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.*;
39 import javax.swing.event.ChangeListener;
40 import javax.swing.event.ChangeEvent;
48 public class AlignFrame 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 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
118 if (viewport.conservation == null)
120 BLOSUM62Colour.setEnabled(false);
121 conservationMenuItem.setEnabled(false);
122 modifyConservation.setEnabled(false);
123 // PIDColour.setEnabled(false);
124 // abovePIDThreshold.setEnabled(false);
125 // modifyPID.setEnabled(false);
128 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
130 if (sortby.equals("Id"))
131 sortIDMenuItem_actionPerformed(null);
132 else if (sortby.equals("Pairwise Identity"))
133 sortPairwiseMenuItem_actionPerformed(null);
135 if (Desktop.desktop != null)
137 addServiceListeners();
138 setGUINucleotide(viewport.alignment.isNucleotide());
141 setMenusFromViewport(viewport);
143 if (viewport.wrapAlignment)
145 wrapMenuItem_actionPerformed(null);
152 public void setFileName(String file, String format)
155 currentFileFormat = format;
156 reload.setEnabled(true);
159 void addKeyListener()
161 addKeyListener(new KeyAdapter()
163 public void keyPressed(KeyEvent evt)
165 if (viewport.cursorMode
166 && evt.getKeyCode() >= KeyEvent.VK_0
167 && evt.getKeyCode() <= KeyEvent.VK_9)
169 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
172 switch (evt.getKeyCode())
175 case 27: // escape key
176 deselectAllSequenceMenuItem_actionPerformed(null);
180 case KeyEvent.VK_DOWN:
181 if (viewport.cursorMode)
183 alignPanel.seqPanel.moveCursor(0, 1);
186 moveSelectedSequences(false);
190 if (viewport.cursorMode)
192 alignPanel.seqPanel.moveCursor(0, -1);
195 moveSelectedSequences(true);
198 case KeyEvent.VK_LEFT:
199 if (viewport.cursorMode)
201 alignPanel.seqPanel.moveCursor( -1, 0);
205 case KeyEvent.VK_RIGHT:
206 if (viewport.cursorMode)
208 alignPanel.seqPanel.moveCursor(1, 0);
212 case KeyEvent.VK_SPACE:
213 if (viewport.cursorMode)
215 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
221 case KeyEvent.VK_DELETE:
222 case KeyEvent.VK_BACK_SPACE:
223 if (!viewport.cursorMode)
225 cut_actionPerformed(null);
228 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
235 if (viewport.cursorMode)
237 alignPanel.seqPanel.setCursorRow();
241 if (viewport.cursorMode && !evt.isControlDown())
243 alignPanel.seqPanel.setCursorColumn();
247 if (viewport.cursorMode)
249 alignPanel.seqPanel.setCursorPosition();
253 case KeyEvent.VK_ENTER:
254 case KeyEvent.VK_COMMA:
255 if (viewport.cursorMode)
257 alignPanel.seqPanel.setCursorRowAndColumn();
262 if (viewport.cursorMode)
264 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
268 if (viewport.cursorMode)
270 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
275 viewport.cursorMode = !viewport.cursorMode;
276 statusBar.setText("Keyboard editing mode is " +
277 (viewport.cursorMode ? "on" : "off"));
278 if (viewport.cursorMode)
280 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
281 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
283 alignPanel.seqPanel.seqCanvas.repaint();
289 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
290 java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
291 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
293 javax.help.HelpBroker hb = hs.createHelpBroker();
294 hb.setCurrentID("home");
295 hb.setDisplayed(true);
299 ex.printStackTrace();
305 boolean toggleSeqs = !evt.isControlDown();
306 boolean toggleCols = !evt.isShiftDown();
308 boolean hide = false;
310 SequenceGroup sg = viewport.getSelectionGroup();
313 if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
315 hideSelSequences_actionPerformed(null);
318 else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))
319 showAllSeqs_actionPerformed(null);
324 if (viewport.colSel.getSelected().size() > 0)
326 hideSelColumns_actionPerformed(null);
328 viewport.selectionGroup = sg;
331 showAllColumns_actionPerformed(null);
335 case KeyEvent.VK_PAGE_UP:
336 if (viewport.wrapAlignment)
337 alignPanel.scrollUp(true);
339 alignPanel.setScrollValues(viewport.startRes,
341 - viewport.endSeq + viewport.startSeq);
343 case KeyEvent.VK_PAGE_DOWN:
344 if (viewport.wrapAlignment)
345 alignPanel.scrollUp(false);
347 alignPanel.setScrollValues(viewport.startRes,
349 + viewport.endSeq - viewport.startSeq);
357 public void addAlignmentPanel(final AlignmentPanel ap,
360 ap.alignFrame = this;
362 alignPanels.addElement(ap);
364 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
366 int aSize = alignPanels.size();
368 tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
370 if (aSize == 1 && ap.av.viewName==null)
372 this.getContentPane().add(ap, BorderLayout.CENTER);
378 setInitialTabVisible();
381 expandViews.setEnabled(true);
382 gatherViews.setEnabled(true);
383 tabbedPane.addTab(ap.av.viewName, ap);
385 ap.setVisible(false);
391 ap.av.alignment.padGaps();
392 ap.av.updateConservation(ap);
393 ap.av.updateConsensus(ap);
397 public void setInitialTabVisible()
399 expandViews.setEnabled(true);
400 gatherViews.setEnabled(true);
401 tabbedPane.setVisible(true);
402 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
403 tabbedPane.addTab(first.av.viewName,first);
404 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
408 public AlignViewport getViewport()
413 /* Set up intrinsic listeners for dynamically generated GUI bits. */
414 private void addServiceListeners()
416 final java.beans.PropertyChangeListener thisListener;
417 // Do this once to get current state
418 BuildWebServiceMenu();
419 Desktop.discoverer.addPropertyChangeListener(
420 thisListener = new java.beans.PropertyChangeListener()
422 public void propertyChange(PropertyChangeEvent evt)
424 // System.out.println("Discoverer property change.");
425 if (evt.getPropertyName().equals("services"))
427 // System.out.println("Rebuilding web service menu");
428 BuildWebServiceMenu();
433 addInternalFrameListener(new javax.swing.event.
434 InternalFrameAdapter()
436 public void internalFrameClosed(
437 javax.swing.event.InternalFrameEvent evt)
439 // System.out.println("deregistering discoverer listener");
440 Desktop.discoverer.removePropertyChangeListener(thisListener);
441 closeMenuItem_actionPerformed(true);
447 public void setGUINucleotide(boolean nucleotide)
449 showTranslation.setVisible( nucleotide );
450 conservationMenuItem.setEnabled( !nucleotide );
451 modifyConservation.setEnabled( !nucleotide );
453 //Remember AlignFrame always starts as protein
456 calculateMenu.remove(calculateMenu.getItemCount()-2);
461 * Need to call this method when tabs are selected for multiple views,
462 * or when loading from Jalview2XML.java
463 * @param av AlignViewport
465 void setMenusFromViewport(AlignViewport av)
467 padGapsMenuitem.setSelected(av.padGaps);
468 colourTextMenuItem.setSelected(av.showColourText);
469 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
470 conservationMenuItem.setSelected(av.getConservationSelected());
471 seqLimits.setSelected(av.getShowJVSuffix());
472 idRightAlign.setSelected(av.rightAlignIds);
473 renderGapsMenuItem.setSelected(av.renderGaps);
474 wrapMenuItem.setSelected(av.wrapAlignment);
475 annotationPanelMenuItem.setState(av.showAnnotation);
476 viewBoxesMenuItem.setSelected(av.showBoxes);
477 viewTextMenuItem.setSelected(av.showText);
479 setColourSelected(ColourSchemeProperty.
480 getColourName(av.getGlobalColourScheme()));
482 showSeqFeatures.setSelected(av.showSequenceFeatures);
483 hiddenMarkers.setState(av.showHiddenMarkers);
484 applyToAllGroups.setState(av.colourAppliesToAllGroups);
490 Hashtable progressBars;
491 public void setProgressBar(String message, long id)
493 if(progressBars == null)
494 progressBars = new Hashtable();
496 JPanel progressPanel;
497 GridLayout layout = (GridLayout) statusPanel.getLayout();
498 if(progressBars.get( new Long(id) )!=null)
500 progressPanel = (JPanel)progressBars.get( new Long(id) );
501 statusPanel.remove(progressPanel);
502 progressBars.remove( progressPanel );
503 progressPanel = null;
505 statusBar.setText(message);
507 layout.setRows(layout.getRows() - 1);
511 progressPanel = new JPanel(new BorderLayout(10, 5));
513 JProgressBar progressBar = new JProgressBar();
514 progressBar.setIndeterminate(true);
516 progressPanel.add(new JLabel(message), BorderLayout.WEST);
517 progressPanel.add(progressBar, BorderLayout.CENTER);
519 layout.setRows(layout.getRows() + 1);
520 statusPanel.add(progressPanel);
522 progressBars.put(new Long(id), progressPanel);
532 Added so Castor Mapping file can obtain Jalview Version
534 public String getVersion()
536 return jalview.bin.Cache.getProperty("VERSION");
539 public FeatureRenderer getFeatureRenderer()
541 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
545 public void fetchSequence_actionPerformed(ActionEvent e)
547 new SequenceFetcher(this);
550 public void addFromFile_actionPerformed(ActionEvent e)
552 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
555 public void reload_actionPerformed(ActionEvent e)
559 if(currentFileFormat.equals("Jalview"))
561 JInternalFrame [] frames = Desktop.desktop.getAllFrames();
562 for(int i=0; i<frames.length; i++)
564 if (frames[i] instanceof AlignFrame
566 && ( (AlignFrame) frames[i]).fileName.equals(fileName))
569 frames[i].setSelected(true);
570 Desktop.instance.closeAssociatedWindows();
571 }catch(java.beans.PropertyVetoException ex){}
575 Desktop.instance.closeAssociatedWindows();
580 viewport.alignment.deleteAllGroups();
581 viewport.sequenceColours=null;
582 while (viewport.alignment.getHeight() > 0)
584 viewport.alignment.deleteSequence(0);
587 viewport.historyList.clear();
588 viewport.redoList.clear();
589 Alignment dset = viewport.alignment.getDataset();
590 while (dset.getHeight() > 0)
592 dset.deleteSequence(0);
595 firePropertyChange("Alignment", null, null);
600 FileLoader loader = new FileLoader();
601 String protocol = fileName.startsWith("http:")? "URL":"File";
602 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
608 public void addFromText_actionPerformed(ActionEvent e)
610 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
613 public void addFromURL_actionPerformed(ActionEvent e)
615 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
619 public void save_actionPerformed(ActionEvent e)
621 if(fileName==null || currentFileFormat==null)
622 saveAs_actionPerformed(null);
624 saveAlignment(fileName, currentFileFormat);
630 * @param e DOCUMENT ME!
632 public void saveAs_actionPerformed(ActionEvent e)
634 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
635 getProperty( "LAST_DIRECTORY"),
637 { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" },
639 { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
644 chooser.setFileView(new JalviewFileView());
645 chooser.setDialogTitle("Save Alignment to file");
646 chooser.setToolTipText("Save");
648 int value = chooser.showSaveDialog(this);
650 if (value == JalviewFileChooser.APPROVE_OPTION)
652 currentFileFormat = chooser.getSelectedFormat();
653 if (currentFileFormat == null)
655 JOptionPane.showInternalMessageDialog(Desktop.desktop,
656 "You must select a file format before saving!",
657 "File format not specified",
658 JOptionPane.WARNING_MESSAGE);
659 value = chooser.showSaveDialog(this);
663 fileName = chooser.getSelectedFile().getPath();
665 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
668 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
670 saveAlignment(fileName, currentFileFormat);
674 public boolean saveAlignment(String file, String format)
676 if (format.equalsIgnoreCase("Jalview"))
678 String shortName = title;
680 if (shortName.indexOf(java.io.File.separatorChar) > -1)
682 shortName = shortName.substring(shortName.lastIndexOf(
683 java.io.File.separatorChar) + 1);
686 new Jalview2XML().SaveAlignment(this, file, shortName);
688 statusBar.setText("Successfully saved to file: "
690 +format +" format.");
693 // USE Jalview2XML to save this file
699 String[] omitHidden = null;
701 if (viewport.hasHiddenColumns)
703 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
704 "The Alignment contains hidden columns."
705 + "\nDo you want to save only the visible alignment?",
706 "Save / Omit Hidden Columns",
707 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
709 if (reply == JOptionPane.YES_OPTION)
710 omitHidden = viewport.getViewAsString(false);
713 String output = new FormatAdapter().formatSequences(
715 viewport.alignment.getSequencesArray(),
725 java.io.PrintWriter out = new java.io.PrintWriter(
726 new java.io.FileWriter(file));
731 statusBar.setText("Successfully saved to file: "
733 +format +" format.");
738 ex.printStackTrace();
747 * @param e DOCUMENT ME!
749 protected void outputText_actionPerformed(ActionEvent e)
751 String [] omitHidden = null;
753 if(viewport.hasHiddenColumns)
755 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
756 "The Alignment contains hidden columns."
757 +"\nDo you want to output only the visible alignment?",
758 "Save / Omit Hidden Columns",
759 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
761 if(reply==JOptionPane.YES_OPTION)
763 omitHidden = viewport.getViewAsString(false);
767 CutAndPasteTransfer cap = new CutAndPasteTransfer();
768 cap.setForInput(null);
769 Desktop.addInternalFrame(cap,
770 "Alignment output - " + e.getActionCommand(), 600,
774 cap.setText(new FormatAdapter().formatSequences(
775 e.getActionCommand(),
776 viewport.alignment.getSequencesArray(),
783 * @param e DOCUMENT ME!
785 protected void htmlMenuItem_actionPerformed(ActionEvent e)
787 new HTMLOutput(viewport,
788 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
789 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
792 public void createImageMap(File file, String image)
794 alignPanel.makePNGImageMap(file, image);
800 * @param e DOCUMENT ME!
802 public void createPNG(File f)
804 alignPanel.makePNG(f);
810 * @param e DOCUMENT ME!
812 public void createEPS(File f)
814 alignPanel.makeEPS(f);
820 * @param e DOCUMENT ME!
822 public void printMenuItem_actionPerformed(ActionEvent e)
824 //Putting in a thread avoids Swing painting problems
825 PrintThread thread = new PrintThread();
829 public void exportFeatures_actionPerformed(ActionEvent e)
831 new AnnotationExporter().exportFeatures(alignPanel);
835 public void exportAnnotations_actionPerformed(ActionEvent e)
837 new AnnotationExporter().exportAnnotations(
839 viewport.alignment.getAlignmentAnnotation()
844 public void associatedData_actionPerformed(ActionEvent e)
846 // Pick the tree file
847 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
850 chooser.setFileView(new JalviewFileView());
851 chooser.setDialogTitle("Load Jalview Annotations or Features File");
852 chooser.setToolTipText("Load Jalview Annotations / Features file");
854 int value = chooser.showOpenDialog(null);
856 if (value == JalviewFileChooser.APPROVE_OPTION)
858 String choice = chooser.getSelectedFile().getPath();
859 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
860 loadJalviewDataFile(choice);
869 * @param e DOCUMENT ME!
871 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
873 if(alignPanels!=null && alignPanels.size()<2)
878 if(alignPanels!=null)
881 for (int i = 0; i < alignPanels.size(); i++)
883 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
884 PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
885 PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
886 PaintRefresher.RemoveComponent(ap);
890 int index = tabbedPane.getSelectedIndex();
892 alignPanels.removeElement(alignPanel);
893 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
894 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
895 PaintRefresher.RemoveComponent(alignPanel);
899 tabbedPane.removeTabAt(index);
900 tabbedPane.validate();
902 if(index==tabbedPane.getTabCount())
905 this.tabSelectionChanged(index);
910 this.setClosed(true);
914 ex.printStackTrace();
922 void updateEditMenuBar()
925 if (viewport.historyList.size() > 0)
927 undoMenuItem.setEnabled(true);
928 CommandI command = (CommandI) viewport.historyList.peek();
929 undoMenuItem.setText("Undo " + command.getDescription());
933 undoMenuItem.setEnabled(false);
934 undoMenuItem.setText("Undo");
937 if (viewport.redoList.size() > 0)
939 redoMenuItem.setEnabled(true);
941 CommandI command = (CommandI) viewport.redoList.peek();
942 redoMenuItem.setText("Redo " + command.getDescription());
946 redoMenuItem.setEnabled(false);
947 redoMenuItem.setText("Redo");
952 public void addHistoryItem(CommandI command)
954 if(command.getSize()>0)
956 viewport.historyList.push(command);
957 viewport.redoList.clear();
959 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
968 * @param e DOCUMENT ME!
970 protected void undoMenuItem_actionPerformed(ActionEvent e)
972 CommandI command = (CommandI)viewport.historyList.pop();
973 viewport.redoList.push(command);
974 command.undoCommand();
976 AlignViewport originalSource = getOriginatingSource(command);
979 if(originalSource!=null)
981 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
982 originalSource.firePropertyChange("alignment", null,null);
989 * @param e DOCUMENT ME!
991 protected void redoMenuItem_actionPerformed(ActionEvent e)
993 if(viewport.redoList.size()<1)
996 CommandI command = (CommandI) viewport.redoList.pop();
997 viewport.historyList.push(command);
1000 AlignViewport originalSource = getOriginatingSource(command);
1001 updateEditMenuBar();
1003 if(originalSource!=null)
1005 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1006 originalSource.firePropertyChange("alignment", null,null);
1010 AlignViewport getOriginatingSource(CommandI command)
1012 AlignViewport originalSource = null;
1013 //For sequence removal and addition, we need to fire
1014 //the property change event FROM the viewport where the
1015 //original alignment was altered
1017 if (command instanceof EditCommand)
1019 EditCommand editCommand = (EditCommand) command;
1020 al = editCommand.getAlignment();
1021 Vector comps = (Vector) PaintRefresher.components
1022 .get(viewport.getSequenceSetId());
1024 for (int i = 0; i < comps.size(); i++)
1026 if (comps.elementAt(i) instanceof AlignmentPanel)
1028 if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
1030 originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
1037 if (originalSource == null)
1039 //The original view is closed, we must validate
1040 //the current view against the closed view first
1042 PaintRefresher.validateSequences(al, viewport.alignment);
1044 originalSource = viewport;
1047 return originalSource;
1053 * @param up DOCUMENT ME!
1055 public void moveSelectedSequences(boolean up)
1057 SequenceGroup sg = viewport.getSelectionGroup();
1066 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1068 SequenceI seq = viewport.alignment.getSequenceAt(i);
1070 if (!sg.getSequences(false).contains(seq))
1075 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1077 if (sg.getSequences(false).contains(temp))
1082 viewport.alignment.getSequences().setElementAt(temp, i);
1083 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1088 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1090 SequenceI seq = viewport.alignment.getSequenceAt(i);
1092 if (!sg.getSequences(false).contains(seq))
1097 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1099 if (sg.getSequences(false).contains(temp))
1104 viewport.alignment.getSequences().setElementAt(temp, i);
1105 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1109 alignPanel.repaint();
1117 * @param e DOCUMENT ME!
1119 protected void copy_actionPerformed(ActionEvent e)
1122 if (viewport.getSelectionGroup() == null)
1127 SequenceI [] seqs = viewport.getSelectionAsNewSequence();
1128 String[] omitHidden = null;
1130 if (viewport.hasHiddenColumns)
1132 omitHidden = viewport.getViewAsString(true);
1135 String output = new FormatAdapter().formatSequences(
1140 StringSelection ss = new StringSelection(output);
1144 //Its really worth setting the clipboard contents
1145 //to empty before setting the large StringSelection!!
1146 Toolkit.getDefaultToolkit().getSystemClipboard()
1147 .setContents(new StringSelection(""), null);
1149 Toolkit.getDefaultToolkit().getSystemClipboard()
1150 .setContents(ss, Desktop.instance);
1152 catch (OutOfMemoryError er)
1154 er.printStackTrace();
1155 javax.swing.SwingUtilities.invokeLater(new Runnable()
1159 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1160 "Out of memory copying region!!"
1162 "\nSee help files for increasing Java Virtual Machine memory."
1164 javax.swing.JOptionPane.WARNING_MESSAGE);
1171 Vector hiddenColumns = null;
1172 if(viewport.hasHiddenColumns)
1174 hiddenColumns =new Vector();
1175 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1176 for(int i=0; i<viewport.getColumnSelection().getHiddenColumns().size(); i++)
1178 int[] region = (int[])
1179 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
1181 hiddenColumns.addElement(new int[]{region[0]-hiddenOffset,
1182 region[1]-hiddenOffset});
1188 Desktop.jalviewClipboard = new Object[]{ seqs,
1189 viewport.alignment.getDataset(),
1191 statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
1197 * @param e DOCUMENT ME!
1199 protected void pasteNew_actionPerformed(ActionEvent e)
1207 * @param e DOCUMENT ME!
1209 protected void pasteThis_actionPerformed(ActionEvent e)
1217 * @param newAlignment DOCUMENT ME!
1219 void paste(boolean newAlignment)
1223 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1224 Transferable contents = c.getContents(this);
1226 if (contents == null)
1234 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1235 if (str.length() < 1)
1238 format = new IdentifyFile().Identify(str, "Paste");
1241 catch (OutOfMemoryError er)
1243 er.printStackTrace();
1244 javax.swing.SwingUtilities.invokeLater(new Runnable()
1248 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1249 "Out of memory pasting sequences!!"
1251 "\nSee help files for increasing Java Virtual Machine memory."
1253 javax.swing.JOptionPane.WARNING_MESSAGE);
1260 SequenceI[] sequences;
1263 if(Desktop.jalviewClipboard!=null)
1265 // The clipboard was filled from within Jalview, we must use the sequences
1266 // And dataset from the copied alignment
1267 sequences = (SequenceI[])Desktop.jalviewClipboard[0];
1271 sequences = new FormatAdapter().readFile(str, "Paste", format);
1274 AlignmentI alignment = null;
1278 alignment = new Alignment(sequences);
1280 if (Desktop.jalviewClipboard != null)
1281 alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
1283 alignment.setDataset(null);
1287 alignment = viewport.getAlignment();
1290 SequenceI [] newseqs = new SequenceI[sequences.length];
1291 for (int i = 0; i < sequences.length; i++)
1293 newseqs[i] = new Sequence(sequences[i].getName(),
1294 sequences[i].getSequence(), sequences[i].getStart(),
1295 sequences[i].getEnd());
1297 alignment.addSequence(newseqs[i]);
1303 addHistoryItem(new EditCommand(
1308 alignment.getWidth(),
1313 viewport.setEndSeq(alignment.getHeight());
1314 alignment.getWidth();
1315 viewport.firePropertyChange("alignment", null, alignment.getSequences());
1320 // Add any annotations attached to sequences
1321 for (int i = 0; i < sequences.length; i++)
1323 if (sequences[i].getAnnotation() != null)
1325 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1327 AlignmentAnnotation newAnnot =
1328 new AlignmentAnnotation(
1329 sequences[i].getAnnotation()[a].label,
1330 sequences[i].getAnnotation()[a].description,
1331 sequences[i].getAnnotation()[a].annotations,
1332 sequences[i].getAnnotation()[a].graphMin,
1333 sequences[i].getAnnotation()[a].graphMax,
1334 sequences[i].getAnnotation()[a].graph);
1336 sequences[i].getAnnotation()[a] = newAnnot;
1337 newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].
1339 newAnnot.sequenceRef = sequences[i];
1340 newAnnot.adjustForAlignment();
1341 alignment.addAnnotation(newAnnot);
1342 alignment.setAnnotationIndex(newAnnot, a);
1345 alignPanel.annotationPanel.adjustPanelHeight();
1351 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
1352 String newtitle = new String("Copied sequences");
1354 if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
1356 Vector hc = (Vector)Desktop.jalviewClipboard[2];
1357 for(int i=0; i<hc.size(); i++)
1359 int [] region = (int[]) hc.elementAt(i);
1360 af.viewport.hideColumns(region[0], region[1]);
1365 //>>>This is a fix for the moment, until a better solution is found!!<<<
1366 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
1367 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1370 if (title.startsWith("Copied sequences"))
1376 newtitle = newtitle.concat("- from " + title);
1379 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1386 catch (Exception ex)
1388 ex.printStackTrace();
1389 System.out.println("Exception whilst pasting: "+ex);
1390 // could be anything being pasted in here
1399 * @param e DOCUMENT ME!
1401 protected void cut_actionPerformed(ActionEvent e)
1403 copy_actionPerformed(null);
1404 delete_actionPerformed(null);
1410 * @param e DOCUMENT ME!
1412 protected void delete_actionPerformed(ActionEvent evt)
1415 SequenceGroup sg = viewport.getSelectionGroup();
1421 Vector seqs = new Vector();
1423 for (int i = 0; i < sg.getSize(false); i++)
1425 seq = sg.getSequenceAt(i);
1426 seqs.addElement(seq);
1430 // If the cut affects all sequences, remove highlighted columns
1431 if (sg.getSize(false) == viewport.alignment.getHeight())
1433 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1434 sg.getEndRes() + 1);
1438 SequenceI [] cut = new SequenceI[seqs.size()];
1439 for(int i=0; i<seqs.size(); i++)
1440 cut[i] = (SequenceI)seqs.elementAt(i);
1446 addHistoryItem(new EditCommand("Cut Sequences",
1450 sg.getEndRes()-sg.getStartRes()+1,
1451 viewport.alignment));
1454 viewport.setSelectionGroup(null);
1455 viewport.alignment.deleteGroup(sg);
1457 viewport.firePropertyChange("alignment", null,
1458 viewport.getAlignment().getSequences());
1460 if (viewport.getAlignment().getHeight() < 1)
1464 this.setClosed(true);
1466 catch (Exception ex)
1475 * @param e DOCUMENT ME!
1477 protected void deleteGroups_actionPerformed(ActionEvent e)
1479 viewport.alignment.deleteAllGroups();
1480 viewport.sequenceColours.clear();
1481 viewport.setSelectionGroup(null);
1482 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1483 alignPanel.repaint();
1489 * @param e DOCUMENT ME!
1491 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1493 SequenceGroup sg = new SequenceGroup();
1495 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1498 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1501 sg.setEndRes(viewport.alignment.getWidth() - 1);
1502 viewport.setSelectionGroup(sg);
1503 alignPanel.repaint();
1504 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1510 * @param e DOCUMENT ME!
1512 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1514 if(viewport.cursorMode)
1516 alignPanel.seqPanel.keyboardNo1 = null;
1517 alignPanel.seqPanel.keyboardNo2 = null;
1519 viewport.setSelectionGroup(null);
1520 viewport.getColumnSelection().clear();
1521 viewport.setSelectionGroup(null);
1522 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1523 alignPanel.idPanel.idCanvas.searchResults = null;
1524 alignPanel.repaint();
1525 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1531 * @param e DOCUMENT ME!
1533 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1535 SequenceGroup sg = viewport.getSelectionGroup();
1539 selectAllSequenceMenuItem_actionPerformed(null);
1544 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1547 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1550 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1553 public void invertColSel_actionPerformed(ActionEvent e)
1555 viewport.invertColumnSelection();
1556 alignPanel.repaint();
1563 * @param e DOCUMENT ME!
1565 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1567 trimAlignment(true);
1573 * @param e DOCUMENT ME!
1575 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
1577 trimAlignment(false);
1580 void trimAlignment(boolean trimLeft)
1582 ColumnSelection colSel = viewport.getColumnSelection();
1585 if (colSel.size() > 0)
1588 column = colSel.getMin();
1590 column = colSel.getMax();
1593 if(viewport.getSelectionGroup()!=null)
1594 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
1596 seqs = viewport.alignment.getSequencesArray();
1599 TrimRegionCommand trimRegion;
1602 trimRegion = new TrimRegionCommand("Remove Left",
1603 TrimRegionCommand.TRIM_LEFT,
1608 viewport.selectionGroup);
1609 viewport.setStartRes(0);
1613 trimRegion = new TrimRegionCommand("Remove Right",
1614 TrimRegionCommand.TRIM_RIGHT,
1619 viewport.selectionGroup);
1622 statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
1625 addHistoryItem(trimRegion);
1627 Vector groups = viewport.alignment.getGroups();
1629 for (int i = 0; i < groups.size(); i++)
1631 SequenceGroup sg = (SequenceGroup) groups.get(i);
1633 if ( (trimLeft && !sg.adjustForRemoveLeft(column))
1634 || (!trimLeft && !sg.adjustForRemoveRight(column)))
1636 viewport.alignment.deleteGroup(sg);
1640 viewport.firePropertyChange("alignment", null,
1641 viewport.getAlignment().getSequences());
1648 * @param e DOCUMENT ME!
1650 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1652 int start = 0, end = viewport.alignment.getWidth()-1;
1655 if (viewport.getSelectionGroup() != null)
1657 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
1658 start = viewport.getSelectionGroup().getStartRes();
1659 end = viewport.getSelectionGroup().getEndRes();
1662 seqs = viewport.alignment.getSequencesArray();
1665 RemoveGapColCommand removeGapCols =
1666 new RemoveGapColCommand("Remove Gapped Columns",
1669 viewport.getGapCharacter());
1671 addHistoryItem(removeGapCols);
1673 statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
1675 //This is to maintain viewport position on first residue
1677 SequenceI seq = viewport.alignment.getSequenceAt(0);
1678 int startRes = seq.findPosition(viewport.startRes);
1679 // ShiftList shifts;
1680 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
1681 // edit.alColumnChanges=shifts.getInverse();
1682 // if (viewport.hasHiddenColumns)
1683 // viewport.getColumnSelection().compensateForEdits(shifts);
1684 viewport.setStartRes(seq.findIndex(startRes)-1);
1685 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1692 * @param e DOCUMENT ME!
1694 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1696 int start = 0, end = viewport.alignment.getWidth()-1;
1699 if (viewport.getSelectionGroup() != null)
1701 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
1702 start = viewport.getSelectionGroup().getStartRes();
1703 end = viewport.getSelectionGroup().getEndRes();
1706 seqs = viewport.alignment.getSequencesArray();
1708 //This is to maintain viewport position on first residue
1710 SequenceI seq = viewport.alignment.getSequenceAt(0);
1711 int startRes = seq.findPosition(viewport.startRes);
1713 addHistoryItem(new RemoveGapsCommand("Remove Gaps",
1716 viewport.getGapCharacter()));
1718 viewport.setStartRes(seq.findIndex(startRes)-1);
1720 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1727 * @param e DOCUMENT ME!
1729 public void padGapsMenuitem_actionPerformed(ActionEvent e)
1731 viewport.padGaps = padGapsMenuitem.isSelected();
1733 viewport.firePropertyChange("alignment",
1735 viewport.getAlignment().getSequences());
1741 * @param e DOCUMENT ME!
1743 public void findMenuItem_actionPerformed(ActionEvent e)
1748 public void newView_actionPerformed(ActionEvent e)
1750 AlignmentPanel newap =
1751 new Jalview2XML().copyAlignPanel(alignPanel, true);
1753 if (viewport.viewName == null)
1754 viewport.viewName = "Original";
1756 newap.av.historyList = viewport.historyList;
1757 newap.av.redoList = viewport.redoList;
1759 int index = Desktop.getViewCount(viewport.getSequenceSetId());
1760 String newViewName = "View " +index;
1762 Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
1763 Vector existingNames = new Vector();
1764 for(int i=0; i<comps.size(); i++)
1766 if(comps.elementAt(i) instanceof AlignmentPanel)
1768 AlignmentPanel ap = (AlignmentPanel)comps.elementAt(i);
1769 if(!existingNames.contains(ap.av.viewName))
1770 existingNames.addElement(ap.av.viewName);
1774 while(existingNames.contains(newViewName))
1776 newViewName = "View "+ (++index);
1779 newap.av.viewName = newViewName;
1781 addAlignmentPanel(newap, false);
1783 if(alignPanels.size()==2)
1785 viewport.gatherViewsHere = true;
1787 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
1790 public void expandViews_actionPerformed(ActionEvent e)
1792 Desktop.instance.explodeViews(this);
1795 public void gatherViews_actionPerformed(ActionEvent e)
1797 Desktop.instance.gatherViews(this);
1805 * @param e DOCUMENT ME!
1807 public void font_actionPerformed(ActionEvent e)
1809 new FontChooser(alignPanel);
1816 * @param e DOCUMENT ME!
1818 protected void seqLimit_actionPerformed(ActionEvent e)
1820 viewport.setShowJVSuffix(seqLimits.isSelected());
1822 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
1823 alignPanel.repaint();
1826 public void idRightAlign_actionPerformed(ActionEvent e)
1828 viewport.rightAlignIds = idRightAlign.isSelected();
1829 alignPanel.repaint();
1837 * @param e DOCUMENT ME!
1839 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
1841 viewport.setColourText(colourTextMenuItem.isSelected());
1842 alignPanel.repaint();
1848 * @param e DOCUMENT ME!
1850 public void wrapMenuItem_actionPerformed(ActionEvent e)
1852 scaleAbove.setVisible(wrapMenuItem.isSelected());
1853 scaleLeft.setVisible(wrapMenuItem.isSelected());
1854 scaleRight.setVisible(wrapMenuItem.isSelected());
1855 viewport.setWrapAlignment(wrapMenuItem.isSelected());
1856 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
1859 public void showAllSeqs_actionPerformed(ActionEvent e)
1861 viewport.showAllHiddenSeqs();
1864 public void showAllColumns_actionPerformed(ActionEvent e)
1866 viewport.showAllHiddenColumns();
1870 public void hideSelSequences_actionPerformed(ActionEvent e)
1872 viewport.hideAllSelectedSeqs();
1873 alignPanel.repaint();
1876 public void hideSelColumns_actionPerformed(ActionEvent e)
1878 viewport.hideSelectedColumns();
1879 alignPanel.repaint();
1882 public void hiddenMarkers_actionPerformed(ActionEvent e)
1884 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
1891 * @param e DOCUMENT ME!
1893 protected void scaleAbove_actionPerformed(ActionEvent e)
1895 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
1896 alignPanel.repaint();
1902 * @param e DOCUMENT ME!
1904 protected void scaleLeft_actionPerformed(ActionEvent e)
1906 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
1907 alignPanel.repaint();
1913 * @param e DOCUMENT ME!
1915 protected void scaleRight_actionPerformed(ActionEvent e)
1917 viewport.setScaleRightWrapped(scaleRight.isSelected());
1918 alignPanel.repaint();
1924 * @param e DOCUMENT ME!
1926 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1928 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
1929 alignPanel.repaint();
1935 * @param e DOCUMENT ME!
1937 public void viewTextMenuItem_actionPerformed(ActionEvent e)
1939 viewport.setShowText(viewTextMenuItem.isSelected());
1940 alignPanel.repaint();
1946 * @param e DOCUMENT ME!
1948 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1950 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
1951 alignPanel.repaint();
1955 public FeatureSettings featureSettings;
1956 public void featureSettings_actionPerformed(ActionEvent e)
1958 if(featureSettings !=null )
1960 featureSettings.close();
1961 featureSettings = null;
1963 featureSettings = new FeatureSettings(this);
1969 * @param evt DOCUMENT ME!
1971 public void showSeqFeatures_actionPerformed(ActionEvent evt)
1973 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
1974 alignPanel.repaint();
1975 if (alignPanel.getOverviewPanel() != null)
1977 alignPanel.getOverviewPanel().updateOverviewImage();
1984 * @param e DOCUMENT ME!
1986 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
1988 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
1989 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
1995 * @param e DOCUMENT ME!
1997 public void overviewMenuItem_actionPerformed(ActionEvent e)
1999 if (alignPanel.overviewPanel != null)
2004 JInternalFrame frame = new JInternalFrame();
2005 OverviewPanel overview = new OverviewPanel(alignPanel);
2006 frame.setContentPane(overview);
2007 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2008 frame.getWidth(), frame.getHeight());
2010 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2011 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2013 public void internalFrameClosed(
2014 javax.swing.event.InternalFrameEvent evt)
2016 alignPanel.setOverviewPanel(null);
2021 alignPanel.setOverviewPanel(overview);
2024 public void textColour_actionPerformed(ActionEvent e)
2026 new TextColourChooser().chooseColour(alignPanel, null);
2032 * @param e DOCUMENT ME!
2034 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2042 * @param e DOCUMENT ME!
2044 public void clustalColour_actionPerformed(ActionEvent e)
2046 changeColour(new ClustalxColourScheme(
2047 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
2053 * @param e DOCUMENT ME!
2055 public void zappoColour_actionPerformed(ActionEvent e)
2057 changeColour(new ZappoColourScheme());
2063 * @param e DOCUMENT ME!
2065 public void taylorColour_actionPerformed(ActionEvent e)
2067 changeColour(new TaylorColourScheme());
2073 * @param e DOCUMENT ME!
2075 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2077 changeColour(new HydrophobicColourScheme());
2083 * @param e DOCUMENT ME!
2085 public void helixColour_actionPerformed(ActionEvent e)
2087 changeColour(new HelixColourScheme());
2093 * @param e DOCUMENT ME!
2095 public void strandColour_actionPerformed(ActionEvent e)
2097 changeColour(new StrandColourScheme());
2103 * @param e DOCUMENT ME!
2105 public void turnColour_actionPerformed(ActionEvent e)
2107 changeColour(new TurnColourScheme());
2113 * @param e DOCUMENT ME!
2115 public void buriedColour_actionPerformed(ActionEvent e)
2117 changeColour(new BuriedColourScheme());
2123 * @param e DOCUMENT ME!
2125 public void nucleotideColour_actionPerformed(ActionEvent e)
2127 changeColour(new NucleotideColourScheme());
2130 public void annotationColour_actionPerformed(ActionEvent e)
2132 new AnnotationColourChooser(viewport, alignPanel);
2139 * @param e DOCUMENT ME!
2141 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2143 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2149 * @param cs DOCUMENT ME!
2151 public void changeColour(ColourSchemeI cs)
2157 if (viewport.getAbovePIDThreshold())
2159 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2162 cs.setThreshold(threshold,
2163 viewport.getIgnoreGapsConsensus());
2165 viewport.setGlobalColourScheme(cs);
2169 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2172 if (viewport.getConservationSelected())
2175 Alignment al = (Alignment) viewport.alignment;
2176 Conservation c = new Conservation("All",
2177 ResidueProperties.propHash, 3,
2178 al.getSequences(), 0,
2182 c.verdict(false, viewport.ConsPercGaps);
2184 cs.setConservation(c);
2186 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
2191 cs.setConservation(null);
2194 cs.setConsensus(viewport.hconsensus);
2197 viewport.setGlobalColourScheme(cs);
2199 if (viewport.getColourAppliesToAllGroups())
2201 Vector groups = viewport.alignment.getGroups();
2203 for (int i = 0; i < groups.size(); i++)
2205 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2213 if (cs instanceof ClustalxColourScheme)
2215 sg.cs = new ClustalxColourScheme(
2216 sg.getSequences(true), sg.getWidth());
2218 else if (cs instanceof UserColourScheme)
2220 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
2226 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2228 catch (Exception ex)
2233 if (viewport.getAbovePIDThreshold()
2234 || cs instanceof PIDColourScheme
2235 || cs instanceof Blosum62ColourScheme)
2237 sg.cs.setThreshold(threshold,
2238 viewport.getIgnoreGapsConsensus());
2240 sg.cs.setConsensus(AAFrequency.calculate(
2241 sg.getSequences(true), sg.getStartRes(),
2245 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2248 if (viewport.getConservationSelected())
2250 Conservation c = new Conservation("Group",
2251 ResidueProperties.propHash, 3,
2252 sg.getSequences(true),
2256 c.verdict(false, viewport.ConsPercGaps);
2257 sg.cs.setConservation(c);
2260 sg.cs.setConservation(null);
2264 if (alignPanel.getOverviewPanel() != null)
2266 alignPanel.getOverviewPanel().updateOverviewImage();
2269 alignPanel.repaint();
2275 * @param e DOCUMENT ME!
2277 protected void modifyPID_actionPerformed(ActionEvent e)
2279 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
2281 SliderPanel.setPIDSliderSource(alignPanel,
2282 viewport.getGlobalColourScheme(),
2284 SliderPanel.showPIDSlider();
2291 * @param e DOCUMENT ME!
2293 protected void modifyConservation_actionPerformed(ActionEvent e)
2295 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
2297 SliderPanel.setConservationSlider(alignPanel,
2298 viewport.globalColourScheme,
2300 SliderPanel.showConservationSlider();
2307 * @param e DOCUMENT ME!
2309 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2311 viewport.setConservationSelected(conservationMenuItem.isSelected());
2313 viewport.setAbovePIDThreshold(false);
2314 abovePIDThreshold.setSelected(false);
2316 changeColour(viewport.getGlobalColourScheme());
2318 modifyConservation_actionPerformed(null);
2324 * @param e DOCUMENT ME!
2326 public void abovePIDThreshold_actionPerformed(ActionEvent e)
2328 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
2330 conservationMenuItem.setSelected(false);
2331 viewport.setConservationSelected(false);
2333 changeColour(viewport.getGlobalColourScheme());
2335 modifyPID_actionPerformed(null);
2341 * @param e DOCUMENT ME!
2343 public void userDefinedColour_actionPerformed(ActionEvent e)
2345 if (e.getActionCommand().equals("User Defined..."))
2347 new UserDefinedColours(alignPanel, null);
2351 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
2352 getUserColourSchemes().get(e.getActionCommand());
2358 public void updateUserColourMenu()
2361 Component[] menuItems = colourMenu.getMenuComponents();
2362 int i, iSize = menuItems.length;
2363 for (i = 0; i < iSize; i++)
2365 if (menuItems[i].getName() != null &&
2366 menuItems[i].getName().equals("USER_DEFINED"))
2368 colourMenu.remove(menuItems[i]);
2372 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
2374 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
2375 getUserColourSchemes().keys();
2377 while (userColours.hasMoreElements())
2379 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
2380 nextElement().toString());
2381 radioItem.setName("USER_DEFINED");
2382 radioItem.addMouseListener(new MouseAdapter()
2384 public void mousePressed(MouseEvent evt)
2386 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
2388 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
2390 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
2391 "Remove from default list?",
2392 "Remove user defined colour",
2393 JOptionPane.YES_NO_OPTION);
2394 if(option == JOptionPane.YES_OPTION)
2396 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
2397 colourMenu.remove(radioItem);
2400 radioItem.addActionListener(new ActionListener()
2402 public void actionPerformed(ActionEvent evt)
2404 userDefinedColour_actionPerformed(evt);
2410 radioItem.addActionListener(new ActionListener()
2412 public void actionPerformed(ActionEvent evt)
2414 userDefinedColour_actionPerformed(evt);
2418 colourMenu.insert(radioItem, 15);
2419 colours.add(radioItem);
2427 * @param e DOCUMENT ME!
2429 public void PIDColour_actionPerformed(ActionEvent e)
2431 changeColour(new PIDColourScheme());
2437 * @param e DOCUMENT ME!
2439 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
2441 changeColour(new Blosum62ColourScheme());
2447 * @param e DOCUMENT ME!
2449 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2451 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2452 AlignmentSorter.sortByPID(viewport.getAlignment(),
2453 viewport.getAlignment().getSequenceAt(0));
2454 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));
2455 alignPanel.repaint();
2461 * @param e DOCUMENT ME!
2463 public void sortIDMenuItem_actionPerformed(ActionEvent e)
2465 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2466 AlignmentSorter.sortByID(viewport.getAlignment());
2467 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
2468 alignPanel.repaint();
2474 * @param e DOCUMENT ME!
2476 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
2478 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2479 AlignmentSorter.sortByGroup(viewport.getAlignment());
2480 addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
2482 alignPanel.repaint();
2488 * @param e DOCUMENT ME!
2490 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2492 new RedundancyPanel(alignPanel, this);
2499 * @param e DOCUMENT ME!
2501 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2503 if ( (viewport.getSelectionGroup() == null) ||
2504 (viewport.getSelectionGroup().getSize(false) < 2))
2506 JOptionPane.showInternalMessageDialog(this,
2507 "You must select at least 2 sequences.",
2508 "Invalid Selection",
2509 JOptionPane.WARNING_MESSAGE);
2513 JInternalFrame frame = new JInternalFrame();
2514 frame.setContentPane(new PairwiseAlignPanel(viewport));
2515 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
2522 * @param e DOCUMENT ME!
2524 public void PCAMenuItem_actionPerformed(ActionEvent e)
2526 if ( ( (viewport.getSelectionGroup() != null) &&
2527 (viewport.getSelectionGroup().getSize(false) < 4) &&
2528 (viewport.getSelectionGroup().getSize(false) > 0)) ||
2529 (viewport.getAlignment().getHeight() < 4))
2531 JOptionPane.showInternalMessageDialog(this,
2532 "Principal component analysis must take\n" +
2533 "at least 4 input sequences.",
2534 "Sequence selection insufficient",
2535 JOptionPane.WARNING_MESSAGE);
2540 new PCAPanel(alignPanel);
2544 public void autoCalculate_actionPerformed(ActionEvent e)
2546 viewport.autoCalculateConsensus = autoCalculate.isSelected();
2547 if(viewport.autoCalculateConsensus)
2549 viewport.firePropertyChange("alignment",
2551 viewport.getAlignment().getSequences());
2559 * @param e DOCUMENT ME!
2561 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2563 NewTreePanel("AV", "PID", "Average distance tree using PID");
2569 * @param e DOCUMENT ME!
2571 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2573 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2579 * @param e DOCUMENT ME!
2581 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2583 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2589 * @param e DOCUMENT ME!
2591 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2593 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2599 * @param type DOCUMENT ME!
2600 * @param pwType DOCUMENT ME!
2601 * @param title DOCUMENT ME!
2603 void NewTreePanel(String type, String pwType, String title)
2607 if (viewport.getSelectionGroup() != null) {
2608 if (viewport.getSelectionGroup().getSize(false) < 3) {
2609 JOptionPane.showMessageDialog(Desktop.desktop,
2610 "You need to have more than two sequences selected to build a tree!",
2611 "Not enough sequences",
2612 JOptionPane.WARNING_MESSAGE);
2617 SequenceGroup sg = viewport.getSelectionGroup();
2619 /* Decide if the selection is a column region */
2620 while (s < sg.getSize(false))
2622 if ( ( (SequenceI) sg.getSequences(false).elementAt(s++)).getLength() <
2625 JOptionPane.showMessageDialog(Desktop.desktop,
2626 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
2627 "Try using the Pad function in the edit menu,\n" +
2628 "or one of the multiple sequence alignment web services.",
2629 "Sequences in selection are not aligned",
2630 JOptionPane.WARNING_MESSAGE);
2636 title = title + " on region";
2637 tp = new TreePanel(alignPanel, type, pwType);
2641 //are the sequences aligned?
2642 if (!viewport.alignment.isAligned())
2644 JOptionPane.showMessageDialog(Desktop.desktop,
2645 "The sequences must be aligned before creating a tree.\n" +
2646 "Try using the Pad function in the edit menu,\n" +
2647 "or one of the multiple sequence alignment web services.",
2648 "Sequences not aligned",
2649 JOptionPane.WARNING_MESSAGE);
2654 if(viewport.alignment.getHeight()<2)
2657 tp = new TreePanel(alignPanel, type, pwType);
2660 title = title + " from " + this.title;
2661 if(viewport.viewName!=null)
2662 title+= " ("+viewport.viewName+")";
2664 Desktop.addInternalFrame(tp, title, 600, 500);
2670 * @param title DOCUMENT ME!
2671 * @param order DOCUMENT ME!
2673 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
2675 final JMenuItem item = new JMenuItem("by " + title);
2677 item.addActionListener(new java.awt.event.ActionListener()
2679 public void actionPerformed(ActionEvent e)
2681 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2683 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
2684 AlignmentSorter.sortBy(viewport.getAlignment(), order);
2686 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport.alignment));
2688 alignPanel.repaint();
2694 * Maintain the Order by->Displayed Tree menu.
2695 * Creates a new menu item for a TreePanel with an appropriate
2696 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
2697 * to remove the menu item when the treePanel is closed, and adjust
2698 * the tree leaf to sequence mapping when the alignment is modified.
2699 * @param treePanel Displayed tree window.
2700 * @param title SortBy menu item title.
2702 public void buildTreeMenu()
2704 sortByTreeMenu.removeAll();
2706 Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
2707 Vector treePanels = new Vector();
2708 int i, iSize = comps.size();
2709 for(i=0; i<iSize; i++)
2711 if(comps.elementAt(i) instanceof TreePanel)
2713 treePanels.add(comps.elementAt(i));
2717 iSize = treePanels.size();
2721 sortByTreeMenu.setVisible(false);
2725 sortByTreeMenu.setVisible(true);
2727 for(i=0; i<treePanels.size(); i++)
2729 TreePanel tp = (TreePanel)treePanels.elementAt(i);
2730 final JMenuItem item = new JMenuItem(tp.getTitle());
2731 final NJTree tree = ((TreePanel)treePanels.elementAt(i)).getTree();
2732 item.addActionListener(new java.awt.event.ActionListener()
2734 public void actionPerformed(ActionEvent e)
2736 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2737 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
2739 addHistoryItem(new OrderCommand("Tree Sort",
2741 viewport.alignment));
2743 alignPanel.repaint();
2747 sortByTreeMenu.add(item);
2752 * Work out whether the whole set of sequences
2753 * or just the selected set will be submitted for multiple alignment.
2756 private jalview.datamodel.AlignmentView gatherSequencesForAlignment()
2758 // Now, check we have enough sequences
2759 AlignmentView msa = null;
2761 if ( (viewport.getSelectionGroup() != null) &&
2762 (viewport.getSelectionGroup().getSize(false) > 1))
2764 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
2765 /*SequenceGroup seqs = viewport.getSelectionGroup();
2767 msa = new SequenceI[sz = seqs.getSize(false)];
2769 for (int i = 0; i < sz; i++)
2771 msa[i] = (SequenceI) seqs.getSequenceAt(i);
2773 msa = viewport.getAlignmentView(true);
2777 /*Vector seqs = viewport.getAlignment().getSequences();
2779 if (seqs.size() > 1)
2781 msa = new SequenceI[seqs.size()];
2783 for (int i = 0; i < seqs.size(); i++)
2785 msa[i] = (SequenceI) seqs.elementAt(i);
2788 msa = viewport.getAlignmentView(false);
2794 * Decides what is submitted to a secondary structure prediction service,
2795 * the currently selected sequence, or the currently selected alignment
2796 * (where the first sequence in the set is the one that the prediction
2799 AlignmentView gatherSeqOrMsaForSecStrPrediction()
2801 AlignmentView seqs = null;
2803 if ( (viewport.getSelectionGroup() != null) &&
2804 (viewport.getSelectionGroup().getSize(false) > 0))
2806 seqs = viewport.getAlignmentView(true);
2810 seqs = viewport.getAlignmentView(false);
2812 // limit sequences - JBPNote in future - could spawn multiple prediction jobs
2813 // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment.
2814 if (!viewport.alignment.isAligned())
2816 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] } );
2823 * @param e DOCUMENT ME!
2825 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2827 // Pick the tree file
2828 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
2831 chooser.setFileView(new JalviewFileView());
2832 chooser.setDialogTitle("Select a newick-like tree file");
2833 chooser.setToolTipText("Load a tree file");
2835 int value = chooser.showOpenDialog(null);
2837 if (value == JalviewFileChooser.APPROVE_OPTION)
2839 String choice = chooser.getSelectedFile().getPath();
2840 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
2844 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
2846 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
2848 catch (Exception ex)
2850 JOptionPane.showMessageDialog(Desktop.desktop,
2851 "Problem reading tree file",
2853 JOptionPane.WARNING_MESSAGE);
2854 ex.printStackTrace();
2860 public TreePanel ShowNewickTree(NewickFile nf, String title)
2862 return ShowNewickTree(nf,title,600,500,4,5);
2864 public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input)
2866 return ShowNewickTree(nf,title, input, 600,500,4,5);
2868 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y) {
2869 return ShowNewickTree(nf, title, null, w, h, x, y);
2872 * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
2874 * @param nf the tree
2875 * @param title tree viewer title
2876 * @param input Associated alignment input data (or null)
2881 * @return TreePanel handle
2883 public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input, int w,int h,int x, int y) {
2884 TreePanel tp = null;
2890 if (nf.getTree() != null)
2892 tp = new TreePanel(alignPanel,
2900 tp.setLocation(x,y);
2903 Desktop.addInternalFrame(tp, title, w, h);
2906 catch (Exception ex)
2908 ex.printStackTrace();
2919 PrinterJob printJob = PrinterJob.getPrinterJob();
2920 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
2921 printJob.setPrintable(alignPanel, pf);
2923 if (printJob.printDialog())
2929 catch (Exception PrintException)
2931 PrintException.printStackTrace();
2938 * Generates menu items and listener event actions for web service clients
2941 public void BuildWebServiceMenu()
2943 if ( (Discoverer.services != null)
2944 && (Discoverer.services.size() > 0))
2946 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
2947 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
2948 Vector wsmenu = new Vector();
2949 final AlignFrame af = this;
2952 // Add any Multiple Sequence Alignment Services
2953 final JMenu msawsmenu = new JMenu("Alignment");
2954 for (int i = 0, j = msaws.size(); i < j; i++)
2956 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
2958 final JMenuItem method = new JMenuItem(sh.getName());
2959 method.addActionListener(new ActionListener()
2961 public void actionPerformed(ActionEvent e)
2963 AlignmentView msa = gatherSequencesForAlignment();
2964 new jalview.ws.MsaWSClient(sh, title, msa,
2965 false, true, viewport.getAlignment().getDataset(), af);
2970 msawsmenu.add(method);
2971 // Deal with services that we know accept partial alignments.
2972 if (sh.getName().indexOf("lustal") > -1)
2974 // We know that ClustalWS can accept partial alignments for refinement.
2975 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
2976 methodR.addActionListener(new ActionListener()
2978 public void actionPerformed(ActionEvent e)
2980 AlignmentView msa = gatherSequencesForAlignment();
2981 new jalview.ws.MsaWSClient(sh, title, msa,
2982 true, true, viewport.getAlignment().getDataset(), af);
2987 msawsmenu.add(methodR);
2991 wsmenu.add(msawsmenu);
2993 if (secstrpr != null)
2995 // Add any secondary structure prediction services
2996 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
2997 for (int i = 0, j = secstrpr.size(); i < j; i++)
2999 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
3001 final JMenuItem method = new JMenuItem(sh.getName());
3002 method.addActionListener(new ActionListener()
3004 public void actionPerformed(ActionEvent e)
3006 AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
3007 if (msa.getSequences().length == 1)
3009 // Single Sequence prediction
3010 new jalview.ws.JPredClient(sh, title, false, msa, af, true);
3014 if (msa.getSequences().length > 1)
3016 // Sequence profile based prediction
3017 new jalview.ws.JPredClient(sh,
3018 title, true, msa, af, true);
3023 secstrmenu.add(method);
3025 wsmenu.add(secstrmenu);
3027 this.webService.removeAll();
3028 for (int i = 0, j = wsmenu.size(); i < j; i++)
3030 webService.add( (JMenu) wsmenu.get(i));
3035 this.webService.removeAll();
3036 this.webService.add(this.webServiceNoServices);
3038 // TODO: add in rediscovery function
3039 // TODO: reduce code redundancy.
3040 // TODO: group services by location as well as function.
3043 /* public void vamsasStore_actionPerformed(ActionEvent e)
3045 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
3046 getProperty("LAST_DIRECTORY"));
3048 chooser.setFileView(new JalviewFileView());
3049 chooser.setDialogTitle("Export to Vamsas file");
3050 chooser.setToolTipText("Export");
3052 int value = chooser.showSaveDialog(this);
3054 if (value == JalviewFileChooser.APPROVE_OPTION)
3056 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
3057 //vs.store(chooser.getSelectedFile().getAbsolutePath() );
3058 vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
3065 public void showTranslation_actionPerformed(ActionEvent e)
3067 SequenceI [] selection = viewport.getSelectionAsNewSequence();
3068 String [] seqstring = viewport.getViewAsString(true);
3070 int s, sSize = selection.length;
3071 SequenceI [] newSeq = new SequenceI[sSize];
3074 StringBuffer protein;
3076 for(s=0; s<sSize; s++)
3078 protein = new StringBuffer();
3079 seq = AlignSeq.extractGaps("-. ", seqstring[s]);
3080 resSize = seq.length();
3081 resSize -= resSize%3;
3083 for(res = 0; res < resSize; res+=3)
3085 String codon = seq.substring(res, res+3);
3086 codon = codon.replace('U', 'T');
3087 String aa = ResidueProperties.codonTranslate(codon);
3089 protein.append(viewport.getGapCharacter());
3090 else if(aa.equals("STOP"))
3091 protein.append("X");
3093 protein.append( aa );
3095 newSeq[s] = new Sequence(selection[s].getName(),
3096 protein.toString());
3100 AlignmentI al = new Alignment(newSeq);
3101 al.setDataset(null);
3104 ////////////////////////////////
3105 // Copy annotations across
3106 jalview.datamodel.AlignmentAnnotation[] annotations
3107 = viewport.alignment.getAlignmentAnnotation();
3109 if(annotations!=null)
3111 for (int i = 0; i < annotations.length; i++)
3113 if (annotations[i].label.equals("Quality") ||
3114 annotations[i].label.equals("Conservation") ||
3115 annotations[i].label.equals("Consensus"))
3120 aSize = viewport.alignment.getWidth() / 3;
3121 jalview.datamodel.Annotation[] anots =
3122 new jalview.datamodel.Annotation[aSize];
3124 for (a = 0; a < viewport.alignment.getWidth(); a++)
3126 if (annotations[i].annotations[a] == null
3127 || annotations[i].annotations[a] == null)
3130 anots[a / 3] = new Annotation(
3131 annotations[i].annotations[a].displayCharacter,
3132 annotations[i].annotations[a].description,
3133 annotations[i].annotations[a].secondaryStructure,
3134 annotations[i].annotations[a].value,
3135 annotations[i].annotations[a].colour);
3138 jalview.datamodel.AlignmentAnnotation aa
3139 = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
3140 annotations[i].description, anots);
3141 al.addAnnotation(aa);
3145 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
3146 Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
3158 * @param String DOCUMENT ME!
3160 public boolean parseFeaturesFile(String file, String type)
3162 boolean featuresFile = false;
3164 featuresFile = new FeaturesFile(file, type).parse(viewport.alignment.getDataset(),
3165 alignPanel.seqPanel.seqCanvas.
3166 getFeatureRenderer().featureColours,
3171 ex.printStackTrace();
3176 viewport.showSequenceFeatures = true;
3177 showSeqFeatures.setSelected(true);
3178 alignPanel.repaint();
3181 return featuresFile;
3184 public void dragEnter(DropTargetDragEvent evt)
3187 public void dragExit(DropTargetEvent evt)
3190 public void dragOver(DropTargetDragEvent evt)
3193 public void dropActionChanged(DropTargetDragEvent evt)
3196 public void drop(DropTargetDropEvent evt)
3198 Transferable t = evt.getTransferable();
3199 java.util.List files = null;
3203 DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
3204 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
3206 //Works on Windows and MacOSX
3207 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3208 files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
3210 else if (t.isDataFlavorSupported(uriListFlavor))
3212 // This is used by Unix drag system
3213 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3214 String data = (String) t.getTransferData(uriListFlavor);
3215 files = new java.util.ArrayList(1);
3216 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
3219 st.hasMoreTokens(); )
3221 String s = st.nextToken();
3222 if (s.startsWith("#"))
3224 // the line is a comment (as per the RFC 2483)
3228 java.net.URI uri = new java.net.URI(s);
3229 java.io.File file = new java.io.File(uri);
3236 e.printStackTrace();
3243 for (int i = 0; i < files.size(); i++)
3245 loadJalviewDataFile(files.get(i).toString());
3248 catch (Exception ex)
3250 ex.printStackTrace();
3255 // This method will attempt to load a "dropped" file first by testing
3256 // whether its and Annotation file, then features file. If both are
3257 // false then the user may have dropped an alignment file onto this
3259 public void loadJalviewDataFile(String file)
3262 String protocol = "File";
3264 if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
3269 boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
3274 boolean isGroupsFile = parseFeaturesFile(file,protocol);
3277 String format = new IdentifyFile().Identify(file, protocol);
3279 if(format.equalsIgnoreCase("JnetFile"))
3281 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
3283 new JnetAnnotationMaker().add_annotation(predictions,
3284 viewport.getAlignment(),
3286 alignPanel.adjustAnnotationHeight();
3287 alignPanel.repaint();
3290 new FileLoader().LoadFile(viewport, file, protocol, format);
3296 alignPanel.adjustAnnotationHeight();
3299 }catch(Exception ex)
3301 ex.printStackTrace();
3305 public void tabSelectionChanged(int index)
3309 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
3310 viewport = alignPanel.av;
3311 setMenusFromViewport(viewport);
3315 public void tabbedPane_mousePressed(MouseEvent e)
3317 if(SwingUtilities.isRightMouseButton(e))
3319 String reply = JOptionPane.showInternalInputDialog(this,
3322 JOptionPane.QUESTION_MESSAGE);
3326 viewport.viewName = reply;
3327 tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
3333 public AlignViewport getCurrentView()