2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2006 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.event.*;
28 import java.awt.print.*;
31 import jalview.analysis.*;
32 import jalview.datamodel.*;
34 import jalview.jbgui.*;
35 import jalview.schemes.*;
36 import jalview.commands.*;
38 import java.awt.dnd.*;
46 public class AlignFrame extends GAlignFrame implements DropTargetListener
49 public static final int DEFAULT_WIDTH = 700;
52 public static final int DEFAULT_HEIGHT = 500;
53 public AlignmentPanel alignPanel;
55 AlignViewport viewport;
57 Vector alignPanels = new Vector();
61 public String currentFileFormat = null;
63 private int treeCount = 0;
66 * Creates a new AlignFrame object.
68 * @param al DOCUMENT ME!
70 public AlignFrame(AlignmentI al, int width, int height)
72 this(al, null, width, height);
77 * new alignment window with hidden columns
78 * @param al AlignmentI
79 * @param hiddenColumns ColumnSelection or null
81 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
82 int width, int height)
84 this.setSize(width, height);
85 viewport = new AlignViewport(al, hiddenColumns);
87 alignPanel = new AlignmentPanel(this, viewport);
89 if(al.getDataset()==null)
94 addAlignmentPanel(alignPanel, true);
99 * Make a new AlignFrame from exisiting alignmentPanels
100 * @param ap AlignmentPanel
101 * @param av AlignViewport
103 public AlignFrame(AlignmentPanel ap)
107 addAlignmentPanel(ap, false);
113 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
115 if (viewport.conservation == null)
117 BLOSUM62Colour.setEnabled(false);
118 conservationMenuItem.setEnabled(false);
119 modifyConservation.setEnabled(false);
120 // PIDColour.setEnabled(false);
121 // abovePIDThreshold.setEnabled(false);
122 // modifyPID.setEnabled(false);
125 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
127 if (sortby.equals("Id"))
128 sortIDMenuItem_actionPerformed(null);
129 else if (sortby.equals("Pairwise Identity"))
130 sortPairwiseMenuItem_actionPerformed(null);
132 if (Desktop.desktop != null)
134 addServiceListeners();
135 setGUINucleotide(viewport.alignment.isNucleotide());
138 setMenusFromViewport(viewport);
140 if (viewport.wrapAlignment)
142 wrapMenuItem_actionPerformed(null);
150 void addKeyListener()
152 final AlignFrame af = this;
153 addKeyListener(new KeyAdapter()
155 public void keyPressed(KeyEvent evt)
157 if (viewport.cursorMode
158 && evt.getKeyCode() >= KeyEvent.VK_0
159 && evt.getKeyCode() <= KeyEvent.VK_9)
161 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
164 switch (evt.getKeyCode())
167 if (!evt.isControlDown())
170 if(viewport.hasHiddenRows)
172 al = viewport.alignment.getHiddenSequences().getFullAlignment();
175 al = new Alignment(viewport.alignment.getSequencesArray());
177 AlignViewport newview = new AlignViewport(al);
179 if(viewport.viewName==null)
180 viewport.viewName="View 1";
182 newview.historyList = viewport.historyList;
183 newview.redoList = viewport.redoList;
185 newview.sequenceSetID = viewport.getSequenceSetId();
186 newview.viewName = "View " +
187 (Desktop.getViewCount(viewport.getSequenceSetId())+1);
189 AlignmentPanel newap = new AlignmentPanel(af, newview);
191 PaintRefresher.Register(newap, viewport.getSequenceSetId());
192 PaintRefresher.Register(alignPanel, viewport.getSequenceSetId());
194 addAlignmentPanel(newap, true);
195 tabbedPane.setSelectedIndex(tabbedPane.getTabCount()-1);
199 Desktop.instance.gatherViews(af);
203 if (!evt.isControlDown())
205 Desktop.instance.explodeViews(af);
210 case 27: // escape key
211 deselectAllSequenceMenuItem_actionPerformed(null);
215 case KeyEvent.VK_DOWN:
216 if (viewport.cursorMode)
218 alignPanel.seqPanel.moveCursor(0, 1);
221 moveSelectedSequences(false);
225 if (viewport.cursorMode)
227 alignPanel.seqPanel.moveCursor(0, -1);
230 moveSelectedSequences(true);
233 case KeyEvent.VK_LEFT:
234 if (viewport.cursorMode)
236 alignPanel.seqPanel.moveCursor( -1, 0);
240 case KeyEvent.VK_RIGHT:
241 if (viewport.cursorMode)
243 alignPanel.seqPanel.moveCursor(1, 0);
247 case KeyEvent.VK_SPACE:
248 if (viewport.cursorMode)
250 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
256 case KeyEvent.VK_DELETE:
257 case KeyEvent.VK_BACK_SPACE:
258 if (!viewport.cursorMode)
260 cut_actionPerformed(null);
263 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
270 if (viewport.cursorMode)
272 alignPanel.seqPanel.setCursorRow();
276 if (viewport.cursorMode && !evt.isControlDown())
278 alignPanel.seqPanel.setCursorColumn();
282 if (viewport.cursorMode)
284 alignPanel.seqPanel.setCursorPosition();
288 case KeyEvent.VK_ENTER:
289 case KeyEvent.VK_COMMA:
290 if (viewport.cursorMode)
292 alignPanel.seqPanel.setCursorRowAndColumn();
297 if (viewport.cursorMode)
299 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
303 if (viewport.cursorMode)
305 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
310 viewport.cursorMode = !viewport.cursorMode;
311 statusBar.setText("Keyboard editing mode is " +
312 (viewport.cursorMode ? "on" : "off"));
313 if (viewport.cursorMode)
315 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
316 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
318 alignPanel.seqPanel.seqCanvas.repaint();
324 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
325 java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
326 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
328 javax.help.HelpBroker hb = hs.createHelpBroker();
329 hb.setCurrentID("home");
330 hb.setDisplayed(true);
334 ex.printStackTrace();
340 boolean toggleSeqs = !evt.isControlDown();
341 boolean toggleCols = !evt.isShiftDown();
343 boolean hide = false;
345 SequenceGroup sg = viewport.getSelectionGroup();
348 if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
350 hideSelSequences_actionPerformed(null);
353 else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))
354 showAllSeqs_actionPerformed(null);
359 if (viewport.colSel.getSelected().size() > 0)
361 hideSelColumns_actionPerformed(null);
363 viewport.selectionGroup = sg;
366 showAllColumns_actionPerformed(null);
370 case KeyEvent.VK_PAGE_UP:
371 if (viewport.wrapAlignment)
372 alignPanel.scrollUp(true);
374 alignPanel.setScrollValues(viewport.startRes,
376 - viewport.endSeq + viewport.startSeq);
378 case KeyEvent.VK_PAGE_DOWN:
379 if (viewport.wrapAlignment)
380 alignPanel.scrollUp(false);
382 alignPanel.setScrollValues(viewport.startRes,
384 + viewport.endSeq - viewport.startSeq);
392 public void addAlignmentPanel(final AlignmentPanel ap,
395 ap.alignFrame = this;
397 alignPanels.addElement(ap);
399 int aSize = alignPanels.size();
401 tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
403 if (aSize == 1 && ap.av.viewName==null)
405 this.getContentPane().add(ap, BorderLayout.CENTER);
411 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
412 tabbedPane.addTab(first.av.viewName==null?"Original":first.av.viewName,first);
414 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
417 tabbedPane.addTab(ap.av.viewName==null?"Original":ap.av.viewName, ap);
419 ap.setVisible(false);
424 ap.av.updateConsensus(ap);
425 ap.av.updateConservation(ap);
430 public AlignViewport getViewport()
435 /* Set up intrinsic listeners for dynamically generated GUI bits. */
436 private void addServiceListeners()
438 final java.beans.PropertyChangeListener thisListener;
439 // Do this once to get current state
440 BuildWebServiceMenu();
441 Desktop.discoverer.addPropertyChangeListener(
442 thisListener = new java.beans.PropertyChangeListener()
444 public void propertyChange(PropertyChangeEvent evt)
446 // System.out.println("Discoverer property change.");
447 if (evt.getPropertyName().equals("services"))
449 // System.out.println("Rebuilding web service menu");
450 BuildWebServiceMenu();
455 addInternalFrameListener(new javax.swing.event.
456 InternalFrameAdapter()
458 public void internalFrameClosed(
459 javax.swing.event.InternalFrameEvent evt)
461 // System.out.println("deregistering discoverer listener");
462 Desktop.discoverer.removePropertyChangeListener(thisListener);
463 closeMenuItem_actionPerformed(null);
469 public void setGUINucleotide(boolean nucleotide)
471 showTranslation.setVisible( nucleotide );
472 conservationMenuItem.setEnabled( !nucleotide );
473 modifyConservation.setEnabled( !nucleotide );
475 //Remember AlignFrame always starts as protein
478 calculateMenu.remove(calculateMenu.getItemCount()-2);
483 * Need to call this method when tabs are selected for multiple views,
484 * or when loading from Jalview2XML.java
485 * @param av AlignViewport
487 void setMenusFromViewport(AlignViewport av)
489 colourTextMenuItem.setSelected(av.showColourText);
490 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
491 conservationMenuItem.setSelected(av.getConservationSelected());
492 seqLimits.setSelected(av.getShowJVSuffix());
493 renderGapsMenuItem.setSelected(av.renderGaps);
494 wrapMenuItem.setSelected(av.wrapAlignment);
495 annotationPanelMenuItem.setState(av.showAnnotation);
496 viewBoxesMenuItem.setSelected(av.showBoxes);
497 viewTextMenuItem.setSelected(av.showText);
499 setColourSelected(ColourSchemeProperty.
500 getColourName(av.getGlobalColourScheme()));
502 showSeqFeatures.setSelected(av.showSequenceFeatures);
503 hiddenMarkers.setState(av.showHiddenMarkers);
504 applyToAllGroups.setState(av.colourAppliesToAllGroups);
505 smoothFont.setState(av.antiAlias);
511 Hashtable progressBars;
512 public void setProgressBar(String message, long id)
514 if(progressBars == null)
515 progressBars = new Hashtable();
517 JPanel progressPanel;
518 GridLayout layout = (GridLayout) statusPanel.getLayout();
519 if(progressBars.get( new Long(id) )!=null)
521 progressPanel = (JPanel)progressBars.get( new Long(id) );
522 statusPanel.remove(progressPanel);
523 progressBars.remove( progressPanel );
524 progressPanel = null;
526 statusBar.setText(message);
528 layout.setRows(layout.getRows() - 1);
532 progressPanel = new JPanel(new BorderLayout(10, 5));
534 JProgressBar progressBar = new JProgressBar();
535 progressBar.setIndeterminate(true);
537 progressPanel.add(new JLabel(message), BorderLayout.WEST);
538 progressPanel.add(progressBar, BorderLayout.CENTER);
540 layout.setRows(layout.getRows() + 1);
541 statusPanel.add(progressPanel);
543 progressBars.put(new Long(id), progressPanel);
553 Added so Castor Mapping file can obtain Jalview Version
555 public String getVersion()
557 return jalview.bin.Cache.getProperty("VERSION");
560 public FeatureRenderer getFeatureRenderer()
562 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
566 public void fetchSequence_actionPerformed(ActionEvent e)
568 new SequenceFetcher(this);
571 public void addFromFile_actionPerformed(ActionEvent e)
573 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
576 public void addFromText_actionPerformed(ActionEvent e)
578 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
581 public void addFromURL_actionPerformed(ActionEvent e)
583 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
589 * @param e DOCUMENT ME!
591 public void saveAlignmentMenu_actionPerformed(ActionEvent e)
593 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
594 getProperty( "LAST_DIRECTORY"),
596 { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" },
598 { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
603 chooser.setFileView(new JalviewFileView());
604 chooser.setDialogTitle("Save Alignment to file");
605 chooser.setToolTipText("Save");
607 int value = chooser.showSaveDialog(this);
609 if (value == JalviewFileChooser.APPROVE_OPTION)
611 currentFileFormat = chooser.getSelectedFormat();
613 if (currentFileFormat == null)
615 JOptionPane.showInternalMessageDialog(Desktop.desktop,
616 "You must select a file format before saving!",
617 "File format not specified",
618 JOptionPane.WARNING_MESSAGE);
619 value = chooser.showSaveDialog(this);
623 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
626 String choice = chooser.getSelectedFile().getPath();
627 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
629 saveAlignment(choice, currentFileFormat);
633 public boolean saveAlignment(String file, String format)
635 if (format.equalsIgnoreCase("Jalview"))
637 String shortName = title;
639 if (shortName.indexOf(java.io.File.separatorChar) > -1)
641 shortName = shortName.substring(shortName.lastIndexOf(
642 java.io.File.separatorChar) + 1);
645 new Jalview2XML().SaveAlignment(this, file, shortName);
647 // USE Jalview2XML to save this file
653 String[] omitHidden = null;
655 if (viewport.hasHiddenColumns)
657 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
658 "The Alignment contains hidden columns."
659 + "\nDo you want to save only the visible alignment?",
660 "Save / Omit Hidden Columns",
661 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
663 if (reply == JOptionPane.YES_OPTION)
664 omitHidden = viewport.getViewAsString(false);
667 String output = new FormatAdapter().formatSequences(
669 viewport.alignment.getSequencesArray(),
679 java.io.PrintWriter out = new java.io.PrintWriter(
680 new java.io.FileWriter(file));
689 ex.printStackTrace();
698 * @param e DOCUMENT ME!
700 protected void outputText_actionPerformed(ActionEvent e)
702 String [] omitHidden = null;
704 if(viewport.hasHiddenColumns)
706 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
707 "The Alignment contains hidden columns."
708 +"\nDo you want to output only the visible alignment?",
709 "Save / Omit Hidden Columns",
710 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
712 if(reply==JOptionPane.YES_OPTION)
714 omitHidden = viewport.getViewAsString(false);
718 CutAndPasteTransfer cap = new CutAndPasteTransfer();
719 Desktop.addInternalFrame(cap,
720 "Alignment output - " + e.getActionCommand(), 600,
724 cap.setText(new FormatAdapter().formatSequences(
725 e.getActionCommand(),
726 viewport.alignment.getSequencesArray(),
733 * @param e DOCUMENT ME!
735 protected void htmlMenuItem_actionPerformed(ActionEvent e)
737 new HTMLOutput(viewport,
738 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
739 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
742 public void createImageMap(File file, String image)
744 alignPanel.makePNGImageMap(file, image);
750 * @param e DOCUMENT ME!
752 public void createPNG(File f)
754 alignPanel.makePNG(f);
760 * @param e DOCUMENT ME!
762 public void createEPS(File f)
764 alignPanel.makeEPS(f);
770 * @param e DOCUMENT ME!
772 public void printMenuItem_actionPerformed(ActionEvent e)
774 //Putting in a thread avoids Swing painting problems
775 PrintThread thread = new PrintThread();
779 public void exportFeatures_actionPerformed(ActionEvent e)
781 new AnnotationExporter().exportFeatures(alignPanel);
785 public void exportAnnotations_actionPerformed(ActionEvent e)
787 new AnnotationExporter().exportAnnotations(
789 viewport.alignment.getAlignmentAnnotation()
794 public void associatedData_actionPerformed(ActionEvent e)
796 // Pick the tree file
797 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
800 chooser.setFileView(new JalviewFileView());
801 chooser.setDialogTitle("Load Jalview Annotations or Features File");
802 chooser.setToolTipText("Load Jalview Annotations / Features file");
804 int value = chooser.showOpenDialog(null);
806 if (value == JalviewFileChooser.APPROVE_OPTION)
808 String choice = chooser.getSelectedFile().getPath();
809 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
810 loadJalviewDataFile(choice);
819 * @param e DOCUMENT ME!
821 public void closeMenuItem_actionPerformed(ActionEvent e)
825 if(alignPanels!=null)
827 for (int i = 0; i < alignPanels.size(); i++)
829 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
830 PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
831 PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
832 PaintRefresher.RemoveComponent(ap);
834 // alignPanels = null;
837 System.out.println("null one here");
839 // alignPanel = null;
842 this.setClosed(true);
846 ex.printStackTrace();
854 void updateEditMenuBar()
857 if (viewport.historyList.size() > 0)
859 undoMenuItem.setEnabled(true);
860 CommandI command = (CommandI) viewport.historyList.peek();
861 undoMenuItem.setText("Undo " + command.getDescription());
865 undoMenuItem.setEnabled(false);
866 undoMenuItem.setText("Undo");
869 if (viewport.redoList.size() > 0)
871 redoMenuItem.setEnabled(true);
873 CommandI command = (CommandI) viewport.redoList.peek();
874 redoMenuItem.setText("Redo " + command.getDescription());
878 redoMenuItem.setEnabled(false);
879 redoMenuItem.setText("Redo");
884 public void addHistoryItem(CommandI command)
886 if(command.getSize()>0)
888 viewport.historyList.push(command);
889 viewport.redoList.clear();
891 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
900 * @param e DOCUMENT ME!
902 protected void undoMenuItem_actionPerformed(ActionEvent e)
904 CommandI command = (CommandI)viewport.historyList.pop();
905 viewport.redoList.push(command);
906 command.undoCommand();
908 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
910 viewport.firePropertyChange("alignment", null,
911 viewport.getAlignment().getSequences());
917 * @param e DOCUMENT ME!
919 protected void redoMenuItem_actionPerformed(ActionEvent e)
921 CommandI command = (CommandI) viewport.redoList.pop();
922 viewport.historyList.push(command);
924 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
927 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
934 * @param up DOCUMENT ME!
936 public void moveSelectedSequences(boolean up)
938 SequenceGroup sg = viewport.getSelectionGroup();
947 for (int i = 1; i < viewport.alignment.getHeight(); i++)
949 SequenceI seq = viewport.alignment.getSequenceAt(i);
951 if (!sg.getSequences(false).contains(seq))
956 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
958 if (sg.getSequences(false).contains(temp))
963 viewport.alignment.getSequences().setElementAt(temp, i);
964 viewport.alignment.getSequences().setElementAt(seq, i - 1);
969 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
971 SequenceI seq = viewport.alignment.getSequenceAt(i);
973 if (!sg.getSequences(false).contains(seq))
978 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
980 if (sg.getSequences(false).contains(temp))
985 viewport.alignment.getSequences().setElementAt(temp, i);
986 viewport.alignment.getSequences().setElementAt(seq, i + 1);
990 alignPanel.repaint();
998 * @param e DOCUMENT ME!
1000 protected void copy_actionPerformed(ActionEvent e)
1003 if (viewport.getSelectionGroup() == null)
1008 SequenceI [] seqs = viewport.getSelectionAsNewSequence();
1009 String[] omitHidden = null;
1011 if (viewport.hasHiddenColumns)
1013 omitHidden = viewport.getViewAsString(true);
1016 String output = new FormatAdapter().formatSequences(
1021 StringSelection ss = new StringSelection(output);
1025 //Its really worth setting the clipboard contents
1026 //to empty before setting the large StringSelection!!
1027 Toolkit.getDefaultToolkit().getSystemClipboard()
1028 .setContents(new StringSelection(""), null);
1030 Toolkit.getDefaultToolkit().getSystemClipboard()
1031 .setContents(ss, Desktop.instance);
1033 catch (OutOfMemoryError er)
1035 er.printStackTrace();
1036 javax.swing.SwingUtilities.invokeLater(new Runnable()
1040 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1041 "Out of memory copying region!!"
1043 "\nSee help files for increasing Java Virtual Machine memory."
1045 javax.swing.JOptionPane.WARNING_MESSAGE);
1052 Vector hiddenColumns = null;
1053 if(viewport.hasHiddenColumns)
1055 hiddenColumns =new Vector();
1056 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1057 for(int i=0; i<viewport.getColumnSelection().getHiddenColumns().size(); i++)
1059 int[] region = (int[])
1060 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
1062 hiddenColumns.addElement(new int[]{region[0]-hiddenOffset,
1063 region[1]-hiddenOffset});
1069 Desktop.jalviewClipboard = new Object[]{ seqs,
1070 viewport.alignment.getDataset(),
1072 statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
1078 * @param e DOCUMENT ME!
1080 protected void pasteNew_actionPerformed(ActionEvent e)
1088 * @param e DOCUMENT ME!
1090 protected void pasteThis_actionPerformed(ActionEvent e)
1098 * @param newAlignment DOCUMENT ME!
1100 void paste(boolean newAlignment)
1104 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1105 Transferable contents = c.getContents(this);
1107 if (contents == null)
1115 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1116 if (str.length() < 1)
1119 format = new IdentifyFile().Identify(str, "Paste");
1122 catch (OutOfMemoryError er)
1124 er.printStackTrace();
1125 javax.swing.SwingUtilities.invokeLater(new Runnable()
1129 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1130 "Out of memory pasting sequences!!"
1132 "\nSee help files for increasing Java Virtual Machine memory."
1134 javax.swing.JOptionPane.WARNING_MESSAGE);
1141 SequenceI[] sequences;
1144 if(Desktop.jalviewClipboard!=null)
1146 // The clipboard was filled from within Jalview, we must use the sequences
1147 // And dataset from the copied alignment
1148 sequences = (SequenceI[])Desktop.jalviewClipboard[0];
1152 sequences = new FormatAdapter().readFile(str, "Paste", format);
1155 AlignmentI alignment = null;
1159 alignment = new Alignment(sequences);
1161 if (Desktop.jalviewClipboard != null)
1162 alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
1164 alignment.setDataset(null);
1168 alignment = viewport.getAlignment();
1171 SequenceI [] newseqs = new SequenceI[sequences.length];
1172 for (int i = 0; i < sequences.length; i++)
1174 newseqs[i] = new Sequence(sequences[i].getName(),
1175 sequences[i].getSequence(), sequences[i].getStart(),
1176 sequences[i].getEnd());
1178 alignment.addSequence(newseqs[i]);
1184 addHistoryItem(new EditCommand(
1189 alignment.getWidth(),
1194 viewport.setEndSeq(alignment.getHeight());
1195 alignment.getWidth();
1196 viewport.firePropertyChange("alignment", null, alignment.getSequences());
1201 // Add any annotations attached to sequences
1202 for (int i = 0; i < sequences.length; i++)
1204 if (sequences[i].getAnnotation() != null)
1206 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1208 AlignmentAnnotation newAnnot =
1209 new AlignmentAnnotation(
1210 sequences[i].getAnnotation()[a].label,
1211 sequences[i].getAnnotation()[a].description,
1212 sequences[i].getAnnotation()[a].annotations,
1213 sequences[i].getAnnotation()[a].graphMin,
1214 sequences[i].getAnnotation()[a].graphMax,
1215 sequences[i].getAnnotation()[a].graph);
1217 sequences[i].getAnnotation()[a] = newAnnot;
1218 newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].
1220 newAnnot.sequenceRef = sequences[i];
1221 newAnnot.adjustForAlignment();
1222 alignment.addAnnotation(newAnnot);
1223 alignment.setAnnotationIndex(newAnnot, a);
1226 alignPanel.annotationPanel.adjustPanelHeight();
1232 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
1233 String newtitle = new String("Copied sequences");
1235 if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
1237 Vector hc = (Vector)Desktop.jalviewClipboard[2];
1238 for(int i=0; i<hc.size(); i++)
1240 int [] region = (int[]) hc.elementAt(i);
1241 af.viewport.hideColumns(region[0], region[1]);
1246 //>>>This is a fix for the moment, until a better solution is found!!<<<
1247 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
1248 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1251 if (title.startsWith("Copied sequences"))
1257 newtitle = newtitle.concat("- from " + title);
1260 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1267 catch (Exception ex)
1269 ex.printStackTrace();
1270 System.out.println("Exception whilst pasting: "+ex);
1271 // could be anything being pasted in here
1280 * @param e DOCUMENT ME!
1282 protected void cut_actionPerformed(ActionEvent e)
1284 copy_actionPerformed(null);
1285 delete_actionPerformed(null);
1291 * @param e DOCUMENT ME!
1293 protected void delete_actionPerformed(ActionEvent e)
1296 SequenceGroup sg = viewport.getSelectionGroup();
1302 Vector seqs = new Vector();
1303 int cutLength = sg.getEndRes()-sg.getStartRes()+1;
1304 boolean seqsCut = false;
1306 for (int i = 0; i < sg.getSize(false); i++)
1308 seq = sg.getSequenceAt(i);
1309 seqs.addElement(seq);
1310 if(seq.getLength()<=cutLength)
1315 // If the cut affects all sequences, remove highlighted columns
1316 if (sg.getSize(false) == viewport.alignment.getHeight())
1318 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1319 sg.getEndRes() + 1);
1323 SequenceI [] cut = new SequenceI[seqs.size()];
1324 for(int i=0; i<seqs.size(); i++)
1325 cut[i] = (SequenceI)seqs.elementAt(i);
1331 addHistoryItem(new EditCommand("Cut Sequences",
1335 sg.getEndRes()-sg.getStartRes()+1,
1336 viewport.alignment));
1339 viewport.setSelectionGroup(null);
1340 viewport.alignment.deleteGroup(sg);
1342 viewport.firePropertyChange("alignment", null,
1343 viewport.getAlignment().getSequences());
1345 if (viewport.getAlignment().getHeight() < 1)
1349 this.setClosed(true);
1351 catch (Exception ex)
1360 * @param e DOCUMENT ME!
1362 protected void deleteGroups_actionPerformed(ActionEvent e)
1364 viewport.alignment.deleteAllGroups();
1365 viewport.setSelectionGroup(null);
1366 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1367 alignPanel.repaint();
1373 * @param e DOCUMENT ME!
1375 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1377 SequenceGroup sg = new SequenceGroup();
1379 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1382 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1385 sg.setEndRes(viewport.alignment.getWidth() - 1);
1386 viewport.setSelectionGroup(sg);
1387 alignPanel.repaint();
1388 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1394 * @param e DOCUMENT ME!
1396 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1398 if(viewport.cursorMode)
1400 alignPanel.seqPanel.keyboardNo1 = null;
1401 alignPanel.seqPanel.keyboardNo2 = null;
1403 viewport.setSelectionGroup(null);
1404 viewport.getColumnSelection().clear();
1405 viewport.setSelectionGroup(null);
1406 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1407 alignPanel.idPanel.idCanvas.searchResults = null;
1408 alignPanel.repaint();
1409 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1415 * @param e DOCUMENT ME!
1417 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1419 SequenceGroup sg = viewport.getSelectionGroup();
1423 selectAllSequenceMenuItem_actionPerformed(null);
1428 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1431 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1434 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1437 public void invertColSel_actionPerformed(ActionEvent e)
1439 viewport.invertColumnSelection();
1440 alignPanel.repaint();
1447 * @param e DOCUMENT ME!
1449 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1451 trimAlignment(true);
1457 * @param e DOCUMENT ME!
1459 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
1461 trimAlignment(false);
1464 void trimAlignment(boolean trimLeft)
1466 ColumnSelection colSel = viewport.getColumnSelection();
1469 if (colSel.size() > 0)
1472 column = colSel.getMin();
1474 column = colSel.getMax();
1477 if(viewport.getSelectionGroup()!=null)
1478 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
1480 seqs = viewport.alignment.getSequencesArray();
1483 TrimRegionCommand trimRegion;
1486 trimRegion = new TrimRegionCommand("Remove Left",
1487 TrimRegionCommand.TRIM_LEFT,
1492 viewport.selectionGroup);
1496 trimRegion = new TrimRegionCommand("Remove Right",
1497 TrimRegionCommand.TRIM_RIGHT,
1502 viewport.selectionGroup);
1505 statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
1508 addHistoryItem(trimRegion);
1510 Vector groups = viewport.alignment.getGroups();
1512 for (int i = 0; i < groups.size(); i++)
1514 SequenceGroup sg = (SequenceGroup) groups.get(i);
1516 if ( (trimLeft && !sg.adjustForRemoveLeft(column))
1517 || (!trimLeft && !sg.adjustForRemoveRight(column)))
1519 viewport.alignment.deleteGroup(sg);
1523 viewport.firePropertyChange("alignment", null,
1524 viewport.getAlignment().getSequences());
1531 * @param e DOCUMENT ME!
1533 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1535 int start = 0, end = viewport.alignment.getWidth()-1;
1538 if (viewport.getSelectionGroup() != null)
1540 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
1541 start = viewport.getSelectionGroup().getStartRes();
1542 end = viewport.getSelectionGroup().getEndRes();
1545 seqs = viewport.alignment.getSequencesArray();
1548 RemoveGapColCommand removeGapCols =
1549 new RemoveGapColCommand("Remove Gapped Columns",
1552 viewport.getGapCharacter());
1554 addHistoryItem(removeGapCols);
1556 statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
1558 //This is to maintain viewport position on first residue
1560 SequenceI seq = viewport.alignment.getSequenceAt(0);
1561 int startRes = seq.findPosition(viewport.startRes);
1562 // ShiftList shifts;
1563 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
1564 // edit.alColumnChanges=shifts.getInverse();
1565 // if (viewport.hasHiddenColumns)
1566 // viewport.getColumnSelection().compensateForEdits(shifts);
1567 viewport.setStartRes(seq.findIndex(startRes)-1);
1568 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1575 * @param e DOCUMENT ME!
1577 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1579 int start = 0, end = viewport.alignment.getWidth()-1;
1582 if (viewport.getSelectionGroup() != null)
1584 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
1585 start = viewport.getSelectionGroup().getStartRes();
1586 end = viewport.getSelectionGroup().getEndRes();
1589 seqs = viewport.alignment.getSequencesArray();
1591 //This is to maintain viewport position on first residue
1593 SequenceI seq = viewport.alignment.getSequenceAt(0);
1594 int startRes = seq.findPosition(viewport.startRes);
1596 addHistoryItem(new RemoveGapsCommand("Remove Gaps",
1599 viewport.getGapCharacter()));
1601 viewport.setStartRes(seq.findIndex(startRes)-1);
1603 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1610 * @param e DOCUMENT ME!
1612 public void padGapsMenuitem_actionPerformed(ActionEvent e)
1614 viewport.padGaps = padGapsMenuitem.isSelected();
1616 viewport.firePropertyChange("alignment",
1618 viewport.getAlignment().getSequences());
1624 * @param e DOCUMENT ME!
1626 public void findMenuItem_actionPerformed(ActionEvent e)
1628 JInternalFrame frame = new JInternalFrame();
1629 Finder finder = new Finder(viewport, alignPanel, frame);
1630 frame.setContentPane(finder);
1631 frame.setLayer(JLayeredPane.PALETTE_LAYER);
1632 Desktop.addInternalFrame(frame, "Find", 340, 110);
1638 * @param e DOCUMENT ME!
1640 public void font_actionPerformed(ActionEvent e)
1642 new FontChooser(alignPanel);
1645 public void smoothFont_actionPerformed(ActionEvent e)
1647 viewport.antiAlias = smoothFont.isSelected();
1648 alignPanel.annotationPanel.image = null;
1649 alignPanel.repaint();
1656 * @param e DOCUMENT ME!
1658 protected void seqLimit_actionPerformed(ActionEvent e)
1660 viewport.setShowJVSuffix(seqLimits.isSelected());
1662 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
1663 alignPanel.repaint();
1670 * @param e DOCUMENT ME!
1672 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
1674 viewport.setColourText(colourTextMenuItem.isSelected());
1675 alignPanel.repaint();
1681 * @param e DOCUMENT ME!
1683 public void wrapMenuItem_actionPerformed(ActionEvent e)
1685 scaleAbove.setVisible(wrapMenuItem.isSelected());
1686 scaleLeft.setVisible(wrapMenuItem.isSelected());
1687 scaleRight.setVisible(wrapMenuItem.isSelected());
1688 viewport.setWrapAlignment(wrapMenuItem.isSelected());
1689 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
1692 public void showAllSeqs_actionPerformed(ActionEvent e)
1694 viewport.showAllHiddenSeqs();
1697 public void showAllColumns_actionPerformed(ActionEvent e)
1699 viewport.showAllHiddenColumns();
1703 public void hideSelSequences_actionPerformed(ActionEvent e)
1705 viewport.hideAllSelectedSeqs();
1706 alignPanel.repaint();
1709 public void hideSelColumns_actionPerformed(ActionEvent e)
1711 viewport.hideSelectedColumns();
1712 alignPanel.repaint();
1715 public void hiddenMarkers_actionPerformed(ActionEvent e)
1717 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
1724 * @param e DOCUMENT ME!
1726 protected void scaleAbove_actionPerformed(ActionEvent e)
1728 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
1729 alignPanel.repaint();
1735 * @param e DOCUMENT ME!
1737 protected void scaleLeft_actionPerformed(ActionEvent e)
1739 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
1740 alignPanel.repaint();
1746 * @param e DOCUMENT ME!
1748 protected void scaleRight_actionPerformed(ActionEvent e)
1750 viewport.setScaleRightWrapped(scaleRight.isSelected());
1751 alignPanel.repaint();
1757 * @param e DOCUMENT ME!
1759 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1761 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
1762 alignPanel.repaint();
1768 * @param e DOCUMENT ME!
1770 public void viewTextMenuItem_actionPerformed(ActionEvent e)
1772 viewport.setShowText(viewTextMenuItem.isSelected());
1773 alignPanel.repaint();
1779 * @param e DOCUMENT ME!
1781 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1783 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
1784 alignPanel.repaint();
1788 public FeatureSettings featureSettings;
1789 public void featureSettings_actionPerformed(ActionEvent e)
1791 if(featureSettings !=null )
1793 featureSettings.close();
1794 featureSettings = null;
1796 featureSettings = new FeatureSettings(this);
1802 * @param evt DOCUMENT ME!
1804 public void showSeqFeatures_actionPerformed(ActionEvent evt)
1806 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
1807 alignPanel.repaint();
1808 if (alignPanel.getOverviewPanel() != null)
1810 alignPanel.getOverviewPanel().updateOverviewImage();
1817 * @param e DOCUMENT ME!
1819 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
1821 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
1822 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
1828 * @param e DOCUMENT ME!
1830 public void overviewMenuItem_actionPerformed(ActionEvent e)
1832 if (alignPanel.overviewPanel != null)
1837 JInternalFrame frame = new JInternalFrame();
1838 OverviewPanel overview = new OverviewPanel(alignPanel);
1839 frame.setContentPane(overview);
1840 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
1841 frame.getWidth(), frame.getHeight());
1843 frame.setLayer(JLayeredPane.PALETTE_LAYER);
1844 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
1846 public void internalFrameClosed(
1847 javax.swing.event.InternalFrameEvent evt)
1849 alignPanel.setOverviewPanel(null);
1854 alignPanel.setOverviewPanel(overview);
1860 * @param e DOCUMENT ME!
1862 protected void noColourmenuItem_actionPerformed(ActionEvent e)
1870 * @param e DOCUMENT ME!
1872 public void clustalColour_actionPerformed(ActionEvent e)
1874 changeColour(new ClustalxColourScheme(
1875 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
1881 * @param e DOCUMENT ME!
1883 public void zappoColour_actionPerformed(ActionEvent e)
1885 changeColour(new ZappoColourScheme());
1891 * @param e DOCUMENT ME!
1893 public void taylorColour_actionPerformed(ActionEvent e)
1895 changeColour(new TaylorColourScheme());
1901 * @param e DOCUMENT ME!
1903 public void hydrophobicityColour_actionPerformed(ActionEvent e)
1905 changeColour(new HydrophobicColourScheme());
1911 * @param e DOCUMENT ME!
1913 public void helixColour_actionPerformed(ActionEvent e)
1915 changeColour(new HelixColourScheme());
1921 * @param e DOCUMENT ME!
1923 public void strandColour_actionPerformed(ActionEvent e)
1925 changeColour(new StrandColourScheme());
1931 * @param e DOCUMENT ME!
1933 public void turnColour_actionPerformed(ActionEvent e)
1935 changeColour(new TurnColourScheme());
1941 * @param e DOCUMENT ME!
1943 public void buriedColour_actionPerformed(ActionEvent e)
1945 changeColour(new BuriedColourScheme());
1951 * @param e DOCUMENT ME!
1953 public void nucleotideColour_actionPerformed(ActionEvent e)
1955 changeColour(new NucleotideColourScheme());
1958 public void annotationColour_actionPerformed(ActionEvent e)
1960 new AnnotationColourChooser(viewport, alignPanel);
1967 * @param e DOCUMENT ME!
1969 protected void applyToAllGroups_actionPerformed(ActionEvent e)
1971 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
1977 * @param cs DOCUMENT ME!
1979 public void changeColour(ColourSchemeI cs)
1985 if (viewport.getAbovePIDThreshold())
1987 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
1990 cs.setThreshold(threshold,
1991 viewport.getIgnoreGapsConsensus());
1993 viewport.setGlobalColourScheme(cs);
1997 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2000 if (viewport.getConservationSelected())
2003 Alignment al = (Alignment) viewport.alignment;
2004 Conservation c = new Conservation("All",
2005 ResidueProperties.propHash, 3,
2006 al.getSequences(), 0,
2010 c.verdict(false, viewport.ConsPercGaps);
2012 cs.setConservation(c);
2014 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
2019 cs.setConservation(null);
2022 cs.setConsensus(viewport.hconsensus);
2025 viewport.setGlobalColourScheme(cs);
2027 if (viewport.getColourAppliesToAllGroups())
2029 Vector groups = viewport.alignment.getGroups();
2031 for (int i = 0; i < groups.size(); i++)
2033 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2041 if (cs instanceof ClustalxColourScheme)
2043 sg.cs = new ClustalxColourScheme(
2044 sg.getSequences(true), sg.getWidth());
2046 else if (cs instanceof UserColourScheme)
2048 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
2054 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2056 catch (Exception ex)
2061 if (viewport.getAbovePIDThreshold()
2062 || cs instanceof PIDColourScheme
2063 || cs instanceof Blosum62ColourScheme)
2065 sg.cs.setThreshold(threshold,
2066 viewport.getIgnoreGapsConsensus());
2068 sg.cs.setConsensus(AAFrequency.calculate(
2069 sg.getSequences(true), 0,
2073 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2076 if (viewport.getConservationSelected())
2078 Conservation c = new Conservation("Group",
2079 ResidueProperties.propHash, 3,
2080 sg.getSequences(true), 0,
2081 viewport.alignment.getWidth() - 1);
2083 c.verdict(false, viewport.ConsPercGaps);
2084 sg.cs.setConservation(c);
2087 sg.cs.setConservation(null);
2091 if (alignPanel.getOverviewPanel() != null)
2093 alignPanel.getOverviewPanel().updateOverviewImage();
2096 alignPanel.repaint();
2102 * @param e DOCUMENT ME!
2104 protected void modifyPID_actionPerformed(ActionEvent e)
2106 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
2108 SliderPanel.setPIDSliderSource(alignPanel,
2109 viewport.getGlobalColourScheme(),
2111 SliderPanel.showPIDSlider();
2118 * @param e DOCUMENT ME!
2120 protected void modifyConservation_actionPerformed(ActionEvent e)
2122 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
2124 SliderPanel.setConservationSlider(alignPanel,
2125 viewport.globalColourScheme,
2127 SliderPanel.showConservationSlider();
2134 * @param e DOCUMENT ME!
2136 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2138 viewport.setConservationSelected(conservationMenuItem.isSelected());
2140 viewport.setAbovePIDThreshold(false);
2141 abovePIDThreshold.setSelected(false);
2143 changeColour(viewport.getGlobalColourScheme());
2145 modifyConservation_actionPerformed(null);
2151 * @param e DOCUMENT ME!
2153 public void abovePIDThreshold_actionPerformed(ActionEvent e)
2155 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
2157 conservationMenuItem.setSelected(false);
2158 viewport.setConservationSelected(false);
2160 changeColour(viewport.getGlobalColourScheme());
2162 modifyPID_actionPerformed(null);
2168 * @param e DOCUMENT ME!
2170 public void userDefinedColour_actionPerformed(ActionEvent e)
2172 if (e.getActionCommand().equals("User Defined..."))
2174 new UserDefinedColours(alignPanel, null);
2178 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
2179 getUserColourSchemes().get(e.getActionCommand());
2185 public void updateUserColourMenu()
2188 Component[] menuItems = colourMenu.getMenuComponents();
2189 int i, iSize = menuItems.length;
2190 for (i = 0; i < iSize; i++)
2192 if (menuItems[i].getName() != null &&
2193 menuItems[i].getName().equals("USER_DEFINED"))
2195 colourMenu.remove(menuItems[i]);
2199 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
2201 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
2202 getUserColourSchemes().keys();
2204 while (userColours.hasMoreElements())
2206 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
2207 nextElement().toString());
2208 radioItem.setName("USER_DEFINED");
2209 radioItem.addMouseListener(new MouseAdapter()
2211 public void mousePressed(MouseEvent evt)
2213 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
2215 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
2217 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
2218 "Remove from default list?",
2219 "Remove user defined colour",
2220 JOptionPane.YES_NO_OPTION);
2221 if(option == JOptionPane.YES_OPTION)
2223 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
2224 colourMenu.remove(radioItem);
2227 radioItem.addActionListener(new ActionListener()
2229 public void actionPerformed(ActionEvent evt)
2231 userDefinedColour_actionPerformed(evt);
2237 radioItem.addActionListener(new ActionListener()
2239 public void actionPerformed(ActionEvent evt)
2241 userDefinedColour_actionPerformed(evt);
2245 colourMenu.insert(radioItem, 15);
2246 colours.add(radioItem);
2254 * @param e DOCUMENT ME!
2256 public void PIDColour_actionPerformed(ActionEvent e)
2258 changeColour(new PIDColourScheme());
2264 * @param e DOCUMENT ME!
2266 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
2268 changeColour(new Blosum62ColourScheme());
2274 * @param e DOCUMENT ME!
2276 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2278 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2279 AlignmentSorter.sortByPID(viewport.getAlignment(),
2280 viewport.getAlignment().getSequenceAt(0));
2281 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));
2282 alignPanel.repaint();
2288 * @param e DOCUMENT ME!
2290 public void sortIDMenuItem_actionPerformed(ActionEvent e)
2292 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2293 AlignmentSorter.sortByID(viewport.getAlignment());
2294 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
2295 alignPanel.repaint();
2301 * @param e DOCUMENT ME!
2303 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
2305 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2306 AlignmentSorter.sortByGroup(viewport.getAlignment());
2307 addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
2309 alignPanel.repaint();
2315 * @param e DOCUMENT ME!
2317 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2319 new RedundancyPanel(alignPanel, this);
2326 * @param e DOCUMENT ME!
2328 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2330 if ( (viewport.getSelectionGroup() == null) ||
2331 (viewport.getSelectionGroup().getSize(false) < 2))
2333 JOptionPane.showInternalMessageDialog(this,
2334 "You must select at least 2 sequences.",
2335 "Invalid Selection",
2336 JOptionPane.WARNING_MESSAGE);
2340 JInternalFrame frame = new JInternalFrame();
2341 frame.setContentPane(new PairwiseAlignPanel(viewport));
2342 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
2349 * @param e DOCUMENT ME!
2351 public void PCAMenuItem_actionPerformed(ActionEvent e)
2353 if ( ( (viewport.getSelectionGroup() != null) &&
2354 (viewport.getSelectionGroup().getSize(false) < 4) &&
2355 (viewport.getSelectionGroup().getSize(false) > 0)) ||
2356 (viewport.getAlignment().getHeight() < 4))
2358 JOptionPane.showInternalMessageDialog(this,
2359 "Principal component analysis must take\n" +
2360 "at least 4 input sequences.",
2361 "Sequence selection insufficient",
2362 JOptionPane.WARNING_MESSAGE);
2367 new PCAPanel(viewport);
2371 public void autoCalculate_actionPerformed(ActionEvent e)
2373 viewport.autoCalculateConsensus = autoCalculate.isSelected();
2374 if(viewport.autoCalculateConsensus)
2376 viewport.firePropertyChange("alignment",
2378 viewport.getAlignment().getSequences());
2386 * @param e DOCUMENT ME!
2388 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2390 NewTreePanel("AV", "PID", "Average distance tree using PID");
2396 * @param e DOCUMENT ME!
2398 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2400 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2406 * @param e DOCUMENT ME!
2408 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2410 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2416 * @param e DOCUMENT ME!
2418 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2420 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2426 * @param type DOCUMENT ME!
2427 * @param pwType DOCUMENT ME!
2428 * @param title DOCUMENT ME!
2430 void NewTreePanel(String type, String pwType, String title)
2434 if (viewport.getSelectionGroup() != null) {
2435 if (viewport.getSelectionGroup().getSize(false) < 3) {
2436 JOptionPane.showMessageDialog(Desktop.desktop,
2437 "You need to have more than two sequences selected to build a tree!",
2438 "Not enough sequences",
2439 JOptionPane.WARNING_MESSAGE);
2444 SequenceGroup sg = viewport.getSelectionGroup();
2446 /* Decide if the selection is a column region */
2447 while (s < sg.getSize(false))
2449 if ( ( (SequenceI) sg.getSequences(false).elementAt(s++)).getLength() <
2452 JOptionPane.showMessageDialog(Desktop.desktop,
2453 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
2454 "Try using the Pad function in the edit menu,\n" +
2455 "or one of the multiple sequence alignment web services.",
2456 "Sequences in selection are not aligned",
2457 JOptionPane.WARNING_MESSAGE);
2463 title = title + " on region";
2464 tp = new TreePanel(alignPanel, type, pwType);
2468 //are the sequences aligned?
2469 if (!viewport.alignment.isAligned())
2471 JOptionPane.showMessageDialog(Desktop.desktop,
2472 "The sequences must be aligned before creating a tree.\n" +
2473 "Try using the Pad function in the edit menu,\n" +
2474 "or one of the multiple sequence alignment web services.",
2475 "Sequences not aligned",
2476 JOptionPane.WARNING_MESSAGE);
2481 if(viewport.alignment.getHeight()<2)
2484 tp = new TreePanel(alignPanel, type, pwType);
2487 addTreeMenuItem(tp, title);
2489 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
2495 * @param title DOCUMENT ME!
2496 * @param order DOCUMENT ME!
2498 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
2500 final JMenuItem item = new JMenuItem("by " + title);
2502 item.addActionListener(new java.awt.event.ActionListener()
2504 public void actionPerformed(ActionEvent e)
2506 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2508 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
2509 AlignmentSorter.sortBy(viewport.getAlignment(), order);
2511 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport.alignment));
2513 alignPanel.repaint();
2519 * Maintain the Order by->Displayed Tree menu.
2520 * Creates a new menu item for a TreePanel with an appropriate
2521 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
2522 * to remove the menu item when the treePanel is closed, and adjust
2523 * the tree leaf to sequence mapping when the alignment is modified.
2524 * @param treePanel Displayed tree window.
2525 * @param title SortBy menu item title.
2527 void addTreeMenuItem(final TreePanel treePanel, String title)
2529 final JMenuItem item = new JMenuItem(title);
2535 sort.add(sortByTreeMenu);
2538 sortByTreeMenu.add(item);
2539 item.addActionListener(new java.awt.event.ActionListener()
2541 public void actionPerformed(ActionEvent e)
2543 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2544 AlignmentSorter.sortByTree(viewport.getAlignment(),
2545 treePanel.getTree());
2547 addHistoryItem(new OrderCommand("Tree Sort",
2549 viewport.alignment));
2552 alignPanel.repaint();
2556 treePanel.addInternalFrameListener(new javax.swing.event.
2557 InternalFrameAdapter()
2559 public void internalFrameClosed(
2560 javax.swing.event.InternalFrameEvent evt)
2563 sortByTreeMenu.remove(item);
2567 sort.remove(sortByTreeMenu);
2575 * Work out whether the whole set of sequences
2576 * or just the selected set will be submitted for multiple alignment.
2579 private jalview.datamodel.AlignmentView gatherSequencesForAlignment()
2581 // Now, check we have enough sequences
2582 AlignmentView msa = null;
2584 if ( (viewport.getSelectionGroup() != null) &&
2585 (viewport.getSelectionGroup().getSize(false) > 1))
2587 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
2588 /*SequenceGroup seqs = viewport.getSelectionGroup();
2590 msa = new SequenceI[sz = seqs.getSize(false)];
2592 for (int i = 0; i < sz; i++)
2594 msa[i] = (SequenceI) seqs.getSequenceAt(i);
2596 msa = viewport.getAlignmentView(true);
2600 /*Vector seqs = viewport.getAlignment().getSequences();
2602 if (seqs.size() > 1)
2604 msa = new SequenceI[seqs.size()];
2606 for (int i = 0; i < seqs.size(); i++)
2608 msa[i] = (SequenceI) seqs.elementAt(i);
2611 msa = viewport.getAlignmentView(false);
2617 * Decides what is submitted to a secondary structure prediction service,
2618 * the currently selected sequence, or the currently selected alignment
2619 * (where the first sequence in the set is the one that the prediction
2622 AlignmentView gatherSeqOrMsaForSecStrPrediction()
2624 AlignmentView seqs = null;
2626 if ( (viewport.getSelectionGroup() != null) &&
2627 (viewport.getSelectionGroup().getSize(false) > 0))
2629 seqs = viewport.getAlignmentView(true);
2633 seqs = viewport.getAlignmentView(false);
2635 // limit sequences - JBPNote in future - could spawn multiple prediction jobs
2636 // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment.
2637 if (!viewport.alignment.isAligned())
2639 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] } );
2646 * @param e DOCUMENT ME!
2648 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2650 // Pick the tree file
2651 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
2654 chooser.setFileView(new JalviewFileView());
2655 chooser.setDialogTitle("Select a newick-like tree file");
2656 chooser.setToolTipText("Load a tree file");
2658 int value = chooser.showOpenDialog(null);
2660 if (value == JalviewFileChooser.APPROVE_OPTION)
2662 String choice = chooser.getSelectedFile().getPath();
2663 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
2667 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
2669 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
2671 catch (Exception ex)
2673 JOptionPane.showMessageDialog(Desktop.desktop,
2674 "Problem reading tree file",
2676 JOptionPane.WARNING_MESSAGE);
2677 ex.printStackTrace();
2683 public TreePanel ShowNewickTree(NewickFile nf, String title)
2685 return ShowNewickTree(nf,title,600,500,4,5);
2687 public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input)
2689 return ShowNewickTree(nf,title, input, 600,500,4,5);
2691 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y) {
2692 return ShowNewickTree(nf, title, null, w, h, x, y);
2695 * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
2697 * @param nf the tree
2698 * @param title tree viewer title
2699 * @param input Associated alignment input data (or null)
2704 * @return TreePanel handle
2706 public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input, int w,int h,int x, int y) {
2707 TreePanel tp = null;
2713 if (nf.getTree() != null)
2715 tp = new TreePanel(alignPanel,
2723 tp.setLocation(x,y);
2726 Desktop.addInternalFrame(tp, title, w, h);
2727 addTreeMenuItem(tp, title);
2730 catch (Exception ex)
2732 ex.printStackTrace();
2743 PrinterJob printJob = PrinterJob.getPrinterJob();
2744 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
2745 printJob.setPrintable(alignPanel, pf);
2747 if (printJob.printDialog())
2753 catch (Exception PrintException)
2755 PrintException.printStackTrace();
2762 * Generates menu items and listener event actions for web service clients
2765 public void BuildWebServiceMenu()
2767 if ( (Discoverer.services != null)
2768 && (Discoverer.services.size() > 0))
2770 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
2771 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
2772 Vector wsmenu = new Vector();
2773 final AlignFrame af = this;
2776 // Add any Multiple Sequence Alignment Services
2777 final JMenu msawsmenu = new JMenu("Alignment");
2778 for (int i = 0, j = msaws.size(); i < j; i++)
2780 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
2782 final JMenuItem method = new JMenuItem(sh.getName());
2783 method.addActionListener(new ActionListener()
2785 public void actionPerformed(ActionEvent e)
2787 AlignmentView msa = gatherSequencesForAlignment();
2788 new jalview.ws.MsaWSClient(sh, title, msa,
2789 false, true, viewport.getAlignment().getDataset(), af);
2794 msawsmenu.add(method);
2795 // Deal with services that we know accept partial alignments.
2796 if (sh.getName().indexOf("lustal") > -1)
2798 // We know that ClustalWS can accept partial alignments for refinement.
2799 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
2800 methodR.addActionListener(new ActionListener()
2802 public void actionPerformed(ActionEvent e)
2804 AlignmentView msa = gatherSequencesForAlignment();
2805 new jalview.ws.MsaWSClient(sh, title, msa,
2806 true, true, viewport.getAlignment().getDataset(), af);
2811 msawsmenu.add(methodR);
2815 wsmenu.add(msawsmenu);
2817 if (secstrpr != null)
2819 // Add any secondary structure prediction services
2820 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
2821 for (int i = 0, j = secstrpr.size(); i < j; i++)
2823 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
2825 final JMenuItem method = new JMenuItem(sh.getName());
2826 method.addActionListener(new ActionListener()
2828 public void actionPerformed(ActionEvent e)
2830 AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
2831 if (msa.getSequences().length == 1)
2833 // Single Sequence prediction
2834 new jalview.ws.JPredClient(sh, title, false, msa, af, true);
2838 if (msa.getSequences().length > 1)
2840 // Sequence profile based prediction
2841 new jalview.ws.JPredClient(sh,
2842 title, true, msa, af, true);
2847 secstrmenu.add(method);
2849 wsmenu.add(secstrmenu);
2851 this.webService.removeAll();
2852 for (int i = 0, j = wsmenu.size(); i < j; i++)
2854 webService.add( (JMenu) wsmenu.get(i));
2859 this.webService.removeAll();
2860 this.webService.add(this.webServiceNoServices);
2862 // TODO: add in rediscovery function
2863 // TODO: reduce code redundancy.
2864 // TODO: group services by location as well as function.
2867 /* public void vamsasStore_actionPerformed(ActionEvent e)
2869 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
2870 getProperty("LAST_DIRECTORY"));
2872 chooser.setFileView(new JalviewFileView());
2873 chooser.setDialogTitle("Export to Vamsas file");
2874 chooser.setToolTipText("Export");
2876 int value = chooser.showSaveDialog(this);
2878 if (value == JalviewFileChooser.APPROVE_OPTION)
2880 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
2881 //vs.store(chooser.getSelectedFile().getAbsolutePath() );
2882 vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
2889 public void showTranslation_actionPerformed(ActionEvent e)
2891 SequenceI [] selection = viewport.getSelectionAsNewSequence();
2892 String [] seqstring = viewport.getViewAsString(true);
2894 int s, sSize = selection.length;
2895 SequenceI [] newSeq = new SequenceI[sSize];
2898 StringBuffer protein;
2900 for(s=0; s<sSize; s++)
2902 protein = new StringBuffer();
2903 seq = AlignSeq.extractGaps("-. ", seqstring[s]);
2904 resSize = seq.length();
2905 resSize -= resSize%3;
2907 for(res = 0; res < resSize; res+=3)
2909 String codon = seq.substring(res, res+3);
2910 codon = codon.replace('U', 'T');
2911 String aa = ResidueProperties.codonTranslate(codon);
2913 protein.append(viewport.getGapCharacter());
2914 else if(aa.equals("STOP"))
2915 protein.append("X");
2917 protein.append( aa );
2919 newSeq[s] = new Sequence(selection[s].getName(),
2920 protein.toString());
2924 AlignmentI al = new Alignment(newSeq);
2925 al.setDataset(null);
2928 ////////////////////////////////
2929 // Copy annotations across
2930 jalview.datamodel.AlignmentAnnotation[] annotations
2931 = viewport.alignment.getAlignmentAnnotation();
2933 if(annotations!=null)
2935 for (int i = 0; i < annotations.length; i++)
2937 if (annotations[i].label.equals("Quality") ||
2938 annotations[i].label.equals("Conservation") ||
2939 annotations[i].label.equals("Consensus"))
2944 aSize = viewport.alignment.getWidth() / 3;
2945 jalview.datamodel.Annotation[] anots =
2946 new jalview.datamodel.Annotation[aSize];
2948 for (a = 0; a < viewport.alignment.getWidth(); a++)
2950 if (annotations[i].annotations[a] == null
2951 || annotations[i].annotations[a] == null)
2954 anots[a / 3] = new Annotation(
2955 annotations[i].annotations[a].displayCharacter,
2956 annotations[i].annotations[a].description,
2957 annotations[i].annotations[a].secondaryStructure,
2958 annotations[i].annotations[a].value,
2959 annotations[i].annotations[a].colour);
2962 jalview.datamodel.AlignmentAnnotation aa
2963 = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
2964 annotations[i].description, anots);
2965 al.addAnnotation(aa);
2969 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2970 Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
2982 * @param String DOCUMENT ME!
2984 public boolean parseFeaturesFile(String file, String type)
2986 boolean featuresFile = false;
2988 featuresFile = new FeaturesFile(file, type).parse(viewport.alignment.getDataset(),
2989 alignPanel.seqPanel.seqCanvas.
2990 getFeatureRenderer().featureColours,
2995 ex.printStackTrace();
3000 viewport.showSequenceFeatures = true;
3001 showSeqFeatures.setSelected(true);
3002 alignPanel.repaint();
3005 return featuresFile;
3008 public void dragEnter(DropTargetDragEvent evt)
3011 public void dragExit(DropTargetEvent evt)
3014 public void dragOver(DropTargetDragEvent evt)
3017 public void dropActionChanged(DropTargetDragEvent evt)
3020 public void drop(DropTargetDropEvent evt)
3022 Transferable t = evt.getTransferable();
3023 java.util.List files = null;
3027 DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
3028 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
3030 //Works on Windows and MacOSX
3031 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3032 files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
3034 else if (t.isDataFlavorSupported(uriListFlavor))
3036 // This is used by Unix drag system
3037 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3038 String data = (String) t.getTransferData(uriListFlavor);
3039 files = new java.util.ArrayList(1);
3040 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
3043 st.hasMoreTokens(); )
3045 String s = st.nextToken();
3046 if (s.startsWith("#"))
3048 // the line is a comment (as per the RFC 2483)
3052 java.net.URI uri = new java.net.URI(s);
3053 java.io.File file = new java.io.File(uri);
3060 e.printStackTrace();
3067 for (int i = 0; i < files.size(); i++)
3069 loadJalviewDataFile(files.get(i).toString());
3072 catch (Exception ex)
3074 ex.printStackTrace();
3079 // This method will attempt to load a "dropped" file first by testing
3080 // whether its and Annotation file, then features file. If both are
3081 // false then the user may have dropped an alignment file onto this
3083 public void loadJalviewDataFile(String file)
3086 String protocol = "File";
3088 if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
3093 boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
3098 boolean isGroupsFile = parseFeaturesFile(file,protocol);
3101 String format = new IdentifyFile().Identify(file, protocol);
3103 if(format.equalsIgnoreCase("JnetFile"))
3105 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
3107 new JnetAnnotationMaker().add_annotation(predictions,
3108 viewport.getAlignment(),
3110 alignPanel.adjustAnnotationHeight();
3111 alignPanel.repaint();
3114 new FileLoader().LoadFile(viewport, file, protocol, format);
3120 alignPanel.adjustAnnotationHeight();
3123 }catch(Exception ex)
3125 ex.printStackTrace();
3129 public void tabSelectionChanged(int index)
3133 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
3134 viewport = alignPanel.av;
3135 setMenusFromViewport(viewport);
3139 public void tabbedPane_mousePressed(MouseEvent e)
3141 if(SwingUtilities.isRightMouseButton(e))
3143 String reply = JOptionPane.showInternalInputDialog(this,
3146 JOptionPane.QUESTION_MESSAGE);
3150 viewport.viewName = reply;
3151 tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
3157 public AlignViewport getCurrentView()