0, end = viewport.alignment.getWidth()-1;
2018 if (viewport.getSelectionGroup() != null)
2020 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
2021 hiddenRepSequences);
2022 start = viewport.getSelectionGroup().getStartRes();
2023 end = viewport.getSelectionGroup().getEndRes();
2027 seqs = viewport.alignment.getSequencesArray();
2030 //This is to maintain viewport position on first residue
2032 SequenceI seq = viewport.alignment.getSequenceAt(0);
2033 int startRes = seq.findPosition(viewport.startRes);
2035 addHistoryItem(new RemoveGapsCommand("Remove Gaps",
2038 viewport.alignment));
2040 viewport.setStartRes(seq.findIndex(startRes)-1);
2042 viewport.firePropertyChange("alignment", null,
2043 viewport.getAlignment().getSequences());
2050 * @param e DOCUMENT ME!
2052 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2054 viewport.padGaps = padGapsMenuitem.isSelected();
2056 viewport.firePropertyChange("alignment",
2058 viewport.getAlignment().getSequences());
2064 * @param e DOCUMENT ME!
2066 public void findMenuItem_actionPerformed(ActionEvent e)
2071 public void newView_actionPerformed(ActionEvent e)
2073 AlignmentPanel newap =
2074 new Jalview2XML().copyAlignPanel(alignPanel, true);
2076 newap.av.gatherViewsHere = false;
2078 if (viewport.viewName == null)
2080 viewport.viewName = "Original";
2083 newap.av.historyList = viewport.historyList;
2084 newap.av.redoList = viewport.redoList;
2086 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2087 String newViewName = "View " +index;
2089 Vector comps = (Vector) PaintRefresher.components.get(viewport.
2090 getSequenceSetId());
2091 Vector existingNames = new Vector();
2092 for(int i=0; i<comps.size(); i++)
2094 if(comps.elementAt(i) instanceof AlignmentPanel)
2096 AlignmentPanel ap = (AlignmentPanel)comps.elementAt(i);
2097 if(!existingNames.contains(ap.av.viewName))
2099 existingNames.addElement(ap.av.viewName);
2104 while(existingNames.contains(newViewName))
2106 newViewName = "View "+ (++index);
2109 newap.av.viewName = newViewName;
2111 addAlignmentPanel(newap, false);
2113 if(alignPanels.size()==2)
2115 viewport.gatherViewsHere = true;
2117 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2120 public void expandViews_actionPerformed(ActionEvent e)
2122 Desktop.instance.explodeViews(this);
2125 public void gatherViews_actionPerformed(ActionEvent e)
2127 Desktop.instance.gatherViews(this);
2135 * @param e DOCUMENT ME!
2137 public void font_actionPerformed(ActionEvent e)
2139 new FontChooser(alignPanel);
2146 * @param e DOCUMENT ME!
2148 protected void seqLimit_actionPerformed(ActionEvent e)
2150 viewport.setShowJVSuffix(seqLimits.isSelected());
2152 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
2153 alignPanel.paintAlignment(true);
2156 public void idRightAlign_actionPerformed(ActionEvent e)
2158 viewport.rightAlignIds = idRightAlign.isSelected();
2159 alignPanel.paintAlignment(true);
2167 * @param e DOCUMENT ME!
2169 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2171 viewport.setColourText(colourTextMenuItem.isSelected());
2172 alignPanel.paintAlignment(true);
2178 * @param e DOCUMENT ME!
2180 public void wrapMenuItem_actionPerformed(ActionEvent e)
2182 scaleAbove.setVisible(wrapMenuItem.isSelected());
2183 scaleLeft.setVisible(wrapMenuItem.isSelected());
2184 scaleRight.setVisible(wrapMenuItem.isSelected());
2185 viewport.setWrapAlignment(wrapMenuItem.isSelected());
2186 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2189 public void showAllSeqs_actionPerformed(ActionEvent e)
2191 viewport.showAllHiddenSeqs();
2194 public void showAllColumns_actionPerformed(ActionEvent e)
2196 viewport.showAllHiddenColumns();
2200 public void hideSelSequences_actionPerformed(ActionEvent e)
2202 viewport.hideAllSelectedSeqs();
2203 alignPanel.paintAlignment(true);
2206 public void hideSelColumns_actionPerformed(ActionEvent e)
2208 viewport.hideSelectedColumns();
2209 alignPanel.paintAlignment(true);
2212 public void hiddenMarkers_actionPerformed(ActionEvent e)
2214 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2221 * @param e DOCUMENT ME!
2223 protected void scaleAbove_actionPerformed(ActionEvent e)
2225 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2226 alignPanel.paintAlignment(true);
2232 * @param e DOCUMENT ME!
2234 protected void scaleLeft_actionPerformed(ActionEvent e)
2236 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2237 alignPanel.paintAlignment(true);
2243 * @param e DOCUMENT ME!
2245 protected void scaleRight_actionPerformed(ActionEvent e)
2247 viewport.setScaleRightWrapped(scaleRight.isSelected());
2248 alignPanel.paintAlignment(true);
2254 * @param e DOCUMENT ME!
2256 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2258 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2259 alignPanel.paintAlignment(true);
2265 * @param e DOCUMENT ME!
2267 public void viewTextMenuItem_actionPerformed(ActionEvent e)
2269 viewport.setShowText(viewTextMenuItem.isSelected());
2270 alignPanel.paintAlignment(true);
2276 * @param e DOCUMENT ME!
2278 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2280 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2281 alignPanel.paintAlignment(true);
2285 public FeatureSettings featureSettings;
2286 public void featureSettings_actionPerformed(ActionEvent e)
2288 if(featureSettings !=null )
2290 featureSettings.close();
2291 featureSettings = null;
2293 featureSettings = new FeatureSettings(this);
2299 * @param evt DOCUMENT ME!
2301 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2303 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2304 alignPanel.paintAlignment(true);
2305 if (alignPanel.getOverviewPanel() != null)
2307 alignPanel.getOverviewPanel().updateOverviewImage();
2314 * @param e DOCUMENT ME!
2316 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2318 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2319 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2322 public void alignmentProperties()
2324 JEditorPane editPane = new JEditorPane("text/html","");
2325 editPane.setEditable(false);
2326 StringBuffer contents = new StringBuffer("<html>");
2329 int min=Integer.MAX_VALUE, max=0;
2330 for(int i=0; i<viewport.alignment.getHeight(); i++)
2332 int size = viewport.alignment.getSequenceAt(i).getEnd()
2333 -viewport.alignment.getSequenceAt(i).getStart();
2340 avg = avg/(float)viewport.alignment.getHeight();
2342 contents.append("<br>Sequences: "+ viewport.alignment.getHeight());
2343 contents.append("<br>Minimum Sequence Length: "+min);
2344 contents.append("<br>Maximum Sequence Length: "+max);
2345 contents.append("<br>Average Length: "+(int)avg);
2347 if (((Alignment)viewport.alignment).getProperties() != null)
2349 Hashtable props = ((Alignment)viewport.alignment).getProperties();
2350 Enumeration en = props.keys();
2351 contents.append("<br><br><table border=\"1\">");
2352 while(en.hasMoreElements())
2354 String key = en.nextElement().toString();
2355 StringBuffer val = new StringBuffer();
2356 String vals = props.get(key).toString();
2359 npos = vals.indexOf("\n",pos);
2362 val.append(vals.substring(pos));
2364 val.append(vals.substring(pos, npos));
2369 contents.append("<tr><td>"+key+"</td><td>"+val+"</td></tr>");
2371 contents.append("</table>");
2373 editPane.setText(contents.toString()+"</html>");
2374 JInternalFrame frame = new JInternalFrame();
2375 frame.getContentPane().add(new JScrollPane(editPane));
2377 Desktop.instance.addInternalFrame(frame,"Alignment Properties: "+getTitle(),500,400);
2384 * @param e DOCUMENT ME!
2386 public void overviewMenuItem_actionPerformed(ActionEvent e)
2388 if (alignPanel.overviewPanel != null)
2393 JInternalFrame frame = new JInternalFrame();
2394 OverviewPanel overview = new OverviewPanel(alignPanel);
2395 frame.setContentPane(overview);
2396 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2397 frame.getWidth(), frame.getHeight());
2399 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2400 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2402 public void internalFrameClosed(
2403 javax.swing.event.InternalFrameEvent evt)
2405 alignPanel.setOverviewPanel(null);
2410 alignPanel.setOverviewPanel(overview);
2413 public void textColour_actionPerformed(ActionEvent e)
2415 new TextColourChooser().chooseColour(alignPanel, null);
2421 * @param e DOCUMENT ME!
2423 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2431 * @param e DOCUMENT ME!
2433 public void clustalColour_actionPerformed(ActionEvent e)
2435 changeColour(new ClustalxColourScheme(
2436 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
2442 * @param e DOCUMENT ME!
2444 public void zappoColour_actionPerformed(ActionEvent e)
2446 changeColour(new ZappoColourScheme());
2452 * @param e DOCUMENT ME!
2454 public void taylorColour_actionPerformed(ActionEvent e)
2456 changeColour(new TaylorColourScheme());
2462 * @param e DOCUMENT ME!
2464 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2466 changeColour(new HydrophobicColourScheme());
2472 * @param e DOCUMENT ME!
2474 public void helixColour_actionPerformed(ActionEvent e)
2476 changeColour(new HelixColourScheme());
2482 * @param e DOCUMENT ME!
2484 public void strandColour_actionPerformed(ActionEvent e)
2486 changeColour(new StrandColourScheme());
2492 * @param e DOCUMENT ME!
2494 public void turnColour_actionPerformed(ActionEvent e)
2496 changeColour(new TurnColourScheme());
2502 * @param e DOCUMENT ME!
2504 public void buriedColour_actionPerformed(ActionEvent e)
2506 changeColour(new BuriedColourScheme());
2512 * @param e DOCUMENT ME!
2514 public void nucleotideColour_actionPerformed(ActionEvent e)
2516 changeColour(new NucleotideColourScheme());
2519 public void annotationColour_actionPerformed(ActionEvent e)
2521 new AnnotationColourChooser(viewport, alignPanel);
2528 * @param e DOCUMENT ME!
2530 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2532 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2538 * @param cs DOCUMENT ME!
2540 public void changeColour(ColourSchemeI cs)
2546 if (viewport.getAbovePIDThreshold())
2548 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2551 cs.setThreshold(threshold,
2552 viewport.getIgnoreGapsConsensus());
2554 viewport.setGlobalColourScheme(cs);
2558 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2561 if (viewport.getConservationSelected())
2564 Alignment al = (Alignment) viewport.alignment;
2565 Conservation c = new Conservation("All",
2566 ResidueProperties.propHash, 3,
2567 al.getSequences(), 0,
2571 c.verdict(false, viewport.ConsPercGaps);
2573 cs.setConservation(c);
2575 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
2580 cs.setConservation(null);
2583 cs.setConsensus(viewport.hconsensus);
2586 viewport.setGlobalColourScheme(cs);
2588 if (viewport.getColourAppliesToAllGroups())
2590 Vector groups = viewport.alignment.getGroups();
2592 for (int i = 0; i < groups.size(); i++)
2594 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2602 if (cs instanceof ClustalxColourScheme)
2604 sg.cs = new ClustalxColourScheme(
2605 sg.getSequences(viewport.hiddenRepSequences), sg.getWidth());
2607 else if (cs instanceof UserColourScheme)
2609 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
2615 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2617 catch (Exception ex)
2622 if (viewport.getAbovePIDThreshold()
2623 || cs instanceof PIDColourScheme
2624 || cs instanceof Blosum62ColourScheme)
2626 sg.cs.setThreshold(threshold,
2627 viewport.getIgnoreGapsConsensus());
2629 sg.cs.setConsensus(AAFrequency.calculate(
2630 sg.getSequences(viewport.hiddenRepSequences), sg.getStartRes(),
2635 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2639 if (viewport.getConservationSelected())
2641 Conservation c = new Conservation("Group",
2642 ResidueProperties.propHash, 3,
2643 sg.getSequences(viewport.
2644 hiddenRepSequences),
2648 c.verdict(false, viewport.ConsPercGaps);
2649 sg.cs.setConservation(c);
2653 sg.cs.setConservation(null);
2658 if (alignPanel.getOverviewPanel() != null)
2660 alignPanel.getOverviewPanel().updateOverviewImage();
2666 alignPanel.paintAlignment(true);
2672 * @param e DOCUMENT ME!
2674 protected void modifyPID_actionPerformed(ActionEvent e)
2676 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
2678 SliderPanel.setPIDSliderSource(alignPanel,
2679 viewport.getGlobalColourScheme(),
2681 SliderPanel.showPIDSlider();
2688 * @param e DOCUMENT ME!
2690 protected void modifyConservation_actionPerformed(ActionEvent e)
2692 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
2694 SliderPanel.setConservationSlider(alignPanel,
2695 viewport.globalColourScheme,
2697 SliderPanel.showConservationSlider();
2704 * @param e DOCUMENT ME!
2706 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2708 viewport.setConservationSelected(conservationMenuItem.isSelected());
2710 viewport.setAbovePIDThreshold(false);
2711 abovePIDThreshold.setSelected(false);
2713 changeColour(viewport.getGlobalColourScheme());
2715 modifyConservation_actionPerformed(null);
2721 * @param e DOCUMENT ME!
2723 public void abovePIDThreshold_actionPerformed(ActionEvent e)
2725 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
2727 conservationMenuItem.setSelected(false);
2728 viewport.setConservationSelected(false);
2730 changeColour(viewport.getGlobalColourScheme());
2732 modifyPID_actionPerformed(null);
2738 * @param e DOCUMENT ME!
2740 public void userDefinedColour_actionPerformed(ActionEvent e)
2742 if (e.getActionCommand().equals("User Defined..."))
2744 new UserDefinedColours(alignPanel, null);
2748 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
2749 getUserColourSchemes().get(e.getActionCommand());
2755 public void updateUserColourMenu()
2758 Component[] menuItems = colourMenu.getMenuComponents();
2759 int i, iSize = menuItems.length;
2760 for (i = 0; i < iSize; i++)
2762 if (menuItems[i].getName() != null &&
2763 menuItems[i].getName().equals("USER_DEFINED"))
2765 colourMenu.remove(menuItems[i]);
2769 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
2771 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
2772 getUserColourSchemes().keys();
2774 while (userColours.hasMoreElements())
2776 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
2778 nextElement().toString());
2779 radioItem.setName("USER_DEFINED");
2780 radioItem.addMouseListener(new MouseAdapter()
2782 public void mousePressed(MouseEvent evt)
2784 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
2786 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
2788 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
2790 "Remove from default list?",
2791 "Remove user defined colour",
2792 JOptionPane.YES_NO_OPTION);
2793 if(option == JOptionPane.YES_OPTION)
2795 jalview.gui.UserDefinedColours.removeColourFromDefaults(
2796 radioItem.getText());
2797 colourMenu.remove(radioItem);
2801 radioItem.addActionListener(new ActionListener()
2803 public void actionPerformed(ActionEvent evt)
2805 userDefinedColour_actionPerformed(evt);
2812 radioItem.addActionListener(new ActionListener()
2814 public void actionPerformed(ActionEvent evt)
2816 userDefinedColour_actionPerformed(evt);
2820 colourMenu.insert(radioItem, 15);
2821 colours.add(radioItem);
2829 * @param e DOCUMENT ME!
2831 public void PIDColour_actionPerformed(ActionEvent e)
2833 changeColour(new PIDColourScheme());
2839 * @param e DOCUMENT ME!
2841 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
2843 changeColour(new Blosum62ColourScheme());
2849 * @param e DOCUMENT ME!
2851 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2853 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2854 AlignmentSorter.sortByPID(viewport.getAlignment(),
2855 viewport.getAlignment().getSequenceAt(0));
2856 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2857 viewport.alignment));
2858 alignPanel.paintAlignment(true);
2864 * @param e DOCUMENT ME!
2866 public void sortIDMenuItem_actionPerformed(ActionEvent e)
2868 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2869 AlignmentSorter.sortByID(viewport.getAlignment());
2870 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
2871 alignPanel.paintAlignment(true);
2877 * @param e DOCUMENT ME!
2879 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
2881 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2882 AlignmentSorter.sortByGroup(viewport.getAlignment());
2883 addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
2885 alignPanel.paintAlignment(true);
2890 * @param e DOCUMENT ME!
2892 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2894 new RedundancyPanel(alignPanel, this);
2901 * @param e DOCUMENT ME!
2903 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2905 if ( (viewport.getSelectionGroup() == null) ||
2906 (viewport.getSelectionGroup().getSize() < 2))
2908 JOptionPane.showInternalMessageDialog(this,
2909 "You must select at least 2 sequences.",
2910 "Invalid Selection",
2911 JOptionPane.WARNING_MESSAGE);
2915 JInternalFrame frame = new JInternalFrame();
2916 frame.setContentPane(new PairwiseAlignPanel(viewport));
2917 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
2924 * @param e DOCUMENT ME!
2926 public void PCAMenuItem_actionPerformed(ActionEvent e)
2928 if ( ( (viewport.getSelectionGroup() != null) &&
2929 (viewport.getSelectionGroup().getSize() < 4) &&
2930 (viewport.getSelectionGroup().getSize() > 0)) ||
2931 (viewport.getAlignment().getHeight() < 4))
2933 JOptionPane.showInternalMessageDialog(this,
2934 "Principal component analysis must take\n" +
2935 "at least 4 input sequences.",
2936 "Sequence selection insufficient",
2937 JOptionPane.WARNING_MESSAGE);
2942 new PCAPanel(alignPanel);
2946 public void autoCalculate_actionPerformed(ActionEvent e)
2948 viewport.autoCalculateConsensus = autoCalculate.isSelected();
2949 if(viewport.autoCalculateConsensus)
2951 viewport.firePropertyChange("alignment",
2953 viewport.getAlignment().getSequences());
2961 * @param e DOCUMENT ME!
2963 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2965 NewTreePanel("AV", "PID", "Average distance tree using PID");
2971 * @param e DOCUMENT ME!
2973 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2975 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2981 * @param e DOCUMENT ME!
2983 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2985 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2991 * @param e DOCUMENT ME!
2993 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2995 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3001 * @param type DOCUMENT ME!
3002 * @param pwType DOCUMENT ME!
3003 * @param title DOCUMENT ME!
3005 void NewTreePanel(String type, String pwType, String title)
3009 if (viewport.getSelectionGroup() != null)
3011 if (viewport.getSelectionGroup().getSize() < 3)
3013 JOptionPane.showMessageDialog(Desktop.desktop,
3014 "You need to have more than two sequences selected to build a tree!",
3015 "Not enough sequences",
3016 JOptionPane.WARNING_MESSAGE);
3021 SequenceGroup sg = viewport.getSelectionGroup();
3023 /* Decide if the selection is a column region */
3024 while (s < sg.getSize())
3026 if ( ( (SequenceI) sg.getSequences(null).elementAt(s++)).getLength() <
3029 JOptionPane.showMessageDialog(Desktop.desktop,
3030 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
3031 "Try using the Pad function in the edit menu,\n" +
3032 "or one of the multiple sequence alignment web services.",
3033 "Sequences in selection are not aligned",
3034 JOptionPane.WARNING_MESSAGE);
3040 title = title + " on region";
3041 tp = new TreePanel(alignPanel, type, pwType);
3045 //are the sequences aligned?
3046 if (!viewport.alignment.isAligned())
3048 JOptionPane.showMessageDialog(Desktop.desktop,
3049 "The sequences must be aligned before creating a tree.\n" +
3050 "Try using the Pad function in the edit menu,\n" +
3051 "or one of the multiple sequence alignment web services.",
3052 "Sequences not aligned",
3053 JOptionPane.WARNING_MESSAGE);
3058 if(viewport.alignment.getHeight()<2)
3063 tp = new TreePanel(alignPanel, type, pwType);
3068 if(viewport.viewName!=null)
3070 title+= viewport.viewName+" of ";
3073 title += this.title;
3075 Desktop.addInternalFrame(tp, title, 600, 500);
3081 * @param title DOCUMENT ME!
3082 * @param order DOCUMENT ME!
3084 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
3086 final JMenuItem item = new JMenuItem("by " + title);
3088 item.addActionListener(new java.awt.event.ActionListener()
3090 public void actionPerformed(ActionEvent e)
3092 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
3094 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
3095 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3097 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3098 viewport.alignment));
3100 alignPanel.paintAlignment(true);
3105 * Add a new sort by annotation score menu item
3106 * @param sort the menu to add the option to
3107 * @param scoreLabel the label used to retrieve scores for each sequence on the alignment
3109 public void addSortByAnnotScoreMenuItem(JMenu sort, final String scoreLabel)
3111 final JMenuItem item = new JMenuItem(scoreLabel);
3113 item.addActionListener(new java.awt.event.ActionListener()
3115 public void actionPerformed(ActionEvent e)
3117 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
3118 AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport.getAlignment());
3119 addHistoryItem(new OrderCommand("Sort by "+scoreLabel, oldOrder, viewport.alignment));
3120 alignPanel.paintAlignment(true);
3125 * last hash for alignment's annotation array - used to minimise cost of rebuild.
3127 protected int _annotationScoreVectorHash;
3129 * search the alignment and rebuild the sort by annotation score submenu
3130 * the last alignment annotation vector hash is stored to minimize
3131 * cost of rebuilding in subsequence calls.
3134 public void buildSortByAnnotationScoresMenu()
3136 if(viewport.alignment.getAlignmentAnnotation()==null)
3141 if (viewport.alignment.getAlignmentAnnotation().hashCode()!=_annotationScoreVectorHash)
3143 sortByAnnotScore.removeAll();
3144 // almost certainly a quicker way to do this - but we keep it simple
3145 Hashtable scoreSorts=new Hashtable();
3146 AlignmentAnnotation aann[];
3147 Enumeration sq = viewport.alignment.getSequences().elements();
3148 while (sq.hasMoreElements())
3150 aann = ((SequenceI) sq.nextElement()).getAnnotation();
3151 for (int i=0;aann!=null && i<aann.length; i++)
3153 if (aann[i].hasScore() && aann[i].sequenceRef!=null)
3155 scoreSorts.put(aann[i].label, aann[i].label);
3159 Enumeration labels = scoreSorts.keys();
3160 while (labels.hasMoreElements())
3162 addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels.nextElement());
3164 sortByAnnotScore.setVisible(scoreSorts.size()>0);
3167 _annotationScoreVectorHash =
3168 viewport.alignment.getAlignmentAnnotation().hashCode();
3173 * Maintain the Order by->Displayed Tree menu.
3174 * Creates a new menu item for a TreePanel with an appropriate
3175 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
3176 * to remove the menu item when the treePanel is closed, and adjust
3177 * the tree leaf to sequence mapping when the alignment is modified.
3178 * @param treePanel Displayed tree window.
3179 * @param title SortBy menu item title.
3181 public void buildTreeMenu()
3183 sortByTreeMenu.removeAll();
3185 Vector comps = (Vector) PaintRefresher.components.get(viewport.
3186 getSequenceSetId());
3187 Vector treePanels = new Vector();
3188 int i, iSize = comps.size();
3189 for(i=0; i<iSize; i++)
3191 if(comps.elementAt(i) instanceof TreePanel)
3193 treePanels.add(comps.elementAt(i));
3197 iSize = treePanels.size();
3201 sortByTreeMenu.setVisible(false);
3205 sortByTreeMenu.setVisible(true);
3207 for(i=0; i<treePanels.size(); i++)
3209 TreePanel tp = (TreePanel)treePanels.elementAt(i);
3210 final JMenuItem item = new JMenuItem(tp.getTitle());
3211 final NJTree tree = ((TreePanel)treePanels.elementAt(i)).getTree();
3212 item.addActionListener(new java.awt.event.ActionListener()
3214 public void actionPerformed(ActionEvent e)
3216 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3217 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
3219 addHistoryItem(new OrderCommand("Tree Sort",
3221 viewport.alignment));
3223 alignPanel.paintAlignment(true);
3227 sortByTreeMenu.add(item);
3232 * Work out whether the whole set of sequences
3233 * or just the selected set will be submitted for multiple alignment.
3236 private jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3238 // Now, check we have enough sequences
3239 AlignmentView msa = null;
3241 if ( (viewport.getSelectionGroup() != null) &&
3242 (viewport.getSelectionGroup().getSize() > 1))
3244 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
3245 /*SequenceGroup seqs = viewport.getSelectionGroup();
3247 msa = new SequenceI[sz = seqs.getSize(false)];
3249 for (int i = 0; i < sz; i++)
3251 msa[i] = (SequenceI) seqs.getSequenceAt(i);
3253 msa = viewport.getAlignmentView(true);
3257 /*Vector seqs = viewport.getAlignment().getSequences();
3259 if (seqs.size() > 1)
3261 msa = new SequenceI[seqs.size()];
3263 for (int i = 0; i < seqs.size(); i++)
3265 msa[i] = (SequenceI) seqs.elementAt(i);
3268 msa = viewport.getAlignmentView(false);
3274 * Decides what is submitted to a secondary structure prediction service,
3275 * the currently selected sequence, or the currently selected alignment
3276 * (where the first sequence in the set is the one that the prediction
3279 AlignmentView gatherSeqOrMsaForSecStrPrediction()
3281 AlignmentView seqs = null;
3283 if ( (viewport.getSelectionGroup() != null) &&
3284 (viewport.getSelectionGroup().getSize() > 0))
3286 seqs = viewport.getAlignmentView(true);
3290 seqs = viewport.getAlignmentView(false);
3292 // limit sequences - JBPNote in future - could spawn multiple prediction jobs
3293 // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3294 if (!viewport.alignment.isAligned())
3296 seqs.setSequences(new SeqCigar[]
3297 {seqs.getSequences()[0]});
3304 * @param e DOCUMENT ME!
3306 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3308 // Pick the tree file
3309 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
3312 chooser.setFileView(new JalviewFileView());
3313 chooser.setDialogTitle("Select a newick-like tree file");
3314 chooser.setToolTipText("Load a tree file");
3316 int value = chooser.showOpenDialog(null);
3318 if (value == JalviewFileChooser.APPROVE_OPTION)
3320 String choice = chooser.getSelectedFile().getPath();
3321 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3325 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
3327 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3329 catch (Exception ex)
3331 JOptionPane.showMessageDialog(Desktop.desktop,
3332 "Problem reading tree file",
3334 JOptionPane.WARNING_MESSAGE);
3335 ex.printStackTrace();
3341 public TreePanel ShowNewickTree(NewickFile nf, String title)
3343 return ShowNewickTree(nf,title,600,500,4,5);
3346 public TreePanel ShowNewickTree(NewickFile nf, String title,
3347 AlignmentView input)
3349 return ShowNewickTree(nf,title, input, 600,500,4,5);
3352 public TreePanel ShowNewickTree(NewickFile nf, String title, int w, int h,
3355 return ShowNewickTree(nf, title, null, w, h, x, y);
3358 * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
3360 * @param nf the tree
3361 * @param title tree viewer title
3362 * @param input Associated alignment input data (or null)
3367 * @return TreePanel handle
3369 public TreePanel ShowNewickTree(NewickFile nf, String title,
3370 AlignmentView input, int w, int h, int x,
3373 TreePanel tp = null;
3379 if (nf.getTree() != null)
3381 tp = new TreePanel(alignPanel,
3390 tp.setLocation(x,y);
3394 Desktop.addInternalFrame(tp, title, w, h);
3397 catch (Exception ex)
3399 ex.printStackTrace();
3407 * Generates menu items and listener event actions for web service clients
3410 public void BuildWebServiceMenu()
3412 if ( (Discoverer.services != null)
3413 && (Discoverer.services.size() > 0))
3415 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
3416 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
3417 Vector wsmenu = new Vector();
3418 final AlignFrame af = this;
3421 // Add any Multiple Sequence Alignment Services
3422 final JMenu msawsmenu = new JMenu("Alignment");
3423 for (int i = 0, j = msaws.size(); i < j; i++)
3425 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
3427 final JMenuItem method = new JMenuItem(sh.getName());
3428 method.addActionListener(new ActionListener()
3430 public void actionPerformed(ActionEvent e)
3432 AlignmentView msa = gatherSequencesForAlignment();
3433 new jalview.ws.MsaWSClient(sh, title, msa,
3435 viewport.getAlignment().getDataset(),
3441 msawsmenu.add(method);
3442 // Deal with services that we know accept partial alignments.
3443 if (sh.getName().indexOf("lustal") > -1)
3445 // We know that ClustalWS can accept partial alignments for refinement.
3446 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
3447 methodR.addActionListener(new ActionListener()
3449 public void actionPerformed(ActionEvent e)
3451 AlignmentView msa = gatherSequencesForAlignment();
3452 new jalview.ws.MsaWSClient(sh, title, msa,
3454 viewport.getAlignment().getDataset(),
3460 msawsmenu.add(methodR);
3464 wsmenu.add(msawsmenu);
3466 if (secstrpr != null)
3468 // Add any secondary structure prediction services
3469 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
3470 for (int i = 0, j = secstrpr.size(); i < j; i++)
3472 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
3474 final JMenuItem method = new JMenuItem(sh.getName());
3475 method.addActionListener(new ActionListener()
3477 public void actionPerformed(ActionEvent e)
3479 AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
3480 if (msa.getSequences().length == 1)
3482 // Single Sequence prediction
3483 new jalview.ws.JPredClient(sh, title, false, msa, af, true);
3487 if (msa.getSequences().length > 1)
3489 // Sequence profile based prediction
3490 new jalview.ws.JPredClient(sh,
3491 title, true, msa, af, true);
3496 secstrmenu.add(method);
3498 wsmenu.add(secstrmenu);
3500 resetWebServiceMenu();
3501 for (int i = 0, j = wsmenu.size(); i < j; i++)
3503 webService.add( (JMenu) wsmenu.get(i));
3508 resetWebServiceMenu();
3509 this.webService.add(this.webServiceNoServices);
3511 // TODO: add in rediscovery function
3512 // TODO: reduce code redundancy.
3513 // TODO: group services by location as well as function.
3518 * empty the web service menu and add any ad-hoc functions
3519 * not dynamically discovered.
3522 private void resetWebServiceMenu()
3524 webService.removeAll();
3525 // Temporary hack - DBRef Fetcher always top level ws entry.
3526 JMenuItem rfetch = new JMenuItem("Fetch DB References");
3527 rfetch.setToolTipText("Retrieve and parse uniprot records for the alignment or the currently selected sequences");
3528 webService.add(rfetch);
3529 rfetch.addActionListener(new ActionListener() {
3531 public void actionPerformed(ActionEvent e)
3533 new jalview.ws.DBRefFetcher(
3534 alignPanel.av.getSequenceSelection(),
3535 alignPanel.alignFrame).fetchDBRefs(false);
3541 /* public void vamsasStore_actionPerformed(ActionEvent e)
3543 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
3544 getProperty("LAST_DIRECTORY"));
3546 chooser.setFileView(new JalviewFileView());
3547 chooser.setDialogTitle("Export to Vamsas file");
3548 chooser.setToolTipText("Export");
3550 int value = chooser.showSaveDialog(this);
3552 if (value == JalviewFileChooser.APPROVE_OPTION)
3554 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
3555 //vs.store(chooser.getSelectedFile().getAbsolutePath() );
3556 vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
3560 * prototype of an automatically enabled/disabled analysis function
3563 protected void setShowProductsEnabled()
3565 SequenceI [] selection = viewport.getSequenceSelection();
3566 if (canShowProducts(selection, viewport.getSelectionGroup()!=null, viewport.getAlignment().getDataset()))
3568 showProducts.setEnabled(true);
3571 showProducts.setEnabled(false);
3575 * search selection for sequence xRef products and build the
3576 * show products menu.
3579 * @return true if showProducts menu should be enabled.
3581 public boolean canShowProducts(SequenceI[] selection, boolean isRegionSelection, Alignment dataset)
3583 boolean showp=false;
3585 showProducts.removeAll();
3586 final boolean dna = viewport.getAlignment().isNucleotide();
3587 String[] ptypes = CrossRef.findSequenceXrefTypes(dna, selection, dataset);
3588 //Object[] prods = CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(), selection, dataset, true);
3589 final SequenceI[] sel = selection;
3590 for (int t=0; ptypes!=null && t<ptypes.length; t++)
3593 final boolean isRegSel = isRegionSelection;
3594 final AlignFrame af = this;
3595 final String source = ptypes[t];
3596 JMenuItem xtype = new JMenuItem(ptypes[t]);
3597 xtype.addActionListener(new ActionListener() {
3599 public void actionPerformed(ActionEvent e)
3601 af.showProductsFor(sel, isRegSel, dna, source);
3605 showProducts.add(xtype);
3607 showProducts.setVisible(showp);
3608 showProducts.setEnabled(showp);
3609 } catch (Exception e)
3611 jalview.bin.Cache.log.warn("canTranslate threw an exception - please report to help@jalview.org",e);
3616 protected void showProductsFor(SequenceI[] sel, boolean isRegSel, boolean dna, String source)
3618 Alignment ds = getViewport().alignment.getDataset();
3619 Alignment prods = CrossRef.findXrefSequences(sel, dna, source, ds);
3622 SequenceI[] sprods = new SequenceI[prods.getHeight()];
3623 for (int s=0; s<sprods.length;s++)
3625 sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
3626 if (!ds.getSequences().contains(sprods[s].getDatasetSequence()))
3627 ds.addSequence(sprods[s].getDatasetSequence());
3629 Alignment al = new Alignment(sprods);
3630 AlignedCodonFrame[] cf = prods.getCodonFrames();
3631 for (int s=0; cf!=null && s<cf.length; s++)
3633 al.addCodonFrame(cf[s]);
3637 AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
3638 String newtitle =""+((dna) ? "Proteins " : "Nucleotides ") + " for "+((isRegSel) ? "selected region of " : "")
3640 Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
3643 System.err.println("No Sequences generated for xRef type "+source);
3648 public boolean canShowTranslationProducts(SequenceI[] selection, AlignmentI alignment)
3652 return (jalview.analysis.Dna.canTranslate(selection, viewport.getViewAsVisibleContigs(true)));
3653 } catch (Exception e)
3655 jalview.bin.Cache.log.warn("canTranslate threw an exception - please report to help@jalview.org",e);
3660 public void showProducts_actionPerformed(ActionEvent e)
3662 ///////////////////////////////
3663 // Collect Data to be translated/transferred
3665 SequenceI [] selection = viewport.getSequenceSelection();
3666 AlignmentI al = null;
3668 al = jalview.analysis.Dna.CdnaTranslate(selection, viewport.getViewAsVisibleContigs(true),
3669 viewport.getGapCharacter(), viewport.getAlignment().getDataset());
3670 } catch (Exception ex) {
3672 jalview.bin.Cache.log.debug("Exception during translation.",ex);
3676 JOptionPane.showMessageDialog(Desktop.desktop,
3677 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
3678 "Translation Failed",
3679 JOptionPane.WARNING_MESSAGE);
3681 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
3682 Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
3688 public void showTranslation_actionPerformed(ActionEvent e)
3690 ///////////////////////////////
3691 // Collect Data to be translated/transferred
3693 SequenceI [] selection = viewport.getSequenceSelection();
3694 String [] seqstring = viewport.getViewAsString(true);
3695 AlignmentI al = null;
3697 al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring, viewport.getViewAsVisibleContigs(true),
3698 viewport.getGapCharacter(), viewport.alignment.getAlignmentAnnotation(),
3699 viewport.alignment.getWidth(), viewport.getAlignment().getDataset());
3700 } catch (Exception ex) {
3702 jalview.bin.Cache.log.debug("Exception during translation.",ex);
3706 JOptionPane.showMessageDialog(Desktop.desktop,
3707 "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
3708 "Translation Failed",
3709 JOptionPane.WARNING_MESSAGE);
3711 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
3712 Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
3721 * @param String DOCUMENT ME!
3723 public boolean parseFeaturesFile(String file, String type)
3725 boolean featuresFile = false;
3728 featuresFile = new FeaturesFile(file,
3729 type).parse(viewport.alignment.getDataset(),
3730 alignPanel.seqPanel.seqCanvas.
3731 getFeatureRenderer().featureColours,
3736 ex.printStackTrace();
3741 viewport.showSequenceFeatures = true;
3742 showSeqFeatures.setSelected(true);
3743 alignPanel.paintAlignment(true);
3746 return featuresFile;
3749 public void dragEnter(DropTargetDragEvent evt)
3752 public void dragExit(DropTargetEvent evt)
3755 public void dragOver(DropTargetDragEvent evt)
3758 public void dropActionChanged(DropTargetDragEvent evt)
3761 public void drop(DropTargetDropEvent evt)
3763 Transferable t = evt.getTransferable();
3764 java.util.List files = null;
3768 DataFlavor uriListFlavor = new DataFlavor(
3769 "text/uri-list;class=java.lang.String");
3770 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
3772 //Works on Windows and MacOSX
3773 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3774 files = (java.util.List) t.getTransferData(DataFlavor.
3775 javaFileListFlavor);
3777 else if (t.isDataFlavorSupported(uriListFlavor))
3779 // This is used by Unix drag system
3780 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3781 String data = (String) t.getTransferData(uriListFlavor);
3782 files = new java.util.ArrayList(1);
3783 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
3786 st.hasMoreTokens(); )
3788 String s = st.nextToken();
3789 if (s.startsWith("#"))
3791 // the line is a comment (as per the RFC 2483)
3795 java.net.URI uri = new java.net.URI(s);
3796 java.io.File file = new java.io.File(uri);
3803 e.printStackTrace();
3810 for (int i = 0; i < files.size(); i++)
3812 loadJalviewDataFile(files.get(i).toString());
3815 catch (Exception ex)
3817 ex.printStackTrace();
3822 // This method will attempt to load a "dropped" file first by testing
3823 // whether its and Annotation file, then features file. If both are
3824 // false then the user may have dropped an alignment file onto this
3826 public void loadJalviewDataFile(String file)
3830 String protocol = "File";
3832 if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
3837 boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
3838 alignment, file, protocol);
3842 boolean isGroupsFile = parseFeaturesFile(file,protocol);
3845 String format = new IdentifyFile().Identify(file, protocol);
3847 if(format.equalsIgnoreCase("JnetFile"))
3849 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
3851 new JnetAnnotationMaker().add_annotation(predictions,
3852 viewport.getAlignment(),
3854 alignPanel.adjustAnnotationHeight();
3855 alignPanel.paintAlignment(true);
3859 new FileLoader().LoadFile(viewport, file, protocol, format);
3866 alignPanel.adjustAnnotationHeight();
3867 buildSortByAnnotationScoresMenu();
3871 catch (Exception ex)
3873 ex.printStackTrace();
3877 public void tabSelectionChanged(int index)
3881 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
3882 viewport = alignPanel.av;
3883 setMenusFromViewport(viewport);
3887 public void tabbedPane_mousePressed(MouseEvent e)
3889 if(SwingUtilities.isRightMouseButton(e))
3891 String reply = JOptionPane.showInternalInputDialog(this,
3894 JOptionPane.QUESTION_MESSAGE);
3898 viewport.viewName = reply;
3899 tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
3905 public AlignViewport getCurrentView()
3912 * Open the dialog for regex description parsing.
3914 protected void extractScores_actionPerformed(ActionEvent e)
3916 ParseProperties pp = new jalview.analysis.ParseProperties(viewport.alignment);
3917 if (pp.getScoresFromDescription("col", "score column ", "\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)")>0)
3919 buildSortByAnnotationScoresMenu();
3928 public PrintThread(AlignmentPanel ap)
3932 static PageFormat pf;
3935 PrinterJob printJob = PrinterJob.getPrinterJob();
3939 printJob.setPrintable(ap, pf);
3943 printJob.setPrintable(ap);
3946 if (printJob.printDialog())
3952 catch (Exception PrintException)
3954 PrintException.printStackTrace();