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;
67 private int treeCount = 0;
70 * Creates a new AlignFrame object.
72 * @param al DOCUMENT ME!
74 public AlignFrame(AlignmentI al, int width, int height)
76 this(al, null, width, height);
81 * new alignment window with hidden columns
82 * @param al AlignmentI
83 * @param hiddenColumns ColumnSelection or null
85 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
86 int width, int height)
88 this.setSize(width, height);
89 viewport = new AlignViewport(al, hiddenColumns);
91 alignPanel = new AlignmentPanel(this, viewport);
93 if(al.getDataset()==null)
98 addAlignmentPanel(alignPanel, true);
103 * Make a new AlignFrame from exisiting alignmentPanels
104 * @param ap AlignmentPanel
105 * @param av AlignViewport
107 public AlignFrame(AlignmentPanel ap)
111 addAlignmentPanel(ap, false);
117 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
119 if (viewport.conservation == null)
121 BLOSUM62Colour.setEnabled(false);
122 conservationMenuItem.setEnabled(false);
123 modifyConservation.setEnabled(false);
124 // PIDColour.setEnabled(false);
125 // abovePIDThreshold.setEnabled(false);
126 // modifyPID.setEnabled(false);
129 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
131 if (sortby.equals("Id"))
132 sortIDMenuItem_actionPerformed(null);
133 else if (sortby.equals("Pairwise Identity"))
134 sortPairwiseMenuItem_actionPerformed(null);
136 if (Desktop.desktop != null)
138 addServiceListeners();
139 setGUINucleotide(viewport.alignment.isNucleotide());
142 setMenusFromViewport(viewport);
144 if (viewport.wrapAlignment)
146 wrapMenuItem_actionPerformed(null);
153 public void setFileName(String file, String format)
156 currentFileFormat = format;
157 reload.setEnabled(true);
160 void addKeyListener()
162 final AlignFrame af = this;
163 addKeyListener(new KeyAdapter()
165 public void keyPressed(KeyEvent evt)
167 if (viewport.cursorMode
168 && evt.getKeyCode() >= KeyEvent.VK_0
169 && evt.getKeyCode() <= KeyEvent.VK_9)
171 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
174 switch (evt.getKeyCode())
177 Desktop.instance.gatherViews(af);
181 if (!evt.isControlDown())
183 Desktop.instance.explodeViews(af);
188 case 27: // escape key
189 deselectAllSequenceMenuItem_actionPerformed(null);
193 case KeyEvent.VK_DOWN:
194 if (viewport.cursorMode)
196 alignPanel.seqPanel.moveCursor(0, 1);
199 moveSelectedSequences(false);
203 if (viewport.cursorMode)
205 alignPanel.seqPanel.moveCursor(0, -1);
208 moveSelectedSequences(true);
211 case KeyEvent.VK_LEFT:
212 if (viewport.cursorMode)
214 alignPanel.seqPanel.moveCursor( -1, 0);
218 case KeyEvent.VK_RIGHT:
219 if (viewport.cursorMode)
221 alignPanel.seqPanel.moveCursor(1, 0);
225 case KeyEvent.VK_SPACE:
226 if (viewport.cursorMode)
228 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
234 case KeyEvent.VK_DELETE:
235 case KeyEvent.VK_BACK_SPACE:
236 if (!viewport.cursorMode)
238 cut_actionPerformed(null);
241 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
248 if (viewport.cursorMode)
250 alignPanel.seqPanel.setCursorRow();
254 if (viewport.cursorMode && !evt.isControlDown())
256 alignPanel.seqPanel.setCursorColumn();
260 if (viewport.cursorMode)
262 alignPanel.seqPanel.setCursorPosition();
266 case KeyEvent.VK_ENTER:
267 case KeyEvent.VK_COMMA:
268 if (viewport.cursorMode)
270 alignPanel.seqPanel.setCursorRowAndColumn();
275 if (viewport.cursorMode)
277 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
281 if (viewport.cursorMode)
283 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
288 viewport.cursorMode = !viewport.cursorMode;
289 statusBar.setText("Keyboard editing mode is " +
290 (viewport.cursorMode ? "on" : "off"));
291 if (viewport.cursorMode)
293 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
294 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
296 alignPanel.seqPanel.seqCanvas.repaint();
302 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
303 java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
304 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
306 javax.help.HelpBroker hb = hs.createHelpBroker();
307 hb.setCurrentID("home");
308 hb.setDisplayed(true);
312 ex.printStackTrace();
318 boolean toggleSeqs = !evt.isControlDown();
319 boolean toggleCols = !evt.isShiftDown();
321 boolean hide = false;
323 SequenceGroup sg = viewport.getSelectionGroup();
326 if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
328 hideSelSequences_actionPerformed(null);
331 else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))
332 showAllSeqs_actionPerformed(null);
337 if (viewport.colSel.getSelected().size() > 0)
339 hideSelColumns_actionPerformed(null);
341 viewport.selectionGroup = sg;
344 showAllColumns_actionPerformed(null);
348 case KeyEvent.VK_PAGE_UP:
349 if (viewport.wrapAlignment)
350 alignPanel.scrollUp(true);
352 alignPanel.setScrollValues(viewport.startRes,
354 - viewport.endSeq + viewport.startSeq);
356 case KeyEvent.VK_PAGE_DOWN:
357 if (viewport.wrapAlignment)
358 alignPanel.scrollUp(false);
360 alignPanel.setScrollValues(viewport.startRes,
362 + viewport.endSeq - viewport.startSeq);
370 public void addAlignmentPanel(final AlignmentPanel ap,
373 ap.alignFrame = this;
375 alignPanels.addElement(ap);
377 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
379 int aSize = alignPanels.size();
381 tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
383 if (aSize == 1 && ap.av.viewName==null)
385 this.getContentPane().add(ap, BorderLayout.CENTER);
391 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
392 tabbedPane.addTab(first.av.viewName==null?"Original":first.av.viewName,first);
394 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
397 tabbedPane.addTab(ap.av.viewName==null?"Original":ap.av.viewName, ap);
399 ap.setVisible(false);
405 ap.av.alignment.padGaps();
406 ap.av.updateConservation(ap);
407 ap.av.updateConsensus(ap);
412 public AlignViewport getViewport()
417 /* Set up intrinsic listeners for dynamically generated GUI bits. */
418 private void addServiceListeners()
420 final java.beans.PropertyChangeListener thisListener;
421 // Do this once to get current state
422 BuildWebServiceMenu();
423 Desktop.discoverer.addPropertyChangeListener(
424 thisListener = new java.beans.PropertyChangeListener()
426 public void propertyChange(PropertyChangeEvent evt)
428 // System.out.println("Discoverer property change.");
429 if (evt.getPropertyName().equals("services"))
431 // System.out.println("Rebuilding web service menu");
432 BuildWebServiceMenu();
437 addInternalFrameListener(new javax.swing.event.
438 InternalFrameAdapter()
440 public void internalFrameClosed(
441 javax.swing.event.InternalFrameEvent evt)
443 // System.out.println("deregistering discoverer listener");
444 Desktop.discoverer.removePropertyChangeListener(thisListener);
445 closeMenuItem_actionPerformed(true);
451 public void setGUINucleotide(boolean nucleotide)
453 showTranslation.setVisible( nucleotide );
454 conservationMenuItem.setEnabled( !nucleotide );
455 modifyConservation.setEnabled( !nucleotide );
457 //Remember AlignFrame always starts as protein
460 calculateMenu.remove(calculateMenu.getItemCount()-2);
465 * Need to call this method when tabs are selected for multiple views,
466 * or when loading from Jalview2XML.java
467 * @param av AlignViewport
469 void setMenusFromViewport(AlignViewport av)
471 padGapsMenuitem.setSelected(av.padGaps);
472 colourTextMenuItem.setSelected(av.showColourText);
473 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
474 conservationMenuItem.setSelected(av.getConservationSelected());
475 seqLimits.setSelected(av.getShowJVSuffix());
476 idRightAlign.setSelected(av.idsAlignRight);
477 renderGapsMenuItem.setSelected(av.renderGaps);
478 wrapMenuItem.setSelected(av.wrapAlignment);
479 annotationPanelMenuItem.setState(av.showAnnotation);
480 viewBoxesMenuItem.setSelected(av.showBoxes);
481 viewTextMenuItem.setSelected(av.showText);
483 setColourSelected(ColourSchemeProperty.
484 getColourName(av.getGlobalColourScheme()));
486 showSeqFeatures.setSelected(av.showSequenceFeatures);
487 hiddenMarkers.setState(av.showHiddenMarkers);
488 applyToAllGroups.setState(av.colourAppliesToAllGroups);
494 Hashtable progressBars;
495 public void setProgressBar(String message, long id)
497 if(progressBars == null)
498 progressBars = new Hashtable();
500 JPanel progressPanel;
501 GridLayout layout = (GridLayout) statusPanel.getLayout();
502 if(progressBars.get( new Long(id) )!=null)
504 progressPanel = (JPanel)progressBars.get( new Long(id) );
505 statusPanel.remove(progressPanel);
506 progressBars.remove( progressPanel );
507 progressPanel = null;
509 statusBar.setText(message);
511 layout.setRows(layout.getRows() - 1);
515 progressPanel = new JPanel(new BorderLayout(10, 5));
517 JProgressBar progressBar = new JProgressBar();
518 progressBar.setIndeterminate(true);
520 progressPanel.add(new JLabel(message), BorderLayout.WEST);
521 progressPanel.add(progressBar, BorderLayout.CENTER);
523 layout.setRows(layout.getRows() + 1);
524 statusPanel.add(progressPanel);
526 progressBars.put(new Long(id), progressPanel);
536 Added so Castor Mapping file can obtain Jalview Version
538 public String getVersion()
540 return jalview.bin.Cache.getProperty("VERSION");
543 public FeatureRenderer getFeatureRenderer()
545 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
549 public void fetchSequence_actionPerformed(ActionEvent e)
551 new SequenceFetcher(this);
554 public void addFromFile_actionPerformed(ActionEvent e)
556 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
559 public void reload_actionPerformed(ActionEvent e)
563 if(currentFileFormat.equals("Jalview"))
565 this.closeMenuItem_actionPerformed(true);
569 viewport.alignment.deleteAllGroups();
570 viewport.sequenceColours=null;
571 while (viewport.alignment.getHeight() > 0)
573 viewport.alignment.deleteSequence(0);
576 viewport.historyList.clear();
577 viewport.redoList.clear();
578 Alignment dset = viewport.alignment.getDataset();
579 while (dset.getHeight() > 0)
581 dset.deleteSequence(0);
584 firePropertyChange("Alignment", null, null);
589 FileLoader loader = new FileLoader();
590 String protocol = fileName.startsWith("http:")? "URL":"File";
591 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
597 public void addFromText_actionPerformed(ActionEvent e)
599 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
602 public void addFromURL_actionPerformed(ActionEvent e)
604 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
608 public void save_actionPerformed(ActionEvent e)
610 if(fileName==null || currentFileFormat==null)
611 saveAs_actionPerformed(null);
613 saveAlignment(fileName, currentFileFormat);
619 * @param e DOCUMENT ME!
621 public void saveAs_actionPerformed(ActionEvent e)
623 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
624 getProperty( "LAST_DIRECTORY"),
626 { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" },
628 { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
633 chooser.setFileView(new JalviewFileView());
634 chooser.setDialogTitle("Save Alignment to file");
635 chooser.setToolTipText("Save");
637 int value = chooser.showSaveDialog(this);
639 if (value == JalviewFileChooser.APPROVE_OPTION)
641 currentFileFormat = chooser.getSelectedFormat();
642 if (currentFileFormat == null)
644 JOptionPane.showInternalMessageDialog(Desktop.desktop,
645 "You must select a file format before saving!",
646 "File format not specified",
647 JOptionPane.WARNING_MESSAGE);
648 value = chooser.showSaveDialog(this);
652 fileName = chooser.getSelectedFile().getPath();
654 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
657 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
659 saveAlignment(fileName, currentFileFormat);
663 public boolean saveAlignment(String file, String format)
665 if (format.equalsIgnoreCase("Jalview"))
667 String shortName = title;
669 if (shortName.indexOf(java.io.File.separatorChar) > -1)
671 shortName = shortName.substring(shortName.lastIndexOf(
672 java.io.File.separatorChar) + 1);
675 new Jalview2XML().SaveAlignment(this, file, shortName);
677 statusBar.setText("Successfully saved to file: "
679 +format +" format.");
682 // USE Jalview2XML to save this file
688 String[] omitHidden = null;
690 if (viewport.hasHiddenColumns)
692 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
693 "The Alignment contains hidden columns."
694 + "\nDo you want to save only the visible alignment?",
695 "Save / Omit Hidden Columns",
696 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
698 if (reply == JOptionPane.YES_OPTION)
699 omitHidden = viewport.getViewAsString(false);
702 String output = new FormatAdapter().formatSequences(
704 viewport.alignment.getSequencesArray(),
714 java.io.PrintWriter out = new java.io.PrintWriter(
715 new java.io.FileWriter(file));
720 statusBar.setText("Successfully saved to file: "
722 +format +" format.");
727 ex.printStackTrace();
736 * @param e DOCUMENT ME!
738 protected void outputText_actionPerformed(ActionEvent e)
740 String [] omitHidden = null;
742 if(viewport.hasHiddenColumns)
744 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
745 "The Alignment contains hidden columns."
746 +"\nDo you want to output only the visible alignment?",
747 "Save / Omit Hidden Columns",
748 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
750 if(reply==JOptionPane.YES_OPTION)
752 omitHidden = viewport.getViewAsString(false);
756 CutAndPasteTransfer cap = new CutAndPasteTransfer();
757 cap.setForInput(null);
758 Desktop.addInternalFrame(cap,
759 "Alignment output - " + e.getActionCommand(), 600,
763 cap.setText(new FormatAdapter().formatSequences(
764 e.getActionCommand(),
765 viewport.alignment.getSequencesArray(),
772 * @param e DOCUMENT ME!
774 protected void htmlMenuItem_actionPerformed(ActionEvent e)
776 new HTMLOutput(viewport,
777 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
778 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
781 public void createImageMap(File file, String image)
783 alignPanel.makePNGImageMap(file, image);
789 * @param e DOCUMENT ME!
791 public void createPNG(File f)
793 alignPanel.makePNG(f);
799 * @param e DOCUMENT ME!
801 public void createEPS(File f)
803 alignPanel.makeEPS(f);
809 * @param e DOCUMENT ME!
811 public void printMenuItem_actionPerformed(ActionEvent e)
813 //Putting in a thread avoids Swing painting problems
814 PrintThread thread = new PrintThread();
818 public void exportFeatures_actionPerformed(ActionEvent e)
820 new AnnotationExporter().exportFeatures(alignPanel);
824 public void exportAnnotations_actionPerformed(ActionEvent e)
826 new AnnotationExporter().exportAnnotations(
828 viewport.alignment.getAlignmentAnnotation()
833 public void associatedData_actionPerformed(ActionEvent e)
835 // Pick the tree file
836 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
839 chooser.setFileView(new JalviewFileView());
840 chooser.setDialogTitle("Load Jalview Annotations or Features File");
841 chooser.setToolTipText("Load Jalview Annotations / Features file");
843 int value = chooser.showOpenDialog(null);
845 if (value == JalviewFileChooser.APPROVE_OPTION)
847 String choice = chooser.getSelectedFile().getPath();
848 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
849 loadJalviewDataFile(choice);
858 * @param e DOCUMENT ME!
860 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
862 if(alignPanels!=null && alignPanels.size()<2)
867 if(alignPanels!=null)
870 for (int i = 0; i < alignPanels.size(); i++)
872 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
873 PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
874 PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
875 PaintRefresher.RemoveComponent(ap);
879 int index = tabbedPane.getSelectedIndex();
881 tabbedPane.removeTabAt(index);
882 alignPanels.removeElement(alignPanel);
883 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
884 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
885 PaintRefresher.RemoveComponent(alignPanel);
888 tabbedPane.validate();
890 if(index==tabbedPane.getTabCount())
893 this.tabSelectionChanged(index);
898 this.setClosed(true);
902 ex.printStackTrace();
910 void updateEditMenuBar()
913 if (viewport.historyList.size() > 0)
915 undoMenuItem.setEnabled(true);
916 CommandI command = (CommandI) viewport.historyList.peek();
917 undoMenuItem.setText("Undo " + command.getDescription());
921 undoMenuItem.setEnabled(false);
922 undoMenuItem.setText("Undo");
925 if (viewport.redoList.size() > 0)
927 redoMenuItem.setEnabled(true);
929 CommandI command = (CommandI) viewport.redoList.peek();
930 redoMenuItem.setText("Redo " + command.getDescription());
934 redoMenuItem.setEnabled(false);
935 redoMenuItem.setText("Redo");
940 public void addHistoryItem(CommandI command)
942 if(command.getSize()>0)
944 viewport.historyList.push(command);
945 viewport.redoList.clear();
947 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
956 * @param e DOCUMENT ME!
958 protected void undoMenuItem_actionPerformed(ActionEvent e)
960 CommandI command = (CommandI)viewport.historyList.pop();
961 viewport.redoList.push(command);
962 command.undoCommand();
965 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
967 viewport.firePropertyChange("alignment", null,null);
973 * @param e DOCUMENT ME!
975 protected void redoMenuItem_actionPerformed(ActionEvent e)
977 CommandI command = (CommandI) viewport.redoList.pop();
978 viewport.historyList.push(command);
980 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
983 viewport.firePropertyChange("alignment", null, null);
990 * @param up DOCUMENT ME!
992 public void moveSelectedSequences(boolean up)
994 SequenceGroup sg = viewport.getSelectionGroup();
1003 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1005 SequenceI seq = viewport.alignment.getSequenceAt(i);
1007 if (!sg.getSequences(false).contains(seq))
1012 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1014 if (sg.getSequences(false).contains(temp))
1019 viewport.alignment.getSequences().setElementAt(temp, i);
1020 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1025 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1027 SequenceI seq = viewport.alignment.getSequenceAt(i);
1029 if (!sg.getSequences(false).contains(seq))
1034 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1036 if (sg.getSequences(false).contains(temp))
1041 viewport.alignment.getSequences().setElementAt(temp, i);
1042 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1046 alignPanel.repaint();
1054 * @param e DOCUMENT ME!
1056 protected void copy_actionPerformed(ActionEvent e)
1059 if (viewport.getSelectionGroup() == null)
1064 SequenceI [] seqs = viewport.getSelectionAsNewSequence();
1065 String[] omitHidden = null;
1067 if (viewport.hasHiddenColumns)
1069 omitHidden = viewport.getViewAsString(true);
1072 String output = new FormatAdapter().formatSequences(
1077 StringSelection ss = new StringSelection(output);
1081 //Its really worth setting the clipboard contents
1082 //to empty before setting the large StringSelection!!
1083 Toolkit.getDefaultToolkit().getSystemClipboard()
1084 .setContents(new StringSelection(""), null);
1086 Toolkit.getDefaultToolkit().getSystemClipboard()
1087 .setContents(ss, Desktop.instance);
1089 catch (OutOfMemoryError er)
1091 er.printStackTrace();
1092 javax.swing.SwingUtilities.invokeLater(new Runnable()
1096 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1097 "Out of memory copying region!!"
1099 "\nSee help files for increasing Java Virtual Machine memory."
1101 javax.swing.JOptionPane.WARNING_MESSAGE);
1108 Vector hiddenColumns = null;
1109 if(viewport.hasHiddenColumns)
1111 hiddenColumns =new Vector();
1112 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1113 for(int i=0; i<viewport.getColumnSelection().getHiddenColumns().size(); i++)
1115 int[] region = (int[])
1116 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
1118 hiddenColumns.addElement(new int[]{region[0]-hiddenOffset,
1119 region[1]-hiddenOffset});
1125 Desktop.jalviewClipboard = new Object[]{ seqs,
1126 viewport.alignment.getDataset(),
1128 statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
1134 * @param e DOCUMENT ME!
1136 protected void pasteNew_actionPerformed(ActionEvent e)
1144 * @param e DOCUMENT ME!
1146 protected void pasteThis_actionPerformed(ActionEvent e)
1154 * @param newAlignment DOCUMENT ME!
1156 void paste(boolean newAlignment)
1160 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1161 Transferable contents = c.getContents(this);
1163 if (contents == null)
1171 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1172 if (str.length() < 1)
1175 format = new IdentifyFile().Identify(str, "Paste");
1178 catch (OutOfMemoryError er)
1180 er.printStackTrace();
1181 javax.swing.SwingUtilities.invokeLater(new Runnable()
1185 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1186 "Out of memory pasting sequences!!"
1188 "\nSee help files for increasing Java Virtual Machine memory."
1190 javax.swing.JOptionPane.WARNING_MESSAGE);
1197 SequenceI[] sequences;
1200 if(Desktop.jalviewClipboard!=null)
1202 // The clipboard was filled from within Jalview, we must use the sequences
1203 // And dataset from the copied alignment
1204 sequences = (SequenceI[])Desktop.jalviewClipboard[0];
1208 sequences = new FormatAdapter().readFile(str, "Paste", format);
1211 AlignmentI alignment = null;
1215 alignment = new Alignment(sequences);
1217 if (Desktop.jalviewClipboard != null)
1218 alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
1220 alignment.setDataset(null);
1224 alignment = viewport.getAlignment();
1227 SequenceI [] newseqs = new SequenceI[sequences.length];
1228 for (int i = 0; i < sequences.length; i++)
1230 newseqs[i] = new Sequence(sequences[i].getName(),
1231 sequences[i].getSequence(), sequences[i].getStart(),
1232 sequences[i].getEnd());
1234 alignment.addSequence(newseqs[i]);
1240 addHistoryItem(new EditCommand(
1245 alignment.getWidth(),
1250 viewport.setEndSeq(alignment.getHeight());
1251 alignment.getWidth();
1252 viewport.firePropertyChange("alignment", null, alignment.getSequences());
1257 // Add any annotations attached to sequences
1258 for (int i = 0; i < sequences.length; i++)
1260 if (sequences[i].getAnnotation() != null)
1262 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1264 AlignmentAnnotation newAnnot =
1265 new AlignmentAnnotation(
1266 sequences[i].getAnnotation()[a].label,
1267 sequences[i].getAnnotation()[a].description,
1268 sequences[i].getAnnotation()[a].annotations,
1269 sequences[i].getAnnotation()[a].graphMin,
1270 sequences[i].getAnnotation()[a].graphMax,
1271 sequences[i].getAnnotation()[a].graph);
1273 sequences[i].getAnnotation()[a] = newAnnot;
1274 newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].
1276 newAnnot.sequenceRef = sequences[i];
1277 newAnnot.adjustForAlignment();
1278 alignment.addAnnotation(newAnnot);
1279 alignment.setAnnotationIndex(newAnnot, a);
1282 alignPanel.annotationPanel.adjustPanelHeight();
1288 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
1289 String newtitle = new String("Copied sequences");
1291 if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
1293 Vector hc = (Vector)Desktop.jalviewClipboard[2];
1294 for(int i=0; i<hc.size(); i++)
1296 int [] region = (int[]) hc.elementAt(i);
1297 af.viewport.hideColumns(region[0], region[1]);
1302 //>>>This is a fix for the moment, until a better solution is found!!<<<
1303 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
1304 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1307 if (title.startsWith("Copied sequences"))
1313 newtitle = newtitle.concat("- from " + title);
1316 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1323 catch (Exception ex)
1325 ex.printStackTrace();
1326 System.out.println("Exception whilst pasting: "+ex);
1327 // could be anything being pasted in here
1336 * @param e DOCUMENT ME!
1338 protected void cut_actionPerformed(ActionEvent e)
1340 copy_actionPerformed(null);
1341 delete_actionPerformed(null);
1347 * @param e DOCUMENT ME!
1349 protected void delete_actionPerformed(ActionEvent evt)
1352 SequenceGroup sg = viewport.getSelectionGroup();
1358 Vector seqs = new Vector();
1360 for (int i = 0; i < sg.getSize(false); i++)
1362 seq = sg.getSequenceAt(i);
1363 seqs.addElement(seq);
1367 // If the cut affects all sequences, remove highlighted columns
1368 if (sg.getSize(false) == viewport.alignment.getHeight())
1370 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1371 sg.getEndRes() + 1);
1375 SequenceI [] cut = new SequenceI[seqs.size()];
1376 for(int i=0; i<seqs.size(); i++)
1377 cut[i] = (SequenceI)seqs.elementAt(i);
1383 addHistoryItem(new EditCommand("Cut Sequences",
1387 sg.getEndRes()-sg.getStartRes()+1,
1388 viewport.alignment));
1391 viewport.setSelectionGroup(null);
1392 viewport.alignment.deleteGroup(sg);
1394 viewport.firePropertyChange("alignment", null,
1395 viewport.getAlignment().getSequences());
1397 if (viewport.getAlignment().getHeight() < 1)
1401 this.setClosed(true);
1403 catch (Exception ex)
1412 * @param e DOCUMENT ME!
1414 protected void deleteGroups_actionPerformed(ActionEvent e)
1416 viewport.alignment.deleteAllGroups();
1417 viewport.sequenceColours.clear();
1418 viewport.setSelectionGroup(null);
1419 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1420 alignPanel.repaint();
1426 * @param e DOCUMENT ME!
1428 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1430 SequenceGroup sg = new SequenceGroup();
1432 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1435 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1438 sg.setEndRes(viewport.alignment.getWidth() - 1);
1439 viewport.setSelectionGroup(sg);
1440 alignPanel.repaint();
1441 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1447 * @param e DOCUMENT ME!
1449 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1451 if(viewport.cursorMode)
1453 alignPanel.seqPanel.keyboardNo1 = null;
1454 alignPanel.seqPanel.keyboardNo2 = null;
1456 viewport.setSelectionGroup(null);
1457 viewport.getColumnSelection().clear();
1458 viewport.setSelectionGroup(null);
1459 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1460 alignPanel.idPanel.idCanvas.searchResults = null;
1461 alignPanel.repaint();
1462 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1468 * @param e DOCUMENT ME!
1470 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1472 SequenceGroup sg = viewport.getSelectionGroup();
1476 selectAllSequenceMenuItem_actionPerformed(null);
1481 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1484 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1487 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1490 public void invertColSel_actionPerformed(ActionEvent e)
1492 viewport.invertColumnSelection();
1493 alignPanel.repaint();
1500 * @param e DOCUMENT ME!
1502 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1504 trimAlignment(true);
1510 * @param e DOCUMENT ME!
1512 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
1514 trimAlignment(false);
1517 void trimAlignment(boolean trimLeft)
1519 ColumnSelection colSel = viewport.getColumnSelection();
1522 if (colSel.size() > 0)
1525 column = colSel.getMin();
1527 column = colSel.getMax();
1530 if(viewport.getSelectionGroup()!=null)
1531 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
1533 seqs = viewport.alignment.getSequencesArray();
1536 TrimRegionCommand trimRegion;
1539 trimRegion = new TrimRegionCommand("Remove Left",
1540 TrimRegionCommand.TRIM_LEFT,
1545 viewport.selectionGroup);
1546 viewport.setStartRes(0);
1550 trimRegion = new TrimRegionCommand("Remove Right",
1551 TrimRegionCommand.TRIM_RIGHT,
1556 viewport.selectionGroup);
1559 statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
1562 addHistoryItem(trimRegion);
1564 Vector groups = viewport.alignment.getGroups();
1566 for (int i = 0; i < groups.size(); i++)
1568 SequenceGroup sg = (SequenceGroup) groups.get(i);
1570 if ( (trimLeft && !sg.adjustForRemoveLeft(column))
1571 || (!trimLeft && !sg.adjustForRemoveRight(column)))
1573 viewport.alignment.deleteGroup(sg);
1577 viewport.firePropertyChange("alignment", null,
1578 viewport.getAlignment().getSequences());
1585 * @param e DOCUMENT ME!
1587 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1589 int start = 0, end = viewport.alignment.getWidth()-1;
1592 if (viewport.getSelectionGroup() != null)
1594 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
1595 start = viewport.getSelectionGroup().getStartRes();
1596 end = viewport.getSelectionGroup().getEndRes();
1599 seqs = viewport.alignment.getSequencesArray();
1602 RemoveGapColCommand removeGapCols =
1603 new RemoveGapColCommand("Remove Gapped Columns",
1606 viewport.getGapCharacter());
1608 addHistoryItem(removeGapCols);
1610 statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
1612 //This is to maintain viewport position on first residue
1614 SequenceI seq = viewport.alignment.getSequenceAt(0);
1615 int startRes = seq.findPosition(viewport.startRes);
1616 // ShiftList shifts;
1617 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
1618 // edit.alColumnChanges=shifts.getInverse();
1619 // if (viewport.hasHiddenColumns)
1620 // viewport.getColumnSelection().compensateForEdits(shifts);
1621 viewport.setStartRes(seq.findIndex(startRes)-1);
1622 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1629 * @param e DOCUMENT ME!
1631 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1633 int start = 0, end = viewport.alignment.getWidth()-1;
1636 if (viewport.getSelectionGroup() != null)
1638 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
1639 start = viewport.getSelectionGroup().getStartRes();
1640 end = viewport.getSelectionGroup().getEndRes();
1643 seqs = viewport.alignment.getSequencesArray();
1645 //This is to maintain viewport position on first residue
1647 SequenceI seq = viewport.alignment.getSequenceAt(0);
1648 int startRes = seq.findPosition(viewport.startRes);
1650 addHistoryItem(new RemoveGapsCommand("Remove Gaps",
1653 viewport.getGapCharacter()));
1655 viewport.setStartRes(seq.findIndex(startRes)-1);
1657 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1664 * @param e DOCUMENT ME!
1666 public void padGapsMenuitem_actionPerformed(ActionEvent e)
1668 viewport.padGaps = padGapsMenuitem.isSelected();
1670 viewport.firePropertyChange("alignment",
1672 viewport.getAlignment().getSequences());
1678 * @param e DOCUMENT ME!
1680 public void findMenuItem_actionPerformed(ActionEvent e)
1682 JInternalFrame frame = new JInternalFrame();
1683 Finder finder = new Finder(viewport, alignPanel, frame);
1684 frame.setContentPane(finder);
1685 frame.setLayer(JLayeredPane.PALETTE_LAYER);
1686 Desktop.addInternalFrame(frame, "Find", 340, 110);
1689 public void newView_actionPerformed(ActionEvent e)
1691 AlignmentPanel newap =
1692 new Jalview2XML().copyAlignPanel(alignPanel, true);
1694 if (viewport.viewName == null)
1695 viewport.viewName = "View 1";
1697 newap.av.historyList = viewport.historyList;
1698 newap.av.redoList = viewport.redoList;
1699 newap.av.viewName = "View " +
1700 (Desktop.getViewCount(viewport.getSequenceSetId()) + 1);
1702 addAlignmentPanel(newap, false);
1704 if(alignPanels.size()==2)
1706 viewport.gatherViewsHere = true;
1708 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
1715 * @param e DOCUMENT ME!
1717 public void font_actionPerformed(ActionEvent e)
1719 new FontChooser(alignPanel);
1726 * @param e DOCUMENT ME!
1728 protected void seqLimit_actionPerformed(ActionEvent e)
1730 viewport.setShowJVSuffix(seqLimits.isSelected());
1732 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
1733 alignPanel.repaint();
1736 public void idRightAlign_actionPerformed(ActionEvent e)
1738 viewport.idsAlignRight = idRightAlign.isSelected();
1739 alignPanel.repaint();
1747 * @param e DOCUMENT ME!
1749 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
1751 viewport.setColourText(colourTextMenuItem.isSelected());
1752 alignPanel.repaint();
1758 * @param e DOCUMENT ME!
1760 public void wrapMenuItem_actionPerformed(ActionEvent e)
1762 scaleAbove.setVisible(wrapMenuItem.isSelected());
1763 scaleLeft.setVisible(wrapMenuItem.isSelected());
1764 scaleRight.setVisible(wrapMenuItem.isSelected());
1765 viewport.setWrapAlignment(wrapMenuItem.isSelected());
1766 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
1769 public void showAllSeqs_actionPerformed(ActionEvent e)
1771 viewport.showAllHiddenSeqs();
1774 public void showAllColumns_actionPerformed(ActionEvent e)
1776 viewport.showAllHiddenColumns();
1780 public void hideSelSequences_actionPerformed(ActionEvent e)
1782 viewport.hideAllSelectedSeqs();
1783 alignPanel.repaint();
1786 public void hideSelColumns_actionPerformed(ActionEvent e)
1788 viewport.hideSelectedColumns();
1789 alignPanel.repaint();
1792 public void hiddenMarkers_actionPerformed(ActionEvent e)
1794 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
1801 * @param e DOCUMENT ME!
1803 protected void scaleAbove_actionPerformed(ActionEvent e)
1805 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
1806 alignPanel.repaint();
1812 * @param e DOCUMENT ME!
1814 protected void scaleLeft_actionPerformed(ActionEvent e)
1816 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
1817 alignPanel.repaint();
1823 * @param e DOCUMENT ME!
1825 protected void scaleRight_actionPerformed(ActionEvent e)
1827 viewport.setScaleRightWrapped(scaleRight.isSelected());
1828 alignPanel.repaint();
1834 * @param e DOCUMENT ME!
1836 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1838 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
1839 alignPanel.repaint();
1845 * @param e DOCUMENT ME!
1847 public void viewTextMenuItem_actionPerformed(ActionEvent e)
1849 viewport.setShowText(viewTextMenuItem.isSelected());
1850 alignPanel.repaint();
1856 * @param e DOCUMENT ME!
1858 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1860 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
1861 alignPanel.repaint();
1865 public FeatureSettings featureSettings;
1866 public void featureSettings_actionPerformed(ActionEvent e)
1868 if(featureSettings !=null )
1870 featureSettings.close();
1871 featureSettings = null;
1873 featureSettings = new FeatureSettings(this);
1879 * @param evt DOCUMENT ME!
1881 public void showSeqFeatures_actionPerformed(ActionEvent evt)
1883 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
1884 alignPanel.repaint();
1885 if (alignPanel.getOverviewPanel() != null)
1887 alignPanel.getOverviewPanel().updateOverviewImage();
1894 * @param e DOCUMENT ME!
1896 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
1898 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
1899 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
1905 * @param e DOCUMENT ME!
1907 public void overviewMenuItem_actionPerformed(ActionEvent e)
1909 if (alignPanel.overviewPanel != null)
1914 JInternalFrame frame = new JInternalFrame();
1915 OverviewPanel overview = new OverviewPanel(alignPanel);
1916 frame.setContentPane(overview);
1917 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
1918 frame.getWidth(), frame.getHeight());
1920 frame.setLayer(JLayeredPane.PALETTE_LAYER);
1921 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
1923 public void internalFrameClosed(
1924 javax.swing.event.InternalFrameEvent evt)
1926 alignPanel.setOverviewPanel(null);
1931 alignPanel.setOverviewPanel(overview);
1934 public void textColour_actionPerformed(ActionEvent e)
1936 int original1 = viewport.textColour.getRGB();
1937 int original2 = viewport.textColour2.getRGB();
1938 int thresh = viewport.thresholdTextColour;
1939 final JSlider slider = new JSlider(0, 750, viewport.thresholdTextColour);
1940 final JButton col1 = new JButton("DARK");
1941 col1.setBackground(viewport.textColour);
1942 col1.setForeground(viewport.textColour);
1943 final JButton col2 = new JButton("LIGHT");
1944 col2.setBackground(viewport.textColour2);
1945 col2.setForeground(viewport.textColour2);
1946 final JPanel bigpanel = new JPanel(new BorderLayout());
1947 JPanel panel = new JPanel();
1948 bigpanel.add(panel, BorderLayout.CENTER);
1949 bigpanel.add(new JLabel(
1950 "<html><i>Select a dark and light text colour, then set the threshold to"
1951 +"<br>switch between colours, based on background colour</i></html>"),
1952 BorderLayout.NORTH);
1957 col1.addActionListener(new ActionListener()
1959 public void actionPerformed(ActionEvent e)
1961 Color col = JColorChooser.showDialog(bigpanel,
1962 "Select Colour for Text",
1963 viewport.textColour);
1966 viewport.textColour = col;
1967 col1.setBackground(col);
1968 col1.setForeground(col);
1969 if(viewport.colourAppliesToAllGroups)
1970 setGroupTextColour();
1972 alignPanel.repaint();
1976 col2.addActionListener(new ActionListener()
1978 public void actionPerformed(ActionEvent e)
1980 Color col = JColorChooser.showDialog(bigpanel,
1981 "Select Colour for Text",
1982 viewport.textColour);
1985 viewport.textColour2 = col;
1986 col2.setBackground(col);
1987 col2.setForeground(col);
1988 if(viewport.colourAppliesToAllGroups)
1989 setGroupTextColour();
1991 alignPanel.repaint();
1996 slider.addChangeListener(new ChangeListener()
1998 public void stateChanged(ChangeEvent evt)
2000 viewport.thresholdTextColour = slider.getValue();
2001 if(viewport.colourAppliesToAllGroups)
2002 setGroupTextColour();
2003 alignPanel.repaint();
2007 int reply = JOptionPane.showInternalOptionDialog(this,
2009 "Adjust Foreground Text Colour Threshold",
2010 JOptionPane.OK_CANCEL_OPTION,
2011 JOptionPane.QUESTION_MESSAGE,
2015 if(reply==JOptionPane.CANCEL_OPTION)
2017 viewport.textColour = new Color(original1);
2018 viewport.textColour2 = new Color(original2);
2019 viewport.thresholdTextColour = thresh;
2023 void setGroupTextColour()
2025 if(viewport.alignment.getGroups()==null)
2028 Vector groups = viewport.alignment.getGroups();
2030 for(int i=0; i<groups.size(); i++)
2032 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
2033 sg.textColour = viewport.textColour;
2034 sg.textColour2 = viewport.textColour2;
2035 sg.thresholdTextColour = viewport.thresholdTextColour;
2045 * @param e DOCUMENT ME!
2047 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2055 * @param e DOCUMENT ME!
2057 public void clustalColour_actionPerformed(ActionEvent e)
2059 changeColour(new ClustalxColourScheme(
2060 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
2066 * @param e DOCUMENT ME!
2068 public void zappoColour_actionPerformed(ActionEvent e)
2070 changeColour(new ZappoColourScheme());
2076 * @param e DOCUMENT ME!
2078 public void taylorColour_actionPerformed(ActionEvent e)
2080 changeColour(new TaylorColourScheme());
2086 * @param e DOCUMENT ME!
2088 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2090 changeColour(new HydrophobicColourScheme());
2096 * @param e DOCUMENT ME!
2098 public void helixColour_actionPerformed(ActionEvent e)
2100 changeColour(new HelixColourScheme());
2106 * @param e DOCUMENT ME!
2108 public void strandColour_actionPerformed(ActionEvent e)
2110 changeColour(new StrandColourScheme());
2116 * @param e DOCUMENT ME!
2118 public void turnColour_actionPerformed(ActionEvent e)
2120 changeColour(new TurnColourScheme());
2126 * @param e DOCUMENT ME!
2128 public void buriedColour_actionPerformed(ActionEvent e)
2130 changeColour(new BuriedColourScheme());
2136 * @param e DOCUMENT ME!
2138 public void nucleotideColour_actionPerformed(ActionEvent e)
2140 changeColour(new NucleotideColourScheme());
2143 public void annotationColour_actionPerformed(ActionEvent e)
2145 new AnnotationColourChooser(viewport, alignPanel);
2152 * @param e DOCUMENT ME!
2154 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2156 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2162 * @param cs DOCUMENT ME!
2164 public void changeColour(ColourSchemeI cs)
2170 if (viewport.getAbovePIDThreshold())
2172 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2175 cs.setThreshold(threshold,
2176 viewport.getIgnoreGapsConsensus());
2178 viewport.setGlobalColourScheme(cs);
2182 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2185 if (viewport.getConservationSelected())
2188 Alignment al = (Alignment) viewport.alignment;
2189 Conservation c = new Conservation("All",
2190 ResidueProperties.propHash, 3,
2191 al.getSequences(), 0,
2195 c.verdict(false, viewport.ConsPercGaps);
2197 cs.setConservation(c);
2199 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
2204 cs.setConservation(null);
2207 cs.setConsensus(viewport.hconsensus);
2210 viewport.setGlobalColourScheme(cs);
2212 if (viewport.getColourAppliesToAllGroups())
2214 Vector groups = viewport.alignment.getGroups();
2216 for (int i = 0; i < groups.size(); i++)
2218 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2226 if (cs instanceof ClustalxColourScheme)
2228 sg.cs = new ClustalxColourScheme(
2229 sg.getSequences(true), sg.getWidth());
2231 else if (cs instanceof UserColourScheme)
2233 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
2239 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2241 catch (Exception ex)
2246 if (viewport.getAbovePIDThreshold()
2247 || cs instanceof PIDColourScheme
2248 || cs instanceof Blosum62ColourScheme)
2250 sg.cs.setThreshold(threshold,
2251 viewport.getIgnoreGapsConsensus());
2253 sg.cs.setConsensus(AAFrequency.calculate(
2254 sg.getSequences(true), sg.getStartRes(),
2258 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2261 if (viewport.getConservationSelected())
2263 Conservation c = new Conservation("Group",
2264 ResidueProperties.propHash, 3,
2265 sg.getSequences(true),
2269 c.verdict(false, viewport.ConsPercGaps);
2270 sg.cs.setConservation(c);
2273 sg.cs.setConservation(null);
2277 if (alignPanel.getOverviewPanel() != null)
2279 alignPanel.getOverviewPanel().updateOverviewImage();
2282 alignPanel.repaint();
2288 * @param e DOCUMENT ME!
2290 protected void modifyPID_actionPerformed(ActionEvent e)
2292 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
2294 SliderPanel.setPIDSliderSource(alignPanel,
2295 viewport.getGlobalColourScheme(),
2297 SliderPanel.showPIDSlider();
2304 * @param e DOCUMENT ME!
2306 protected void modifyConservation_actionPerformed(ActionEvent e)
2308 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
2310 SliderPanel.setConservationSlider(alignPanel,
2311 viewport.globalColourScheme,
2313 SliderPanel.showConservationSlider();
2320 * @param e DOCUMENT ME!
2322 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2324 viewport.setConservationSelected(conservationMenuItem.isSelected());
2326 viewport.setAbovePIDThreshold(false);
2327 abovePIDThreshold.setSelected(false);
2329 changeColour(viewport.getGlobalColourScheme());
2331 modifyConservation_actionPerformed(null);
2337 * @param e DOCUMENT ME!
2339 public void abovePIDThreshold_actionPerformed(ActionEvent e)
2341 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
2343 conservationMenuItem.setSelected(false);
2344 viewport.setConservationSelected(false);
2346 changeColour(viewport.getGlobalColourScheme());
2348 modifyPID_actionPerformed(null);
2354 * @param e DOCUMENT ME!
2356 public void userDefinedColour_actionPerformed(ActionEvent e)
2358 if (e.getActionCommand().equals("User Defined..."))
2360 new UserDefinedColours(alignPanel, null);
2364 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
2365 getUserColourSchemes().get(e.getActionCommand());
2371 public void updateUserColourMenu()
2374 Component[] menuItems = colourMenu.getMenuComponents();
2375 int i, iSize = menuItems.length;
2376 for (i = 0; i < iSize; i++)
2378 if (menuItems[i].getName() != null &&
2379 menuItems[i].getName().equals("USER_DEFINED"))
2381 colourMenu.remove(menuItems[i]);
2385 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
2387 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
2388 getUserColourSchemes().keys();
2390 while (userColours.hasMoreElements())
2392 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
2393 nextElement().toString());
2394 radioItem.setName("USER_DEFINED");
2395 radioItem.addMouseListener(new MouseAdapter()
2397 public void mousePressed(MouseEvent evt)
2399 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
2401 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
2403 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
2404 "Remove from default list?",
2405 "Remove user defined colour",
2406 JOptionPane.YES_NO_OPTION);
2407 if(option == JOptionPane.YES_OPTION)
2409 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
2410 colourMenu.remove(radioItem);
2413 radioItem.addActionListener(new ActionListener()
2415 public void actionPerformed(ActionEvent evt)
2417 userDefinedColour_actionPerformed(evt);
2423 radioItem.addActionListener(new ActionListener()
2425 public void actionPerformed(ActionEvent evt)
2427 userDefinedColour_actionPerformed(evt);
2431 colourMenu.insert(radioItem, 15);
2432 colours.add(radioItem);
2440 * @param e DOCUMENT ME!
2442 public void PIDColour_actionPerformed(ActionEvent e)
2444 changeColour(new PIDColourScheme());
2450 * @param e DOCUMENT ME!
2452 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
2454 changeColour(new Blosum62ColourScheme());
2460 * @param e DOCUMENT ME!
2462 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2464 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2465 AlignmentSorter.sortByPID(viewport.getAlignment(),
2466 viewport.getAlignment().getSequenceAt(0));
2467 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));
2468 alignPanel.repaint();
2474 * @param e DOCUMENT ME!
2476 public void sortIDMenuItem_actionPerformed(ActionEvent e)
2478 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2479 AlignmentSorter.sortByID(viewport.getAlignment());
2480 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
2481 alignPanel.repaint();
2487 * @param e DOCUMENT ME!
2489 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
2491 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2492 AlignmentSorter.sortByGroup(viewport.getAlignment());
2493 addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
2495 alignPanel.repaint();
2501 * @param e DOCUMENT ME!
2503 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2505 new RedundancyPanel(alignPanel, this);
2512 * @param e DOCUMENT ME!
2514 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2516 if ( (viewport.getSelectionGroup() == null) ||
2517 (viewport.getSelectionGroup().getSize(false) < 2))
2519 JOptionPane.showInternalMessageDialog(this,
2520 "You must select at least 2 sequences.",
2521 "Invalid Selection",
2522 JOptionPane.WARNING_MESSAGE);
2526 JInternalFrame frame = new JInternalFrame();
2527 frame.setContentPane(new PairwiseAlignPanel(viewport));
2528 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
2535 * @param e DOCUMENT ME!
2537 public void PCAMenuItem_actionPerformed(ActionEvent e)
2539 if ( ( (viewport.getSelectionGroup() != null) &&
2540 (viewport.getSelectionGroup().getSize(false) < 4) &&
2541 (viewport.getSelectionGroup().getSize(false) > 0)) ||
2542 (viewport.getAlignment().getHeight() < 4))
2544 JOptionPane.showInternalMessageDialog(this,
2545 "Principal component analysis must take\n" +
2546 "at least 4 input sequences.",
2547 "Sequence selection insufficient",
2548 JOptionPane.WARNING_MESSAGE);
2553 new PCAPanel(viewport);
2557 public void autoCalculate_actionPerformed(ActionEvent e)
2559 viewport.autoCalculateConsensus = autoCalculate.isSelected();
2560 if(viewport.autoCalculateConsensus)
2562 viewport.firePropertyChange("alignment",
2564 viewport.getAlignment().getSequences());
2572 * @param e DOCUMENT ME!
2574 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2576 NewTreePanel("AV", "PID", "Average distance tree using PID");
2582 * @param e DOCUMENT ME!
2584 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2586 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2592 * @param e DOCUMENT ME!
2594 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2596 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2602 * @param e DOCUMENT ME!
2604 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2606 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2612 * @param type DOCUMENT ME!
2613 * @param pwType DOCUMENT ME!
2614 * @param title DOCUMENT ME!
2616 void NewTreePanel(String type, String pwType, String title)
2620 if (viewport.getSelectionGroup() != null) {
2621 if (viewport.getSelectionGroup().getSize(false) < 3) {
2622 JOptionPane.showMessageDialog(Desktop.desktop,
2623 "You need to have more than two sequences selected to build a tree!",
2624 "Not enough sequences",
2625 JOptionPane.WARNING_MESSAGE);
2630 SequenceGroup sg = viewport.getSelectionGroup();
2632 /* Decide if the selection is a column region */
2633 while (s < sg.getSize(false))
2635 if ( ( (SequenceI) sg.getSequences(false).elementAt(s++)).getLength() <
2638 JOptionPane.showMessageDialog(Desktop.desktop,
2639 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
2640 "Try using the Pad function in the edit menu,\n" +
2641 "or one of the multiple sequence alignment web services.",
2642 "Sequences in selection are not aligned",
2643 JOptionPane.WARNING_MESSAGE);
2649 title = title + " on region";
2650 tp = new TreePanel(alignPanel, type, pwType);
2654 //are the sequences aligned?
2655 if (!viewport.alignment.isAligned())
2657 JOptionPane.showMessageDialog(Desktop.desktop,
2658 "The sequences must be aligned before creating a tree.\n" +
2659 "Try using the Pad function in the edit menu,\n" +
2660 "or one of the multiple sequence alignment web services.",
2661 "Sequences not aligned",
2662 JOptionPane.WARNING_MESSAGE);
2667 if(viewport.alignment.getHeight()<2)
2670 tp = new TreePanel(alignPanel, type, pwType);
2673 addTreeMenuItem(tp, title);
2675 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
2681 * @param title DOCUMENT ME!
2682 * @param order DOCUMENT ME!
2684 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
2686 final JMenuItem item = new JMenuItem("by " + title);
2688 item.addActionListener(new java.awt.event.ActionListener()
2690 public void actionPerformed(ActionEvent e)
2692 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2694 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
2695 AlignmentSorter.sortBy(viewport.getAlignment(), order);
2697 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport.alignment));
2699 alignPanel.repaint();
2705 * Maintain the Order by->Displayed Tree menu.
2706 * Creates a new menu item for a TreePanel with an appropriate
2707 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
2708 * to remove the menu item when the treePanel is closed, and adjust
2709 * the tree leaf to sequence mapping when the alignment is modified.
2710 * @param treePanel Displayed tree window.
2711 * @param title SortBy menu item title.
2713 void addTreeMenuItem(final TreePanel treePanel, String title)
2715 final JMenuItem item = new JMenuItem(title);
2721 sort.add(sortByTreeMenu);
2724 sortByTreeMenu.add(item);
2725 item.addActionListener(new java.awt.event.ActionListener()
2727 public void actionPerformed(ActionEvent e)
2729 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2730 AlignmentSorter.sortByTree(viewport.getAlignment(),
2731 treePanel.getTree());
2733 addHistoryItem(new OrderCommand("Tree Sort",
2735 viewport.alignment));
2738 alignPanel.repaint();
2742 treePanel.addInternalFrameListener(new javax.swing.event.
2743 InternalFrameAdapter()
2745 public void internalFrameClosed(
2746 javax.swing.event.InternalFrameEvent evt)
2749 sortByTreeMenu.remove(item);
2753 sort.remove(sortByTreeMenu);
2761 * Work out whether the whole set of sequences
2762 * or just the selected set will be submitted for multiple alignment.
2765 private jalview.datamodel.AlignmentView gatherSequencesForAlignment()
2767 // Now, check we have enough sequences
2768 AlignmentView msa = null;
2770 if ( (viewport.getSelectionGroup() != null) &&
2771 (viewport.getSelectionGroup().getSize(false) > 1))
2773 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
2774 /*SequenceGroup seqs = viewport.getSelectionGroup();
2776 msa = new SequenceI[sz = seqs.getSize(false)];
2778 for (int i = 0; i < sz; i++)
2780 msa[i] = (SequenceI) seqs.getSequenceAt(i);
2782 msa = viewport.getAlignmentView(true);
2786 /*Vector seqs = viewport.getAlignment().getSequences();
2788 if (seqs.size() > 1)
2790 msa = new SequenceI[seqs.size()];
2792 for (int i = 0; i < seqs.size(); i++)
2794 msa[i] = (SequenceI) seqs.elementAt(i);
2797 msa = viewport.getAlignmentView(false);
2803 * Decides what is submitted to a secondary structure prediction service,
2804 * the currently selected sequence, or the currently selected alignment
2805 * (where the first sequence in the set is the one that the prediction
2808 AlignmentView gatherSeqOrMsaForSecStrPrediction()
2810 AlignmentView seqs = null;
2812 if ( (viewport.getSelectionGroup() != null) &&
2813 (viewport.getSelectionGroup().getSize(false) > 0))
2815 seqs = viewport.getAlignmentView(true);
2819 seqs = viewport.getAlignmentView(false);
2821 // limit sequences - JBPNote in future - could spawn multiple prediction jobs
2822 // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment.
2823 if (!viewport.alignment.isAligned())
2825 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] } );
2832 * @param e DOCUMENT ME!
2834 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2836 // Pick the tree file
2837 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
2840 chooser.setFileView(new JalviewFileView());
2841 chooser.setDialogTitle("Select a newick-like tree file");
2842 chooser.setToolTipText("Load a tree file");
2844 int value = chooser.showOpenDialog(null);
2846 if (value == JalviewFileChooser.APPROVE_OPTION)
2848 String choice = chooser.getSelectedFile().getPath();
2849 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
2853 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
2855 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
2857 catch (Exception ex)
2859 JOptionPane.showMessageDialog(Desktop.desktop,
2860 "Problem reading tree file",
2862 JOptionPane.WARNING_MESSAGE);
2863 ex.printStackTrace();
2869 public TreePanel ShowNewickTree(NewickFile nf, String title)
2871 return ShowNewickTree(nf,title,600,500,4,5);
2873 public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input)
2875 return ShowNewickTree(nf,title, input, 600,500,4,5);
2877 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y) {
2878 return ShowNewickTree(nf, title, null, w, h, x, y);
2881 * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
2883 * @param nf the tree
2884 * @param title tree viewer title
2885 * @param input Associated alignment input data (or null)
2890 * @return TreePanel handle
2892 public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input, int w,int h,int x, int y) {
2893 TreePanel tp = null;
2899 if (nf.getTree() != null)
2901 tp = new TreePanel(alignPanel,
2909 tp.setLocation(x,y);
2912 Desktop.addInternalFrame(tp, title, w, h);
2913 addTreeMenuItem(tp, title);
2916 catch (Exception ex)
2918 ex.printStackTrace();
2929 PrinterJob printJob = PrinterJob.getPrinterJob();
2930 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
2931 printJob.setPrintable(alignPanel, pf);
2933 if (printJob.printDialog())
2939 catch (Exception PrintException)
2941 PrintException.printStackTrace();
2948 * Generates menu items and listener event actions for web service clients
2951 public void BuildWebServiceMenu()
2953 if ( (Discoverer.services != null)
2954 && (Discoverer.services.size() > 0))
2956 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
2957 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
2958 Vector wsmenu = new Vector();
2959 final AlignFrame af = this;
2962 // Add any Multiple Sequence Alignment Services
2963 final JMenu msawsmenu = new JMenu("Alignment");
2964 for (int i = 0, j = msaws.size(); i < j; i++)
2966 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
2968 final JMenuItem method = new JMenuItem(sh.getName());
2969 method.addActionListener(new ActionListener()
2971 public void actionPerformed(ActionEvent e)
2973 AlignmentView msa = gatherSequencesForAlignment();
2974 new jalview.ws.MsaWSClient(sh, title, msa,
2975 false, true, viewport.getAlignment().getDataset(), af);
2980 msawsmenu.add(method);
2981 // Deal with services that we know accept partial alignments.
2982 if (sh.getName().indexOf("lustal") > -1)
2984 // We know that ClustalWS can accept partial alignments for refinement.
2985 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
2986 methodR.addActionListener(new ActionListener()
2988 public void actionPerformed(ActionEvent e)
2990 AlignmentView msa = gatherSequencesForAlignment();
2991 new jalview.ws.MsaWSClient(sh, title, msa,
2992 true, true, viewport.getAlignment().getDataset(), af);
2997 msawsmenu.add(methodR);
3001 wsmenu.add(msawsmenu);
3003 if (secstrpr != null)
3005 // Add any secondary structure prediction services
3006 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
3007 for (int i = 0, j = secstrpr.size(); i < j; i++)
3009 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
3011 final JMenuItem method = new JMenuItem(sh.getName());
3012 method.addActionListener(new ActionListener()
3014 public void actionPerformed(ActionEvent e)
3016 AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
3017 if (msa.getSequences().length == 1)
3019 // Single Sequence prediction
3020 new jalview.ws.JPredClient(sh, title, false, msa, af, true);
3024 if (msa.getSequences().length > 1)
3026 // Sequence profile based prediction
3027 new jalview.ws.JPredClient(sh,
3028 title, true, msa, af, true);
3033 secstrmenu.add(method);
3035 wsmenu.add(secstrmenu);
3037 this.webService.removeAll();
3038 for (int i = 0, j = wsmenu.size(); i < j; i++)
3040 webService.add( (JMenu) wsmenu.get(i));
3045 this.webService.removeAll();
3046 this.webService.add(this.webServiceNoServices);
3048 // TODO: add in rediscovery function
3049 // TODO: reduce code redundancy.
3050 // TODO: group services by location as well as function.
3053 /* public void vamsasStore_actionPerformed(ActionEvent e)
3055 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
3056 getProperty("LAST_DIRECTORY"));
3058 chooser.setFileView(new JalviewFileView());
3059 chooser.setDialogTitle("Export to Vamsas file");
3060 chooser.setToolTipText("Export");
3062 int value = chooser.showSaveDialog(this);
3064 if (value == JalviewFileChooser.APPROVE_OPTION)
3066 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
3067 //vs.store(chooser.getSelectedFile().getAbsolutePath() );
3068 vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
3075 public void showTranslation_actionPerformed(ActionEvent e)
3077 SequenceI [] selection = viewport.getSelectionAsNewSequence();
3078 String [] seqstring = viewport.getViewAsString(true);
3080 int s, sSize = selection.length;
3081 SequenceI [] newSeq = new SequenceI[sSize];
3084 StringBuffer protein;
3086 for(s=0; s<sSize; s++)
3088 protein = new StringBuffer();
3089 seq = AlignSeq.extractGaps("-. ", seqstring[s]);
3090 resSize = seq.length();
3091 resSize -= resSize%3;
3093 for(res = 0; res < resSize; res+=3)
3095 String codon = seq.substring(res, res+3);
3096 codon = codon.replace('U', 'T');
3097 String aa = ResidueProperties.codonTranslate(codon);
3099 protein.append(viewport.getGapCharacter());
3100 else if(aa.equals("STOP"))
3101 protein.append("X");
3103 protein.append( aa );
3105 newSeq[s] = new Sequence(selection[s].getName(),
3106 protein.toString());
3110 AlignmentI al = new Alignment(newSeq);
3111 al.setDataset(null);
3114 ////////////////////////////////
3115 // Copy annotations across
3116 jalview.datamodel.AlignmentAnnotation[] annotations
3117 = viewport.alignment.getAlignmentAnnotation();
3119 if(annotations!=null)
3121 for (int i = 0; i < annotations.length; i++)
3123 if (annotations[i].label.equals("Quality") ||
3124 annotations[i].label.equals("Conservation") ||
3125 annotations[i].label.equals("Consensus"))
3130 aSize = viewport.alignment.getWidth() / 3;
3131 jalview.datamodel.Annotation[] anots =
3132 new jalview.datamodel.Annotation[aSize];
3134 for (a = 0; a < viewport.alignment.getWidth(); a++)
3136 if (annotations[i].annotations[a] == null
3137 || annotations[i].annotations[a] == null)
3140 anots[a / 3] = new Annotation(
3141 annotations[i].annotations[a].displayCharacter,
3142 annotations[i].annotations[a].description,
3143 annotations[i].annotations[a].secondaryStructure,
3144 annotations[i].annotations[a].value,
3145 annotations[i].annotations[a].colour);
3148 jalview.datamodel.AlignmentAnnotation aa
3149 = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
3150 annotations[i].description, anots);
3151 al.addAnnotation(aa);
3155 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
3156 Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
3168 * @param String DOCUMENT ME!
3170 public boolean parseFeaturesFile(String file, String type)
3172 boolean featuresFile = false;
3174 featuresFile = new FeaturesFile(file, type).parse(viewport.alignment.getDataset(),
3175 alignPanel.seqPanel.seqCanvas.
3176 getFeatureRenderer().featureColours,
3181 ex.printStackTrace();
3186 viewport.showSequenceFeatures = true;
3187 showSeqFeatures.setSelected(true);
3188 alignPanel.repaint();
3191 return featuresFile;
3194 public void dragEnter(DropTargetDragEvent evt)
3197 public void dragExit(DropTargetEvent evt)
3200 public void dragOver(DropTargetDragEvent evt)
3203 public void dropActionChanged(DropTargetDragEvent evt)
3206 public void drop(DropTargetDropEvent evt)
3208 Transferable t = evt.getTransferable();
3209 java.util.List files = null;
3213 DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
3214 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
3216 //Works on Windows and MacOSX
3217 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3218 files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
3220 else if (t.isDataFlavorSupported(uriListFlavor))
3222 // This is used by Unix drag system
3223 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3224 String data = (String) t.getTransferData(uriListFlavor);
3225 files = new java.util.ArrayList(1);
3226 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
3229 st.hasMoreTokens(); )
3231 String s = st.nextToken();
3232 if (s.startsWith("#"))
3234 // the line is a comment (as per the RFC 2483)
3238 java.net.URI uri = new java.net.URI(s);
3239 java.io.File file = new java.io.File(uri);
3246 e.printStackTrace();
3253 for (int i = 0; i < files.size(); i++)
3255 loadJalviewDataFile(files.get(i).toString());
3258 catch (Exception ex)
3260 ex.printStackTrace();
3265 // This method will attempt to load a "dropped" file first by testing
3266 // whether its and Annotation file, then features file. If both are
3267 // false then the user may have dropped an alignment file onto this
3269 public void loadJalviewDataFile(String file)
3272 String protocol = "File";
3274 if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
3279 boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
3284 boolean isGroupsFile = parseFeaturesFile(file,protocol);
3287 String format = new IdentifyFile().Identify(file, protocol);
3289 if(format.equalsIgnoreCase("JnetFile"))
3291 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
3293 new JnetAnnotationMaker().add_annotation(predictions,
3294 viewport.getAlignment(),
3296 alignPanel.adjustAnnotationHeight();
3297 alignPanel.repaint();
3300 new FileLoader().LoadFile(viewport, file, protocol, format);
3306 alignPanel.adjustAnnotationHeight();
3309 }catch(Exception ex)
3311 ex.printStackTrace();
3315 public void tabSelectionChanged(int index)
3319 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
3320 viewport = alignPanel.av;
3321 setMenusFromViewport(viewport);
3325 public void tabbedPane_mousePressed(MouseEvent e)
3327 if(SwingUtilities.isRightMouseButton(e))
3329 String reply = JOptionPane.showInternalInputDialog(this,
3332 JOptionPane.QUESTION_MESSAGE);
3336 viewport.viewName = reply;
3337 tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
3343 public AlignViewport getCurrentView()