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.util.ShiftList;
37 import jalview.commands.*;
39 import java.awt.dnd.*;
47 public class AlignFrame extends GAlignFrame implements DropTargetListener
50 public static final int DEFAULT_WIDTH = 700;
53 public static final int DEFAULT_HEIGHT = 500;
54 public AlignmentPanel alignPanel;
55 AlignViewport viewport;
58 Vector alignPanels = new Vector();
62 public String currentFileFormat = null;
63 Stack historyList = new Stack();
64 Stack redoList = new Stack();
65 private int treeCount = 0;
68 * Creates a new AlignFrame object.
70 * @param al DOCUMENT ME!
72 public AlignFrame(AlignmentI al, int width, int height)
74 this(al, null, width, height);
79 * new alignment window with hidden columns
80 * @param al AlignmentI
81 * @param hiddenColumns ColumnSelection or null
83 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
84 int width, int height)
86 this.setSize(width, height);
87 viewport = new AlignViewport(al, hiddenColumns);
89 alignPanel = new AlignmentPanel(this, viewport);
91 if(al.getDataset()==null)
96 addAlignmentPanel(alignPanel);
101 * Make a new AlignFrame from exisiting alignmentPanels
102 * @param ap AlignmentPanel
103 * @param av AlignViewport
105 public AlignFrame(AlignmentPanel ap)
109 alignPanel.alignFrame = this;
110 addAlignmentPanel(ap);
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 if (jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))
143 wrapMenuItem.setSelected(true);
144 wrapMenuItem_actionPerformed(null);
150 void addKeyListener()
152 final AlignFrame af = this;
153 addKeyListener(new KeyAdapter()
155 public void keyPressed(KeyEvent evt)
157 if (viewport.cursorMode
158 && evt.getKeyCode() >= KeyEvent.VK_0
159 && evt.getKeyCode() <= KeyEvent.VK_9)
161 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
164 switch (evt.getKeyCode())
167 if (!evt.isControlDown())
170 if(viewport.hasHiddenRows)
172 al = viewport.alignment.getHiddenSequences().getFullAlignment();
175 al = new Alignment(viewport.alignment.getSequencesArray());
177 AlignViewport newview = new AlignViewport(al);
179 AlignmentPanel copy = new AlignmentPanel(af, newview);
181 if(viewport.viewName==null)
182 viewport.viewName="View 1";
184 copy.av.sequenceSetID = viewport.getSequenceSetId();
185 copy.av.viewName = "View " +
186 (Desktop.getViewCount(viewport.getSequenceSetId())+1);
189 addAlignmentPanel(copy);
190 PaintRefresher.Register(copy, viewport.getSequenceSetId());
191 PaintRefresher.Register(alignPanel,
192 viewport.getSequenceSetId());
197 Desktop.instance.gatherViews(af);
201 if (!evt.isControlDown())
203 Desktop.instance.explodeViews(af);
208 case 27: // escape key
209 deselectAllSequenceMenuItem_actionPerformed(null);
213 case KeyEvent.VK_DOWN:
214 if (viewport.cursorMode)
216 alignPanel.seqPanel.moveCursor(0, 1);
219 moveSelectedSequences(false);
223 if (viewport.cursorMode)
225 alignPanel.seqPanel.moveCursor(0, -1);
228 moveSelectedSequences(true);
231 case KeyEvent.VK_LEFT:
232 if (viewport.cursorMode)
234 alignPanel.seqPanel.moveCursor( -1, 0);
238 case KeyEvent.VK_RIGHT:
239 if (viewport.cursorMode)
241 alignPanel.seqPanel.moveCursor(1, 0);
245 case KeyEvent.VK_SPACE:
246 if (viewport.cursorMode)
248 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
254 case KeyEvent.VK_DELETE:
255 case KeyEvent.VK_BACK_SPACE:
256 if (!viewport.cursorMode)
258 cut_actionPerformed(null);
261 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
268 if (viewport.cursorMode)
270 alignPanel.seqPanel.setCursorRow();
274 if (viewport.cursorMode && !evt.isControlDown())
276 alignPanel.seqPanel.setCursorColumn();
280 if (viewport.cursorMode)
282 alignPanel.seqPanel.setCursorPosition();
286 case KeyEvent.VK_ENTER:
287 case KeyEvent.VK_COMMA:
288 if (viewport.cursorMode)
290 alignPanel.seqPanel.setCursorRowAndColumn();
295 if (viewport.cursorMode)
297 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
301 if (viewport.cursorMode)
303 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
308 viewport.cursorMode = !viewport.cursorMode;
309 statusBar.setText("Keyboard editing mode is " +
310 (viewport.cursorMode ? "on" : "off"));
311 if (viewport.cursorMode)
313 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
314 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
316 alignPanel.seqPanel.seqCanvas.repaint();
322 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
323 java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
324 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
326 javax.help.HelpBroker hb = hs.createHelpBroker();
327 hb.setCurrentID("home");
328 hb.setDisplayed(true);
332 ex.printStackTrace();
338 boolean toggleSeqs = !evt.isControlDown();
339 boolean toggleCols = !evt.isShiftDown();
341 boolean hide = false;
343 SequenceGroup sg = viewport.getSelectionGroup();
346 if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
348 hideSelSequences_actionPerformed(null);
351 else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))
352 showAllSeqs_actionPerformed(null);
357 if (viewport.colSel.getSelected().size() > 0)
359 hideSelColumns_actionPerformed(null);
361 viewport.selectionGroup = sg;
364 showAllColumns_actionPerformed(null);
368 case KeyEvent.VK_PAGE_UP:
369 if (viewport.wrapAlignment)
370 alignPanel.scrollUp(true);
372 alignPanel.setScrollValues(viewport.startRes,
374 - viewport.endSeq + viewport.startSeq);
376 case KeyEvent.VK_PAGE_DOWN:
377 if (viewport.wrapAlignment)
378 alignPanel.scrollUp(false);
380 alignPanel.setScrollValues(viewport.startRes,
382 + viewport.endSeq - viewport.startSeq);
392 public void addAlignmentPanel(final AlignmentPanel ap)
394 alignPanels.addElement(ap);
396 int aSize = alignPanels.size();
398 tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
400 if (aSize == 1 && ap.av.viewName==null)
402 this.getContentPane().add(ap, BorderLayout.CENTER);
408 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
409 tabbedPane.addTab(first.av.viewName==null?"Original":first.av.viewName,first);
411 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
414 tabbedPane.addTab(ap.av.viewName==null?"Original":ap.av.viewName, ap);
417 ap.av.updateConsensus(ap);
418 ap.av.updateConservation(ap);
421 ap.av.addPropertyChangeListener(new PropertyChangeListener()
423 public void propertyChange(PropertyChangeEvent evt)
425 if (evt.getPropertyName().equals("alignment"))
427 PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
438 public AlignViewport getViewport()
443 /* Set up intrinsic listeners for dynamically generated GUI bits. */
444 private void addServiceListeners()
446 final java.beans.PropertyChangeListener thisListener;
447 // Do this once to get current state
448 BuildWebServiceMenu();
449 Desktop.discoverer.addPropertyChangeListener(
450 thisListener = new java.beans.PropertyChangeListener()
452 public void propertyChange(PropertyChangeEvent evt)
454 // System.out.println("Discoverer property change.");
455 if (evt.getPropertyName().equals("services"))
457 // System.out.println("Rebuilding web service menu");
458 BuildWebServiceMenu();
463 addInternalFrameListener(new javax.swing.event.
464 InternalFrameAdapter()
466 public void internalFrameClosed(
467 javax.swing.event.InternalFrameEvent evt)
469 // System.out.println("deregistering discoverer listener");
470 Desktop.discoverer.removePropertyChangeListener(thisListener);
471 closeMenuItem_actionPerformed(null);
477 public void setGUINucleotide(boolean nucleotide)
479 showTranslation.setVisible( nucleotide );
480 //sequenceFeatures.setVisible(!nucleotide );
481 //featureSettings.setVisible( !nucleotide );
482 conservationMenuItem.setVisible( !nucleotide );
483 modifyConservation.setVisible( !nucleotide );
485 //Remember AlignFrame always starts as protein
488 calculateMenu.remove(calculateMenu.getItemCount()-2);
493 Hashtable progressBars;
494 public void setProgressBar(String message, long id)
496 if(progressBars == null)
497 progressBars = new Hashtable();
499 JPanel progressPanel;
500 GridLayout layout = (GridLayout) statusPanel.getLayout();
501 if(progressBars.get( new Long(id) )!=null)
503 progressPanel = (JPanel)progressBars.get( new Long(id) );
504 statusPanel.remove(progressPanel);
505 progressBars.remove( progressPanel );
506 progressPanel = null;
508 statusBar.setText(message);
510 layout.setRows(layout.getRows() - 1);
514 progressPanel = new JPanel(new BorderLayout(10, 5));
516 JProgressBar progressBar = new JProgressBar();
517 progressBar.setIndeterminate(true);
519 progressPanel.add(new JLabel(message), BorderLayout.WEST);
520 progressPanel.add(progressBar, BorderLayout.CENTER);
522 layout.setRows(layout.getRows() + 1);
523 statusPanel.add(progressPanel);
525 progressBars.put(new Long(id), progressPanel);
535 Added so Castor Mapping file can obtain Jalview Version
537 public String getVersion()
539 return jalview.bin.Cache.getProperty("VERSION");
542 public FeatureRenderer getFeatureRenderer()
544 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
548 public void fetchSequence_actionPerformed(ActionEvent e)
550 new SequenceFetcher(this);
553 public void addFromFile_actionPerformed(ActionEvent e)
555 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
558 public void addFromText_actionPerformed(ActionEvent e)
560 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
563 public void addFromURL_actionPerformed(ActionEvent e)
565 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
571 * @param e DOCUMENT ME!
573 public void saveAlignmentMenu_actionPerformed(ActionEvent e)
575 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
576 getProperty( "LAST_DIRECTORY"),
578 { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" },
580 { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
585 chooser.setFileView(new JalviewFileView());
586 chooser.setDialogTitle("Save Alignment to file");
587 chooser.setToolTipText("Save");
589 int value = chooser.showSaveDialog(this);
591 if (value == JalviewFileChooser.APPROVE_OPTION)
593 currentFileFormat = chooser.getSelectedFormat();
595 if (currentFileFormat == null)
597 JOptionPane.showInternalMessageDialog(Desktop.desktop,
598 "You must select a file format before saving!",
599 "File format not specified",
600 JOptionPane.WARNING_MESSAGE);
601 value = chooser.showSaveDialog(this);
605 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
608 String choice = chooser.getSelectedFile().getPath();
609 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
611 saveAlignment(choice, currentFileFormat);
615 public boolean saveAlignment(String file, String format)
617 if (format.equalsIgnoreCase("Jalview"))
619 String shortName = title;
621 if (shortName.indexOf(java.io.File.separatorChar) > -1)
623 shortName = shortName.substring(shortName.lastIndexOf(
624 java.io.File.separatorChar) + 1);
627 new Jalview2XML().SaveAlignment(this, file, shortName);
629 // USE Jalview2XML to save this file
635 String[] omitHidden = null;
637 if (viewport.hasHiddenColumns)
639 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
640 "The Alignment contains hidden columns."
641 + "\nDo you want to save only the visible alignment?",
642 "Save / Omit Hidden Columns",
643 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
645 if (reply == JOptionPane.YES_OPTION)
646 omitHidden = viewport.getViewAsString(false);
649 String output = new FormatAdapter().formatSequences(
651 viewport.alignment.getSequencesArray(),
661 java.io.PrintWriter out = new java.io.PrintWriter(
662 new java.io.FileWriter(file));
671 ex.printStackTrace();
680 * @param e DOCUMENT ME!
682 protected void outputText_actionPerformed(ActionEvent e)
684 String [] omitHidden = null;
686 if(viewport.hasHiddenColumns)
688 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
689 "The Alignment contains hidden columns."
690 +"\nDo you want to output only the visible alignment?",
691 "Save / Omit Hidden Columns",
692 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
694 if(reply==JOptionPane.YES_OPTION)
696 omitHidden = viewport.getViewAsString(false);
700 CutAndPasteTransfer cap = new CutAndPasteTransfer();
701 Desktop.addInternalFrame(cap,
702 "Alignment output - " + e.getActionCommand(), 600,
706 cap.setText(new FormatAdapter().formatSequences(
707 e.getActionCommand(),
708 viewport.alignment.getSequencesArray(),
715 * @param e DOCUMENT ME!
717 protected void htmlMenuItem_actionPerformed(ActionEvent e)
719 new HTMLOutput(viewport,
720 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
721 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
724 public void createImageMap(File file, String image)
726 alignPanel.makePNGImageMap(file, image);
732 * @param e DOCUMENT ME!
734 public void createPNG(File f)
736 alignPanel.makePNG(f);
742 * @param e DOCUMENT ME!
744 public void createEPS(File f)
746 alignPanel.makeEPS(f);
752 * @param e DOCUMENT ME!
754 public void printMenuItem_actionPerformed(ActionEvent e)
756 //Putting in a thread avoids Swing painting problems
757 PrintThread thread = new PrintThread();
761 public void exportFeatures_actionPerformed(ActionEvent e)
763 new AnnotationExporter().exportFeatures(alignPanel);
767 public void exportAnnotations_actionPerformed(ActionEvent e)
769 new AnnotationExporter().exportAnnotations(
771 viewport.alignment.getAlignmentAnnotation()
776 public void associatedData_actionPerformed(ActionEvent e)
778 // Pick the tree file
779 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
782 chooser.setFileView(new JalviewFileView());
783 chooser.setDialogTitle("Load Jalview Annotations or Features File");
784 chooser.setToolTipText("Load Jalview Annotations / Features file");
786 int value = chooser.showOpenDialog(null);
788 if (value == JalviewFileChooser.APPROVE_OPTION)
790 String choice = chooser.getSelectedFile().getPath();
791 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
792 loadJalviewDataFile(choice);
801 * @param e DOCUMENT ME!
803 public void closeMenuItem_actionPerformed(ActionEvent e)
807 for(int i=0; i<alignPanels.size(); i++)
809 AlignmentPanel ap = (AlignmentPanel)alignPanels.elementAt(i);
810 PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
811 PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
812 PaintRefresher.RemoveComponent(ap);
815 this.setClosed(true);
826 void updateEditMenuBar()
829 if (historyList.size() > 0)
831 undoMenuItem.setEnabled(true);
832 CommandI command = (CommandI) historyList.peek();
833 undoMenuItem.setText("Undo " + command.getDescription());
837 undoMenuItem.setEnabled(false);
838 undoMenuItem.setText("Undo");
841 if (redoList.size() > 0)
843 redoMenuItem.setEnabled(true);
845 CommandI command = (CommandI) redoList.peek();
846 redoMenuItem.setText("Redo " + command.getDescription());
850 redoMenuItem.setEnabled(false);
851 redoMenuItem.setText("Redo");
856 public void addHistoryItem(CommandI command)
858 historyList.push(command);
862 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
870 * @param e DOCUMENT ME!
872 protected void undoMenuItem_actionPerformed(ActionEvent e)
874 CommandI command = (CommandI)historyList.pop();
875 redoList.push(command);
876 command.undoCommand();
878 // HistoryItem nh,hi = (HistoryItem) historyList.pop();
879 // redoList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment,
880 // HistoryItem.HIDE));
881 // if (hi.alColumnChanges!=null)
882 // nh.alColumnChanges = hi.alColumnChanges.getInverse();
883 // restoreHistoryItem(hi);
884 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
886 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
892 * @param e DOCUMENT ME!
894 protected void redoMenuItem_actionPerformed(ActionEvent e)
896 CommandI command = (CommandI) redoList.pop();
897 historyList.push(command);
899 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
901 // HistoryItem nh,hi = (HistoryItem) redoList.pop();
902 // historyList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment,
903 // HistoryItem.HIDE));
904 // if (hi.alColumnChanges!=null)
905 // nh.alColumnChanges=hi.alColumnChanges.getInverse();
906 // restoreHistoryItem(hi);
908 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
915 * @param up DOCUMENT ME!
917 public void moveSelectedSequences(boolean up)
919 SequenceGroup sg = viewport.getSelectionGroup();
928 for (int i = 1; i < viewport.alignment.getHeight(); i++)
930 SequenceI seq = viewport.alignment.getSequenceAt(i);
932 if (!sg.getSequences(false).contains(seq))
937 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
939 if (sg.getSequences(false).contains(temp))
944 viewport.alignment.getSequences().setElementAt(temp, i);
945 viewport.alignment.getSequences().setElementAt(seq, i - 1);
950 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
952 SequenceI seq = viewport.alignment.getSequenceAt(i);
954 if (!sg.getSequences(false).contains(seq))
959 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
961 if (sg.getSequences(false).contains(temp))
966 viewport.alignment.getSequences().setElementAt(temp, i);
967 viewport.alignment.getSequences().setElementAt(seq, i + 1);
971 alignPanel.repaint();
979 * @param e DOCUMENT ME!
981 protected void copy_actionPerformed(ActionEvent e)
984 if (viewport.getSelectionGroup() == null)
989 SequenceI [] seqs = viewport.getSelectionAsNewSequence();
990 String[] omitHidden = null;
992 if (viewport.hasHiddenColumns)
994 omitHidden = viewport.getViewAsString(true);
997 String output = new FormatAdapter().formatSequences(
1002 StringSelection ss = new StringSelection(output);
1006 //Its really worth setting the clipboard contents
1007 //to empty before setting the large StringSelection!!
1008 Toolkit.getDefaultToolkit().getSystemClipboard()
1009 .setContents(new StringSelection(""), null);
1011 Toolkit.getDefaultToolkit().getSystemClipboard()
1012 .setContents(ss, Desktop.instance);
1014 catch (OutOfMemoryError er)
1016 er.printStackTrace();
1017 javax.swing.SwingUtilities.invokeLater(new Runnable()
1021 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1022 "Out of memory copying region!!"
1024 "\nSee help files for increasing Java Virtual Machine memory."
1026 javax.swing.JOptionPane.WARNING_MESSAGE);
1033 Vector hiddenColumns = null;
1034 if(viewport.hasHiddenColumns)
1036 hiddenColumns =new Vector();
1037 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1038 for(int i=0; i<viewport.getColumnSelection().getHiddenColumns().size(); i++)
1040 int[] region = (int[])
1041 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
1043 hiddenColumns.addElement(new int[]{region[0]-hiddenOffset,
1044 region[1]-hiddenOffset});
1050 Desktop.jalviewClipboard = new Object[]{ seqs,
1051 viewport.alignment.getDataset(),
1053 statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
1059 * @param e DOCUMENT ME!
1061 protected void pasteNew_actionPerformed(ActionEvent e)
1069 * @param e DOCUMENT ME!
1071 protected void pasteThis_actionPerformed(ActionEvent e)
1079 * @param newAlignment DOCUMENT ME!
1081 void paste(boolean newAlignment)
1085 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1086 Transferable contents = c.getContents(this);
1088 if (contents == null)
1096 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1097 if (str.length() < 1)
1100 format = new IdentifyFile().Identify(str, "Paste");
1103 catch (OutOfMemoryError er)
1105 er.printStackTrace();
1106 javax.swing.SwingUtilities.invokeLater(new Runnable()
1110 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1111 "Out of memory pasting sequences!!"
1113 "\nSee help files for increasing Java Virtual Machine memory."
1115 javax.swing.JOptionPane.WARNING_MESSAGE);
1122 SequenceI[] sequences;
1125 if(Desktop.jalviewClipboard!=null)
1127 // The clipboard was filled from within Jalview, we must use the sequences
1128 // And dataset from the copied alignment
1129 sequences = (SequenceI[])Desktop.jalviewClipboard[0];
1133 sequences = new FormatAdapter().readFile(str, "Paste", format);
1136 AlignmentI alignment = null;
1140 alignment = new Alignment(sequences);
1142 if (Desktop.jalviewClipboard != null)
1143 alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
1145 alignment.setDataset(null);
1149 alignment = viewport.getAlignment();
1152 SequenceI [] newseqs = new SequenceI[sequences.length];
1153 for (int i = 0; i < sequences.length; i++)
1155 newseqs[i] = new Sequence(sequences[i].getName(),
1156 sequences[i].getSequence(), sequences[i].getStart(),
1157 sequences[i].getEnd());
1159 alignment.addSequence(newseqs[i]);
1160 PaintRefresher.Refresh(alignPanel,
1161 alignPanel.av.getSequenceSetId(),
1169 addHistoryItem(new EditCommand(
1174 alignment.getWidth(),
1179 viewport.setEndSeq(alignment.getHeight());
1180 alignment.getWidth();
1181 viewport.firePropertyChange("alignment", null, alignment.getSequences());
1186 // Add any annotations attached to sequences
1187 for (int i = 0; i < sequences.length; i++)
1189 if (sequences[i].getAnnotation() != null)
1191 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1193 AlignmentAnnotation newAnnot =
1194 new AlignmentAnnotation(
1195 sequences[i].getAnnotation()[a].label,
1196 sequences[i].getAnnotation()[a].description,
1197 sequences[i].getAnnotation()[a].annotations,
1198 sequences[i].getAnnotation()[a].graphMin,
1199 sequences[i].getAnnotation()[a].graphMax,
1200 sequences[i].getAnnotation()[a].graph);
1202 sequences[i].getAnnotation()[a] = newAnnot;
1203 newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].
1205 newAnnot.sequenceRef = sequences[i];
1206 newAnnot.adjustForAlignment();
1207 alignment.addAnnotation(newAnnot);
1208 alignment.setAnnotationIndex(newAnnot, a);
1211 alignPanel.annotationPanel.adjustPanelHeight();
1217 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
1218 String newtitle = new String("Copied sequences");
1220 if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
1222 Vector hc = (Vector)Desktop.jalviewClipboard[2];
1223 for(int i=0; i<hc.size(); i++)
1225 int [] region = (int[]) hc.elementAt(i);
1226 af.viewport.hideColumns(region[0], region[1]);
1231 //>>>This is a fix for the moment, until a better solution is found!!<<<
1232 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
1233 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1236 if (title.startsWith("Copied sequences"))
1242 newtitle = newtitle.concat("- from " + title);
1245 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1252 catch (Exception ex)
1254 ex.printStackTrace();
1255 System.out.println("Exception whilst pasting: "+ex);
1256 // could be anything being pasted in here
1265 * @param e DOCUMENT ME!
1267 protected void cut_actionPerformed(ActionEvent e)
1269 copy_actionPerformed(null);
1270 delete_actionPerformed(null);
1276 * @param e DOCUMENT ME!
1278 protected void delete_actionPerformed(ActionEvent e)
1281 SequenceGroup sg = viewport.getSelectionGroup();
1287 Vector seqs = new Vector();
1288 int cutLength = sg.getEndRes()-sg.getStartRes()+1;
1290 for (int i = 0; i < sg.getSize(false); i++)
1292 seq = sg.getSequenceAt(i);
1293 seqs.addElement(seq);
1294 if(seq.getLength()<=cutLength)
1295 PaintRefresher.Refresh(alignPanel,
1296 alignPanel.av.getSequenceSetId(),
1301 // If the cut affects all sequences, remove highlighted columns
1302 if (sg.getSize(false) == viewport.alignment.getHeight())
1304 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1305 sg.getEndRes() + 1);
1309 SequenceI [] cut = new SequenceI[seqs.size()];
1310 for(int i=0; i<seqs.size(); i++)
1311 cut[i] = (SequenceI)seqs.elementAt(i);
1317 addHistoryItem(new EditCommand("Cut Sequences",
1321 sg.getEndRes()-sg.getStartRes()+1,
1322 viewport.alignment));
1324 viewport.setSelectionGroup(null);
1325 viewport.alignment.deleteGroup(sg);
1327 viewport.firePropertyChange("alignment", null,
1328 viewport.getAlignment().getSequences());
1330 if (viewport.getAlignment().getHeight() < 1)
1334 this.setClosed(true);
1336 catch (Exception ex)
1345 * @param e DOCUMENT ME!
1347 protected void deleteGroups_actionPerformed(ActionEvent e)
1349 viewport.alignment.deleteAllGroups();
1350 viewport.setSelectionGroup(null);
1351 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1352 alignPanel.repaint();
1358 * @param e DOCUMENT ME!
1360 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1362 SequenceGroup sg = new SequenceGroup();
1364 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1367 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1370 sg.setEndRes(viewport.alignment.getWidth() - 1);
1371 viewport.setSelectionGroup(sg);
1372 alignPanel.repaint();
1373 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1379 * @param e DOCUMENT ME!
1381 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1383 if(viewport.cursorMode)
1385 alignPanel.seqPanel.keyboardNo1 = null;
1386 alignPanel.seqPanel.keyboardNo2 = null;
1388 viewport.setSelectionGroup(null);
1389 viewport.getColumnSelection().clear();
1390 viewport.setSelectionGroup(null);
1391 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1392 alignPanel.idPanel.idCanvas.searchResults = null;
1393 alignPanel.repaint();
1394 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1400 * @param e DOCUMENT ME!
1402 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1404 SequenceGroup sg = viewport.getSelectionGroup();
1408 selectAllSequenceMenuItem_actionPerformed(null);
1413 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1416 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1419 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1422 public void invertColSel_actionPerformed(ActionEvent e)
1424 viewport.invertColumnSelection();
1425 alignPanel.repaint();
1432 * @param e DOCUMENT ME!
1434 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1436 trimAlignment(true);
1442 * @param e DOCUMENT ME!
1444 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
1446 trimAlignment(false);
1449 void trimAlignment(boolean trimLeft)
1451 ColumnSelection colSel = viewport.getColumnSelection();
1454 if (colSel.size() > 0)
1457 column = colSel.getMin();
1459 column = colSel.getMax();
1462 if(viewport.getSelectionGroup()!=null)
1463 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
1465 seqs = viewport.alignment.getSequencesArray();
1468 TrimRegionCommand trimRegion;
1471 trimRegion = new TrimRegionCommand("Remove Left",
1472 TrimRegionCommand.TRIM_LEFT,
1477 viewport.selectionGroup);
1481 trimRegion = new TrimRegionCommand("Remove Right",
1482 TrimRegionCommand.TRIM_RIGHT,
1487 viewport.selectionGroup);
1490 addHistoryItem(trimRegion);
1492 Vector groups = viewport.alignment.getGroups();
1494 for (int i = 0; i < groups.size(); i++)
1496 SequenceGroup sg = (SequenceGroup) groups.get(i);
1498 if ( (trimLeft && !sg.adjustForRemoveLeft(column))
1499 || (!trimLeft && !sg.adjustForRemoveRight(column)))
1501 viewport.alignment.deleteGroup(sg);
1505 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1512 * @param e DOCUMENT ME!
1514 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1516 int start = 0, end = viewport.alignment.getWidth()-1;
1519 if (viewport.getSelectionGroup() != null)
1521 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
1522 start = viewport.getSelectionGroup().getStartRes();
1523 end = viewport.getSelectionGroup().getEndRes();
1526 seqs = viewport.alignment.getSequencesArray();
1529 addHistoryItem(new RemoveGapColCommand("Remove Gapped Columns",
1532 viewport.getGapCharacter()));
1534 //This is to maintain viewport position on first residue
1536 SequenceI seq = viewport.alignment.getSequenceAt(0);
1537 int startRes = seq.findPosition(viewport.startRes);
1538 // ShiftList shifts;
1539 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
1540 // edit.alColumnChanges=shifts.getInverse();
1541 // if (viewport.hasHiddenColumns)
1542 // viewport.getColumnSelection().compensateForEdits(shifts);
1543 viewport.setStartRes(seq.findIndex(startRes)-1);
1544 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1551 * @param e DOCUMENT ME!
1553 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1555 int start = 0, end = viewport.alignment.getWidth()-1;
1558 if (viewport.getSelectionGroup() != null)
1560 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
1561 start = viewport.getSelectionGroup().getStartRes();
1562 end = viewport.getSelectionGroup().getEndRes();
1565 seqs = viewport.alignment.getSequencesArray();
1567 //This is to maintain viewport position on first residue
1569 SequenceI seq = viewport.alignment.getSequenceAt(0);
1570 int startRes = seq.findPosition(viewport.startRes);
1572 addHistoryItem(new RemoveGapsCommand("Remove Gaps",
1575 viewport.getGapCharacter()));
1577 viewport.setStartRes(seq.findIndex(startRes)-1);
1579 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1583 public void alignmentChanged()
1588 for(int i=0; i<alignPanels.size(); i++)
1590 ap = (AlignmentPanel) alignPanels.elementAt(i);
1594 av.getAlignment().padGaps();
1596 if (av.hconsensus != null && av.autoCalculateConsensus)
1598 av.updateConsensus(ap);
1599 av.updateConservation(ap);
1600 ap.annotationPanel.repaint();
1603 resetAllColourSchemes();
1605 av.alignment.adjustSequenceAnnotations();
1607 if (ap.overviewPanel != null)
1608 ap.overviewPanel.updateOverviewImage();
1614 void resetAllColourSchemes()
1616 ColourSchemeI cs = viewport.globalColourScheme;
1619 if (cs instanceof ClustalxColourScheme)
1621 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
1622 resetClustalX(viewport.alignment.getSequences(),
1623 viewport.alignment.getWidth());
1626 cs.setConsensus(viewport.hconsensus);
1627 if (cs.conservationApplied())
1629 Alignment al = (Alignment) viewport.alignment;
1630 Conservation c = new Conservation("All",
1631 ResidueProperties.propHash, 3,
1632 al.getSequences(), 0,
1635 c.verdict(false, viewport.ConsPercGaps);
1637 cs.setConservation(c);
1641 int s, sSize = viewport.alignment.getGroups().size();
1642 for(s=0; s<sSize; s++)
1644 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
1645 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
1647 ((ClustalxColourScheme)sg.cs).resetClustalX(
1648 sg.getSequences(true), sg.getWidth());
1650 sg.recalcConservation();
1657 * @param e DOCUMENT ME!
1659 public void padGapsMenuitem_actionPerformed(ActionEvent e)
1661 // addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
1662 // HistoryItem.HIDE));
1664 viewport.padGaps = padGapsMenuitem.isSelected();
1666 viewport.firePropertyChange("alignment",
1668 viewport.getAlignment().getSequences());
1674 * @param e DOCUMENT ME!
1676 public void findMenuItem_actionPerformed(ActionEvent e)
1678 JInternalFrame frame = new JInternalFrame();
1679 Finder finder = new Finder(viewport, alignPanel, frame);
1680 frame.setContentPane(finder);
1681 frame.setLayer(JLayeredPane.PALETTE_LAYER);
1682 Desktop.addInternalFrame(frame, "Find", 340, 110);
1688 * @param e DOCUMENT ME!
1690 public void font_actionPerformed(ActionEvent e)
1692 new FontChooser(alignPanel);
1695 public void smoothFont_actionPerformed(ActionEvent e)
1697 viewport.antiAlias = smoothFont.isSelected();
1698 alignPanel.annotationPanel.image = null;
1699 alignPanel.repaint();
1706 * @param e DOCUMENT ME!
1708 protected void seqLimit_actionPerformed(ActionEvent e)
1710 viewport.setShowJVSuffix(seqLimits.isSelected());
1712 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
1713 alignPanel.repaint();
1720 * @param e DOCUMENT ME!
1722 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
1724 viewport.setColourText(colourTextMenuItem.isSelected());
1725 alignPanel.repaint();
1731 * @param e DOCUMENT ME!
1733 public void wrapMenuItem_actionPerformed(ActionEvent e)
1735 scaleAbove.setVisible(wrapMenuItem.isSelected());
1736 scaleLeft.setVisible(wrapMenuItem.isSelected());
1737 scaleRight.setVisible(wrapMenuItem.isSelected());
1738 viewport.setWrapAlignment(wrapMenuItem.isSelected());
1739 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
1742 public void showAllSeqs_actionPerformed(ActionEvent e)
1744 viewport.showAllHiddenSeqs();
1747 public void showAllColumns_actionPerformed(ActionEvent e)
1749 viewport.showAllHiddenColumns();
1753 public void hideSelSequences_actionPerformed(ActionEvent e)
1755 viewport.hideAllSelectedSeqs();
1756 alignPanel.repaint();
1759 public void hideSelColumns_actionPerformed(ActionEvent e)
1761 viewport.hideSelectedColumns();
1762 alignPanel.repaint();
1765 public void hiddenMarkers_actionPerformed(ActionEvent e)
1767 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
1774 * @param e DOCUMENT ME!
1776 protected void scaleAbove_actionPerformed(ActionEvent e)
1778 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
1779 alignPanel.repaint();
1785 * @param e DOCUMENT ME!
1787 protected void scaleLeft_actionPerformed(ActionEvent e)
1789 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
1790 alignPanel.repaint();
1796 * @param e DOCUMENT ME!
1798 protected void scaleRight_actionPerformed(ActionEvent e)
1800 viewport.setScaleRightWrapped(scaleRight.isSelected());
1801 alignPanel.repaint();
1807 * @param e DOCUMENT ME!
1809 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1811 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
1812 alignPanel.repaint();
1818 * @param e DOCUMENT ME!
1820 public void viewTextMenuItem_actionPerformed(ActionEvent e)
1822 viewport.setShowText(viewTextMenuItem.isSelected());
1823 alignPanel.repaint();
1829 * @param e DOCUMENT ME!
1831 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1833 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
1834 alignPanel.repaint();
1838 public FeatureSettings featureSettings;
1839 public void featureSettings_actionPerformed(ActionEvent e)
1841 if(featureSettings !=null )
1843 featureSettings.close();
1844 featureSettings = null;
1846 featureSettings = new FeatureSettings(this);
1852 * @param evt DOCUMENT ME!
1854 public void showSeqFeatures_actionPerformed(ActionEvent evt)
1856 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
1857 alignPanel.repaint();
1858 if (alignPanel.getOverviewPanel() != null)
1860 alignPanel.getOverviewPanel().updateOverviewImage();
1867 * @param e DOCUMENT ME!
1869 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
1871 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
1872 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
1878 * @param e DOCUMENT ME!
1880 public void overviewMenuItem_actionPerformed(ActionEvent e)
1882 if (alignPanel.overviewPanel != null)
1887 JInternalFrame frame = new JInternalFrame();
1888 OverviewPanel overview = new OverviewPanel(alignPanel);
1889 frame.setContentPane(overview);
1890 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
1891 frame.getWidth(), frame.getHeight());
1893 frame.setLayer(JLayeredPane.PALETTE_LAYER);
1894 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
1896 public void internalFrameClosed(
1897 javax.swing.event.InternalFrameEvent evt)
1899 alignPanel.setOverviewPanel(null);
1904 alignPanel.setOverviewPanel(overview);
1910 * @param e DOCUMENT ME!
1912 protected void noColourmenuItem_actionPerformed(ActionEvent e)
1920 * @param e DOCUMENT ME!
1922 public void clustalColour_actionPerformed(ActionEvent e)
1924 changeColour(new ClustalxColourScheme(
1925 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
1931 * @param e DOCUMENT ME!
1933 public void zappoColour_actionPerformed(ActionEvent e)
1935 changeColour(new ZappoColourScheme());
1941 * @param e DOCUMENT ME!
1943 public void taylorColour_actionPerformed(ActionEvent e)
1945 changeColour(new TaylorColourScheme());
1951 * @param e DOCUMENT ME!
1953 public void hydrophobicityColour_actionPerformed(ActionEvent e)
1955 changeColour(new HydrophobicColourScheme());
1961 * @param e DOCUMENT ME!
1963 public void helixColour_actionPerformed(ActionEvent e)
1965 changeColour(new HelixColourScheme());
1971 * @param e DOCUMENT ME!
1973 public void strandColour_actionPerformed(ActionEvent e)
1975 changeColour(new StrandColourScheme());
1981 * @param e DOCUMENT ME!
1983 public void turnColour_actionPerformed(ActionEvent e)
1985 changeColour(new TurnColourScheme());
1991 * @param e DOCUMENT ME!
1993 public void buriedColour_actionPerformed(ActionEvent e)
1995 changeColour(new BuriedColourScheme());
2001 * @param e DOCUMENT ME!
2003 public void nucleotideColour_actionPerformed(ActionEvent e)
2005 changeColour(new NucleotideColourScheme());
2008 public void annotationColour_actionPerformed(ActionEvent e)
2010 new AnnotationColourChooser(viewport, alignPanel);
2017 * @param e DOCUMENT ME!
2019 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2021 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2027 * @param cs DOCUMENT ME!
2029 public void changeColour(ColourSchemeI cs)
2035 if (viewport.getAbovePIDThreshold())
2037 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2040 cs.setThreshold(threshold,
2041 viewport.getIgnoreGapsConsensus());
2043 viewport.setGlobalColourScheme(cs);
2047 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2050 if (viewport.getConservationSelected())
2053 Alignment al = (Alignment) viewport.alignment;
2054 Conservation c = new Conservation("All",
2055 ResidueProperties.propHash, 3,
2056 al.getSequences(), 0,
2060 c.verdict(false, viewport.ConsPercGaps);
2062 cs.setConservation(c);
2064 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
2069 cs.setConservation(null);
2072 cs.setConsensus(viewport.hconsensus);
2075 viewport.setGlobalColourScheme(cs);
2077 if (viewport.getColourAppliesToAllGroups())
2079 Vector groups = viewport.alignment.getGroups();
2081 for (int i = 0; i < groups.size(); i++)
2083 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2091 if (cs instanceof ClustalxColourScheme)
2093 sg.cs = new ClustalxColourScheme(
2094 sg.getSequences(true), sg.getWidth());
2096 else if (cs instanceof UserColourScheme)
2098 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
2104 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2106 catch (Exception ex)
2111 if (viewport.getAbovePIDThreshold()
2112 || cs instanceof PIDColourScheme
2113 || cs instanceof Blosum62ColourScheme)
2115 sg.cs.setThreshold(threshold,
2116 viewport.getIgnoreGapsConsensus());
2118 sg.cs.setConsensus(AAFrequency.calculate(
2119 sg.getSequences(true), 0,
2123 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2126 if (viewport.getConservationSelected())
2128 Conservation c = new Conservation("Group",
2129 ResidueProperties.propHash, 3,
2130 sg.getSequences(true), 0,
2131 viewport.alignment.getWidth() - 1);
2133 c.verdict(false, viewport.ConsPercGaps);
2134 sg.cs.setConservation(c);
2137 sg.cs.setConservation(null);
2141 if (alignPanel.getOverviewPanel() != null)
2143 alignPanel.getOverviewPanel().updateOverviewImage();
2146 alignPanel.repaint();
2152 * @param e DOCUMENT ME!
2154 protected void modifyPID_actionPerformed(ActionEvent e)
2156 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
2158 SliderPanel.setPIDSliderSource(alignPanel,
2159 viewport.getGlobalColourScheme(),
2161 SliderPanel.showPIDSlider();
2168 * @param e DOCUMENT ME!
2170 protected void modifyConservation_actionPerformed(ActionEvent e)
2172 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
2174 SliderPanel.setConservationSlider(alignPanel,
2175 viewport.globalColourScheme,
2177 SliderPanel.showConservationSlider();
2184 * @param e DOCUMENT ME!
2186 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2188 viewport.setConservationSelected(conservationMenuItem.isSelected());
2190 viewport.setAbovePIDThreshold(false);
2191 abovePIDThreshold.setSelected(false);
2193 changeColour(viewport.getGlobalColourScheme());
2195 modifyConservation_actionPerformed(null);
2201 * @param e DOCUMENT ME!
2203 public void abovePIDThreshold_actionPerformed(ActionEvent e)
2205 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
2207 conservationMenuItem.setSelected(false);
2208 viewport.setConservationSelected(false);
2210 changeColour(viewport.getGlobalColourScheme());
2212 modifyPID_actionPerformed(null);
2218 * @param e DOCUMENT ME!
2220 public void userDefinedColour_actionPerformed(ActionEvent e)
2222 if (e.getActionCommand().equals("User Defined..."))
2224 new UserDefinedColours(alignPanel, null);
2228 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
2229 getUserColourSchemes().get(e.getActionCommand());
2235 public void updateUserColourMenu()
2238 Component[] menuItems = colourMenu.getMenuComponents();
2239 int i, iSize = menuItems.length;
2240 for (i = 0; i < iSize; i++)
2242 if (menuItems[i].getName() != null &&
2243 menuItems[i].getName().equals("USER_DEFINED"))
2245 colourMenu.remove(menuItems[i]);
2249 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
2251 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
2252 getUserColourSchemes().keys();
2254 while (userColours.hasMoreElements())
2256 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
2257 nextElement().toString());
2258 radioItem.setName("USER_DEFINED");
2259 radioItem.addMouseListener(new MouseAdapter()
2261 public void mousePressed(MouseEvent evt)
2263 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
2265 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
2267 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
2268 "Remove from default list?",
2269 "Remove user defined colour",
2270 JOptionPane.YES_NO_OPTION);
2271 if(option == JOptionPane.YES_OPTION)
2273 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
2274 colourMenu.remove(radioItem);
2277 radioItem.addActionListener(new ActionListener()
2279 public void actionPerformed(ActionEvent evt)
2281 userDefinedColour_actionPerformed(evt);
2287 radioItem.addActionListener(new ActionListener()
2289 public void actionPerformed(ActionEvent evt)
2291 userDefinedColour_actionPerformed(evt);
2295 colourMenu.insert(radioItem, 15);
2296 colours.add(radioItem);
2304 * @param e DOCUMENT ME!
2306 public void PIDColour_actionPerformed(ActionEvent e)
2308 changeColour(new PIDColourScheme());
2314 * @param e DOCUMENT ME!
2316 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
2318 changeColour(new Blosum62ColourScheme());
2324 * @param e DOCUMENT ME!
2326 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2328 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2329 AlignmentSorter.sortByPID(viewport.getAlignment(),
2330 viewport.getAlignment().getSequenceAt(0));
2331 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));
2332 alignPanel.repaint();
2338 * @param e DOCUMENT ME!
2340 public void sortIDMenuItem_actionPerformed(ActionEvent e)
2342 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2343 AlignmentSorter.sortByID(viewport.getAlignment());
2344 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
2345 alignPanel.repaint();
2351 * @param e DOCUMENT ME!
2353 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
2355 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2356 AlignmentSorter.sortByGroup(viewport.getAlignment());
2357 addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
2359 alignPanel.repaint();
2365 * @param e DOCUMENT ME!
2367 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2369 new RedundancyPanel(alignPanel, this);
2376 * @param e DOCUMENT ME!
2378 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2380 if ( (viewport.getSelectionGroup() == null) ||
2381 (viewport.getSelectionGroup().getSize(false) < 2))
2383 JOptionPane.showInternalMessageDialog(this,
2384 "You must select at least 2 sequences.",
2385 "Invalid Selection",
2386 JOptionPane.WARNING_MESSAGE);
2390 JInternalFrame frame = new JInternalFrame();
2391 frame.setContentPane(new PairwiseAlignPanel(viewport));
2392 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
2399 * @param e DOCUMENT ME!
2401 public void PCAMenuItem_actionPerformed(ActionEvent e)
2403 if ( ( (viewport.getSelectionGroup() != null) &&
2404 (viewport.getSelectionGroup().getSize(false) < 4) &&
2405 (viewport.getSelectionGroup().getSize(false) > 0)) ||
2406 (viewport.getAlignment().getHeight() < 4))
2408 JOptionPane.showInternalMessageDialog(this,
2409 "Principal component analysis must take\n" +
2410 "at least 4 input sequences.",
2411 "Sequence selection insufficient",
2412 JOptionPane.WARNING_MESSAGE);
2417 new PCAPanel(viewport);
2421 public void autoCalculate_actionPerformed(ActionEvent e)
2423 viewport.autoCalculateConsensus = autoCalculate.isSelected();
2424 if(viewport.autoCalculateConsensus)
2426 viewport.firePropertyChange("alignment",
2428 viewport.getAlignment().getSequences());
2436 * @param e DOCUMENT ME!
2438 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2440 NewTreePanel("AV", "PID", "Average distance tree using PID");
2446 * @param e DOCUMENT ME!
2448 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2450 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2456 * @param e DOCUMENT ME!
2458 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2460 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2466 * @param e DOCUMENT ME!
2468 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2470 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2476 * @param type DOCUMENT ME!
2477 * @param pwType DOCUMENT ME!
2478 * @param title DOCUMENT ME!
2480 void NewTreePanel(String type, String pwType, String title)
2484 if (viewport.getSelectionGroup() != null) {
2485 if (viewport.getSelectionGroup().getSize(false) < 3) {
2486 JOptionPane.showMessageDialog(Desktop.desktop,
2487 "You need to have more than two sequences selected to build a tree!",
2488 "Not enough sequences",
2489 JOptionPane.WARNING_MESSAGE);
2494 SequenceGroup sg = viewport.getSelectionGroup();
2496 /* Decide if the selection is a column region */
2497 while (s < sg.getSize(false))
2499 if ( ( (SequenceI) sg.getSequences(false).elementAt(s++)).getLength() <
2502 JOptionPane.showMessageDialog(Desktop.desktop,
2503 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
2504 "Try using the Pad function in the edit menu,\n" +
2505 "or one of the multiple sequence alignment web services.",
2506 "Sequences in selection are not aligned",
2507 JOptionPane.WARNING_MESSAGE);
2513 title = title + " on region";
2514 tp = new TreePanel(alignPanel, type, pwType);
2518 //are the sequences aligned?
2519 if (!viewport.alignment.isAligned())
2521 JOptionPane.showMessageDialog(Desktop.desktop,
2522 "The sequences must be aligned before creating a tree.\n" +
2523 "Try using the Pad function in the edit menu,\n" +
2524 "or one of the multiple sequence alignment web services.",
2525 "Sequences not aligned",
2526 JOptionPane.WARNING_MESSAGE);
2531 if(viewport.alignment.getHeight()<2)
2534 tp = new TreePanel(alignPanel, type, pwType);
2537 addTreeMenuItem(tp, title);
2539 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
2545 * @param title DOCUMENT ME!
2546 * @param order DOCUMENT ME!
2548 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
2550 final JMenuItem item = new JMenuItem("by " + title);
2552 item.addActionListener(new java.awt.event.ActionListener()
2554 public void actionPerformed(ActionEvent e)
2556 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2558 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
2559 AlignmentSorter.sortBy(viewport.getAlignment(), order);
2561 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport.alignment));
2563 alignPanel.repaint();
2569 * Maintain the Order by->Displayed Tree menu.
2570 * Creates a new menu item for a TreePanel with an appropriate
2571 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
2572 * to remove the menu item when the treePanel is closed, and adjust
2573 * the tree leaf to sequence mapping when the alignment is modified.
2574 * @param treePanel Displayed tree window.
2575 * @param title SortBy menu item title.
2577 void addTreeMenuItem(final TreePanel treePanel, String title)
2579 final JMenuItem item = new JMenuItem(title);
2585 sort.add(sortByTreeMenu);
2588 sortByTreeMenu.add(item);
2589 item.addActionListener(new java.awt.event.ActionListener()
2591 public void actionPerformed(ActionEvent e)
2593 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2594 AlignmentSorter.sortByTree(viewport.getAlignment(),
2595 treePanel.getTree());
2597 addHistoryItem(new OrderCommand("Tree Sort",
2599 viewport.alignment));
2602 alignPanel.repaint();
2606 treePanel.addInternalFrameListener(new javax.swing.event.
2607 InternalFrameAdapter()
2609 public void internalFrameClosed(
2610 javax.swing.event.InternalFrameEvent evt)
2613 sortByTreeMenu.remove(item);
2617 sort.remove(sortByTreeMenu);
2625 * Work out whether the whole set of sequences
2626 * or just the selected set will be submitted for multiple alignment.
2629 private jalview.datamodel.AlignmentView gatherSequencesForAlignment()
2631 // Now, check we have enough sequences
2632 AlignmentView msa = null;
2634 if ( (viewport.getSelectionGroup() != null) &&
2635 (viewport.getSelectionGroup().getSize(false) > 1))
2637 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
2638 /*SequenceGroup seqs = viewport.getSelectionGroup();
2640 msa = new SequenceI[sz = seqs.getSize(false)];
2642 for (int i = 0; i < sz; i++)
2644 msa[i] = (SequenceI) seqs.getSequenceAt(i);
2646 msa = viewport.getAlignmentView(true);
2650 /*Vector seqs = viewport.getAlignment().getSequences();
2652 if (seqs.size() > 1)
2654 msa = new SequenceI[seqs.size()];
2656 for (int i = 0; i < seqs.size(); i++)
2658 msa[i] = (SequenceI) seqs.elementAt(i);
2661 msa = viewport.getAlignmentView(false);
2667 * Decides what is submitted to a secondary structure prediction service,
2668 * the currently selected sequence, or the currently selected alignment
2669 * (where the first sequence in the set is the one that the prediction
2672 AlignmentView gatherSeqOrMsaForSecStrPrediction()
2674 AlignmentView seqs = null;
2676 if ( (viewport.getSelectionGroup() != null) &&
2677 (viewport.getSelectionGroup().getSize(false) > 0))
2679 seqs = viewport.getAlignmentView(true);
2683 seqs = viewport.getAlignmentView(false);
2685 // limit sequences - JBPNote in future - could spawn multiple prediction jobs
2686 // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment.
2687 if (!viewport.alignment.isAligned())
2689 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] } );
2696 * @param e DOCUMENT ME!
2698 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2700 // Pick the tree file
2701 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
2704 chooser.setFileView(new JalviewFileView());
2705 chooser.setDialogTitle("Select a newick-like tree file");
2706 chooser.setToolTipText("Load a tree file");
2708 int value = chooser.showOpenDialog(null);
2710 if (value == JalviewFileChooser.APPROVE_OPTION)
2712 String choice = chooser.getSelectedFile().getPath();
2713 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
2717 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
2719 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
2721 catch (Exception ex)
2723 JOptionPane.showMessageDialog(Desktop.desktop,
2724 "Problem reading tree file",
2726 JOptionPane.WARNING_MESSAGE);
2727 ex.printStackTrace();
2733 public TreePanel ShowNewickTree(NewickFile nf, String title)
2735 return ShowNewickTree(nf,title,600,500,4,5);
2737 public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input)
2739 return ShowNewickTree(nf,title, input, 600,500,4,5);
2741 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y) {
2742 return ShowNewickTree(nf, title, null, w, h, x, y);
2745 * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
2747 * @param nf the tree
2748 * @param title tree viewer title
2749 * @param input Associated alignment input data (or null)
2754 * @return TreePanel handle
2756 public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input, int w,int h,int x, int y) {
2757 TreePanel tp = null;
2763 if (nf.getTree() != null)
2765 tp = new TreePanel(alignPanel,
2773 tp.setLocation(x,y);
2776 Desktop.addInternalFrame(tp, title, w, h);
2777 addTreeMenuItem(tp, title);
2780 catch (Exception ex)
2782 ex.printStackTrace();
2793 PrinterJob printJob = PrinterJob.getPrinterJob();
2794 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
2795 printJob.setPrintable(alignPanel, pf);
2797 if (printJob.printDialog())
2803 catch (Exception PrintException)
2805 PrintException.printStackTrace();
2812 * Generates menu items and listener event actions for web service clients
2815 public void BuildWebServiceMenu()
2817 if ( (Discoverer.services != null)
2818 && (Discoverer.services.size() > 0))
2820 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
2821 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
2822 Vector wsmenu = new Vector();
2823 final AlignFrame af = this;
2826 // Add any Multiple Sequence Alignment Services
2827 final JMenu msawsmenu = new JMenu("Alignment");
2828 for (int i = 0, j = msaws.size(); i < j; i++)
2830 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
2832 final JMenuItem method = new JMenuItem(sh.getName());
2833 method.addActionListener(new ActionListener()
2835 public void actionPerformed(ActionEvent e)
2837 AlignmentView msa = gatherSequencesForAlignment();
2838 new jalview.ws.MsaWSClient(sh, title, msa,
2839 false, true, viewport.getAlignment().getDataset(), af);
2844 msawsmenu.add(method);
2845 // Deal with services that we know accept partial alignments.
2846 if (sh.getName().indexOf("lustal") > -1)
2848 // We know that ClustalWS can accept partial alignments for refinement.
2849 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
2850 methodR.addActionListener(new ActionListener()
2852 public void actionPerformed(ActionEvent e)
2854 AlignmentView msa = gatherSequencesForAlignment();
2855 new jalview.ws.MsaWSClient(sh, title, msa,
2856 true, true, viewport.getAlignment().getDataset(), af);
2861 msawsmenu.add(methodR);
2865 wsmenu.add(msawsmenu);
2867 if (secstrpr != null)
2869 // Add any secondary structure prediction services
2870 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
2871 for (int i = 0, j = secstrpr.size(); i < j; i++)
2873 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
2875 final JMenuItem method = new JMenuItem(sh.getName());
2876 method.addActionListener(new ActionListener()
2878 public void actionPerformed(ActionEvent e)
2880 AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
2881 if (msa.getSequences().length == 1)
2883 // Single Sequence prediction
2884 new jalview.ws.JPredClient(sh, title, false, msa, af, true);
2888 if (msa.getSequences().length > 1)
2890 // Sequence profile based prediction
2891 new jalview.ws.JPredClient(sh,
2892 title, true, msa, af, true);
2897 secstrmenu.add(method);
2899 wsmenu.add(secstrmenu);
2901 this.webService.removeAll();
2902 for (int i = 0, j = wsmenu.size(); i < j; i++)
2904 webService.add( (JMenu) wsmenu.get(i));
2909 this.webService.removeAll();
2910 this.webService.add(this.webServiceNoServices);
2912 // TODO: add in rediscovery function
2913 // TODO: reduce code redundancy.
2914 // TODO: group services by location as well as function.
2917 /* public void vamsasStore_actionPerformed(ActionEvent e)
2919 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
2920 getProperty("LAST_DIRECTORY"));
2922 chooser.setFileView(new JalviewFileView());
2923 chooser.setDialogTitle("Export to Vamsas file");
2924 chooser.setToolTipText("Export");
2926 int value = chooser.showSaveDialog(this);
2928 if (value == JalviewFileChooser.APPROVE_OPTION)
2930 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
2931 //vs.store(chooser.getSelectedFile().getAbsolutePath() );
2932 vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
2939 public void showTranslation_actionPerformed(ActionEvent e)
2941 SequenceI [] selection = viewport.getSelectionAsNewSequence();
2942 String [] seqstring = viewport.getViewAsString(true);
2944 int s, sSize = selection.length;
2945 SequenceI [] newSeq = new SequenceI[sSize];
2948 StringBuffer protein;
2950 for(s=0; s<sSize; s++)
2952 protein = new StringBuffer();
2953 seq = AlignSeq.extractGaps("-. ", seqstring[s]);
2954 resSize = seq.length();
2955 resSize -= resSize%3;
2957 for(res = 0; res < resSize; res+=3)
2959 String codon = seq.substring(res, res+3);
2960 codon = codon.replace('U', 'T');
2961 String aa = ResidueProperties.codonTranslate(codon);
2963 protein.append(viewport.getGapCharacter());
2964 else if(aa.equals("STOP"))
2965 protein.append("X");
2967 protein.append( aa );
2969 newSeq[s] = new Sequence(selection[s].getName(),
2970 protein.toString());
2974 AlignmentI al = new Alignment(newSeq);
2975 al.setDataset(null);
2978 ////////////////////////////////
2979 // Copy annotations across
2980 jalview.datamodel.AlignmentAnnotation[] annotations
2981 = viewport.alignment.getAlignmentAnnotation();
2983 if(annotations!=null)
2985 for (int i = 0; i < annotations.length; i++)
2987 if (annotations[i].label.equals("Quality") ||
2988 annotations[i].label.equals("Conservation") ||
2989 annotations[i].label.equals("Consensus"))
2994 aSize = viewport.alignment.getWidth() / 3;
2995 jalview.datamodel.Annotation[] anots =
2996 new jalview.datamodel.Annotation[aSize];
2998 for (a = 0; a < viewport.alignment.getWidth(); a++)
3000 if (annotations[i].annotations[a] == null
3001 || annotations[i].annotations[a] == null)
3004 anots[a / 3] = new Annotation(
3005 annotations[i].annotations[a].displayCharacter,
3006 annotations[i].annotations[a].description,
3007 annotations[i].annotations[a].secondaryStructure,
3008 annotations[i].annotations[a].value,
3009 annotations[i].annotations[a].colour);
3012 jalview.datamodel.AlignmentAnnotation aa
3013 = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
3014 annotations[i].description, anots);
3015 al.addAnnotation(aa);
3019 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
3020 Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
3032 * @param String DOCUMENT ME!
3034 public boolean parseFeaturesFile(String file, String type)
3036 boolean featuresFile = false;
3038 featuresFile = new FeaturesFile(file, type).parse(viewport.alignment.getDataset(),
3039 alignPanel.seqPanel.seqCanvas.
3040 getFeatureRenderer().featureColours,
3045 ex.printStackTrace();
3050 viewport.showSequenceFeatures = true;
3051 showSeqFeatures.setSelected(true);
3052 alignPanel.repaint();
3055 return featuresFile;
3058 public void dragEnter(DropTargetDragEvent evt)
3061 public void dragExit(DropTargetEvent evt)
3064 public void dragOver(DropTargetDragEvent evt)
3067 public void dropActionChanged(DropTargetDragEvent evt)
3070 public void drop(DropTargetDropEvent evt)
3072 Transferable t = evt.getTransferable();
3073 java.util.List files = null;
3077 DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
3078 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
3080 //Works on Windows and MacOSX
3081 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3082 files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
3084 else if (t.isDataFlavorSupported(uriListFlavor))
3086 // This is used by Unix drag system
3087 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3088 String data = (String) t.getTransferData(uriListFlavor);
3089 files = new java.util.ArrayList(1);
3090 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
3093 st.hasMoreTokens(); )
3095 String s = st.nextToken();
3096 if (s.startsWith("#"))
3098 // the line is a comment (as per the RFC 2483)
3102 java.net.URI uri = new java.net.URI(s);
3103 java.io.File file = new java.io.File(uri);
3110 e.printStackTrace();
3117 for (int i = 0; i < files.size(); i++)
3119 loadJalviewDataFile(files.get(i).toString());
3122 catch (Exception ex)
3124 ex.printStackTrace();
3129 // This method will attempt to load a "dropped" file first by testing
3130 // whether its and Annotation file, then features file. If both are
3131 // false then the user may have dropped an alignment file onto this
3133 public void loadJalviewDataFile(String file)
3136 String protocol = "File";
3138 if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
3143 boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
3148 boolean isGroupsFile = parseFeaturesFile(file,protocol);
3151 String format = new IdentifyFile().Identify(file, protocol);
3153 if(format.equalsIgnoreCase("JnetFile"))
3155 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
3157 new JnetAnnotationMaker().add_annotation(predictions,
3158 viewport.getAlignment(),
3160 alignPanel.adjustAnnotationHeight();
3161 alignPanel.repaint();
3164 new FileLoader().LoadFile(viewport, file, protocol, format);
3170 alignPanel.adjustAnnotationHeight();
3173 }catch(Exception ex)
3175 ex.printStackTrace();
3179 public void tabSelectionChanged(int index)
3183 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
3184 viewport = alignPanel.av;
3188 public void tabbedPane_mousePressed(MouseEvent e)
3190 if(SwingUtilities.isRightMouseButton(e))
3192 String reply = JOptionPane.showInternalInputDialog(this,
3195 JOptionPane.QUESTION_MESSAGE);
3199 viewport.viewName = reply;
3200 tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
3206 public AlignViewport getCurrentView()