2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Softwarechang
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
26 import java.awt.datatransfer.*;
27 import java.awt.event.*;
28 import java.awt.print.*;
31 import jalview.analysis.*;
32 import jalview.datamodel.*;
34 import jalview.jbgui.*;
35 import jalview.schemes.*;
36 import jalview.commands.*;
38 import java.awt.dnd.*;
39 import javax.swing.event.ChangeListener;
40 import javax.swing.event.ChangeEvent;
48 public class AlignFrame extends GAlignFrame implements DropTargetListener
51 public static final int DEFAULT_WIDTH = 700;
54 public static final int DEFAULT_HEIGHT = 500;
55 public AlignmentPanel alignPanel;
57 AlignViewport viewport;
59 Vector alignPanels = new Vector();
63 String currentFileFormat = null;
65 String fileName = null;
69 * Creates a new AlignFrame object.
71 * @param al DOCUMENT ME!
73 public AlignFrame(AlignmentI al, int width, int height)
75 this(al, null, width, height);
80 * new alignment window with hidden columns
81 * @param al AlignmentI
82 * @param hiddenColumns ColumnSelection or null
84 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
85 int width, int height)
87 this.setSize(width, height);
88 viewport = new AlignViewport(al, hiddenColumns);
90 alignPanel = new AlignmentPanel(this, viewport);
92 if(al.getDataset()==null)
97 addAlignmentPanel(alignPanel, true);
102 * Make a new AlignFrame from exisiting alignmentPanels
103 * @param ap AlignmentPanel
104 * @param av AlignViewport
106 public AlignFrame(AlignmentPanel ap)
110 addAlignmentPanel(ap, false);
116 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
118 if (viewport.conservation == null)
120 BLOSUM62Colour.setEnabled(false);
121 conservationMenuItem.setEnabled(false);
122 modifyConservation.setEnabled(false);
123 // PIDColour.setEnabled(false);
124 // abovePIDThreshold.setEnabled(false);
125 // modifyPID.setEnabled(false);
128 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
130 if (sortby.equals("Id"))
131 sortIDMenuItem_actionPerformed(null);
132 else if (sortby.equals("Pairwise Identity"))
133 sortPairwiseMenuItem_actionPerformed(null);
135 if (Desktop.desktop != null)
137 addServiceListeners();
138 setGUINucleotide(viewport.alignment.isNucleotide());
141 setMenusFromViewport(viewport);
143 if (viewport.wrapAlignment)
145 wrapMenuItem_actionPerformed(null);
152 public void setFileName(String file, String format)
155 currentFileFormat = format;
156 reload.setEnabled(true);
159 void addKeyListener()
161 addKeyListener(new KeyAdapter()
163 public void keyPressed(KeyEvent evt)
165 if (viewport.cursorMode
166 && evt.getKeyCode() >= KeyEvent.VK_0
167 && evt.getKeyCode() <= KeyEvent.VK_9)
169 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
172 switch (evt.getKeyCode())
175 case 27: // escape key
176 deselectAllSequenceMenuItem_actionPerformed(null);
180 case KeyEvent.VK_DOWN:
181 if (viewport.cursorMode)
183 alignPanel.seqPanel.moveCursor(0, 1);
186 moveSelectedSequences(false);
190 if (viewport.cursorMode)
192 alignPanel.seqPanel.moveCursor(0, -1);
195 moveSelectedSequences(true);
198 case KeyEvent.VK_LEFT:
199 if (viewport.cursorMode)
201 alignPanel.seqPanel.moveCursor( -1, 0);
205 case KeyEvent.VK_RIGHT:
206 if (viewport.cursorMode)
208 alignPanel.seqPanel.moveCursor(1, 0);
212 case KeyEvent.VK_SPACE:
213 if (viewport.cursorMode)
215 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
221 case KeyEvent.VK_DELETE:
222 case KeyEvent.VK_BACK_SPACE:
223 if (!viewport.cursorMode)
225 cut_actionPerformed(null);
228 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
235 if (viewport.cursorMode)
237 alignPanel.seqPanel.setCursorRow();
241 if (viewport.cursorMode && !evt.isControlDown())
243 alignPanel.seqPanel.setCursorColumn();
247 if (viewport.cursorMode)
249 alignPanel.seqPanel.setCursorPosition();
253 case KeyEvent.VK_ENTER:
254 case KeyEvent.VK_COMMA:
255 if (viewport.cursorMode)
257 alignPanel.seqPanel.setCursorRowAndColumn();
262 if (viewport.cursorMode)
264 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
268 if (viewport.cursorMode)
270 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
275 viewport.cursorMode = !viewport.cursorMode;
276 statusBar.setText("Keyboard editing mode is " +
277 (viewport.cursorMode ? "on" : "off"));
278 if (viewport.cursorMode)
280 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
281 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
283 alignPanel.seqPanel.seqCanvas.repaint();
289 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
290 java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
291 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
293 javax.help.HelpBroker hb = hs.createHelpBroker();
294 hb.setCurrentID("home");
295 hb.setDisplayed(true);
299 ex.printStackTrace();
305 boolean toggleSeqs = !evt.isControlDown();
306 boolean toggleCols = !evt.isShiftDown();
308 boolean hide = false;
310 SequenceGroup sg = viewport.getSelectionGroup();
313 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
315 hideSelSequences_actionPerformed(null);
318 else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))
319 showAllSeqs_actionPerformed(null);
324 if (viewport.colSel.getSelected().size() > 0)
326 hideSelColumns_actionPerformed(null);
328 viewport.selectionGroup = sg;
331 showAllColumns_actionPerformed(null);
335 case KeyEvent.VK_PAGE_UP:
336 if (viewport.wrapAlignment)
337 alignPanel.scrollUp(true);
339 alignPanel.setScrollValues(viewport.startRes,
341 - viewport.endSeq + viewport.startSeq);
343 case KeyEvent.VK_PAGE_DOWN:
344 if (viewport.wrapAlignment)
345 alignPanel.scrollUp(false);
347 alignPanel.setScrollValues(viewport.startRes,
349 + viewport.endSeq - viewport.startSeq);
357 public void addAlignmentPanel(final AlignmentPanel ap,
360 ap.alignFrame = this;
362 alignPanels.addElement(ap);
364 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
366 int aSize = alignPanels.size();
368 tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
370 if (aSize == 1 && ap.av.viewName==null)
372 this.getContentPane().add(ap, BorderLayout.CENTER);
378 setInitialTabVisible();
381 expandViews.setEnabled(true);
382 gatherViews.setEnabled(true);
383 tabbedPane.addTab(ap.av.viewName, ap);
385 ap.setVisible(false);
391 ap.av.alignment.padGaps();
392 ap.av.updateConservation(ap);
393 ap.av.updateConsensus(ap);
397 public void setInitialTabVisible()
399 expandViews.setEnabled(true);
400 gatherViews.setEnabled(true);
401 tabbedPane.setVisible(true);
402 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
403 tabbedPane.addTab(first.av.viewName,first);
404 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
408 public AlignViewport getViewport()
413 /* Set up intrinsic listeners for dynamically generated GUI bits. */
414 private void addServiceListeners()
416 final java.beans.PropertyChangeListener thisListener;
417 // Do this once to get current state
418 BuildWebServiceMenu();
419 Desktop.discoverer.addPropertyChangeListener(
420 thisListener = new java.beans.PropertyChangeListener()
422 public void propertyChange(PropertyChangeEvent evt)
424 // System.out.println("Discoverer property change.");
425 if (evt.getPropertyName().equals("services"))
427 // System.out.println("Rebuilding web service menu");
428 BuildWebServiceMenu();
433 addInternalFrameListener(new javax.swing.event.
434 InternalFrameAdapter()
436 public void internalFrameClosed(
437 javax.swing.event.InternalFrameEvent evt)
439 // System.out.println("deregistering discoverer listener");
440 Desktop.discoverer.removePropertyChangeListener(thisListener);
441 closeMenuItem_actionPerformed(true);
447 public void setGUINucleotide(boolean nucleotide)
449 showTranslation.setVisible( nucleotide );
450 conservationMenuItem.setEnabled( !nucleotide );
451 modifyConservation.setEnabled( !nucleotide );
453 //Remember AlignFrame always starts as protein
456 calculateMenu.remove(calculateMenu.getItemCount()-2);
461 * Need to call this method when tabs are selected for multiple views,
462 * or when loading from Jalview2XML.java
463 * @param av AlignViewport
465 void setMenusFromViewport(AlignViewport av)
467 padGapsMenuitem.setSelected(av.padGaps);
468 colourTextMenuItem.setSelected(av.showColourText);
469 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
470 conservationMenuItem.setSelected(av.getConservationSelected());
471 seqLimits.setSelected(av.getShowJVSuffix());
472 idRightAlign.setSelected(av.rightAlignIds);
473 renderGapsMenuItem.setSelected(av.renderGaps);
474 wrapMenuItem.setSelected(av.wrapAlignment);
475 annotationPanelMenuItem.setState(av.showAnnotation);
476 viewBoxesMenuItem.setSelected(av.showBoxes);
477 viewTextMenuItem.setSelected(av.showText);
479 setColourSelected(ColourSchemeProperty.
480 getColourName(av.getGlobalColourScheme()));
482 showSeqFeatures.setSelected(av.showSequenceFeatures);
483 hiddenMarkers.setState(av.showHiddenMarkers);
484 applyToAllGroups.setState(av.colourAppliesToAllGroups);
490 Hashtable progressBars;
491 public void setProgressBar(String message, long id)
493 if(progressBars == null)
494 progressBars = new Hashtable();
496 JPanel progressPanel;
497 GridLayout layout = (GridLayout) statusPanel.getLayout();
498 if(progressBars.get( new Long(id) )!=null)
500 progressPanel = (JPanel)progressBars.get( new Long(id) );
501 statusPanel.remove(progressPanel);
502 progressBars.remove( progressPanel );
503 progressPanel = null;
505 statusBar.setText(message);
507 layout.setRows(layout.getRows() - 1);
511 progressPanel = new JPanel(new BorderLayout(10, 5));
513 JProgressBar progressBar = new JProgressBar();
514 progressBar.setIndeterminate(true);
516 progressPanel.add(new JLabel(message), BorderLayout.WEST);
517 progressPanel.add(progressBar, BorderLayout.CENTER);
519 layout.setRows(layout.getRows() + 1);
520 statusPanel.add(progressPanel);
522 progressBars.put(new Long(id), progressPanel);
532 Added so Castor Mapping file can obtain Jalview Version
534 public String getVersion()
536 return jalview.bin.Cache.getProperty("VERSION");
539 public FeatureRenderer getFeatureRenderer()
541 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
545 public void fetchSequence_actionPerformed(ActionEvent e)
547 new SequenceFetcher(this);
550 public void addFromFile_actionPerformed(ActionEvent e)
552 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
555 public void reload_actionPerformed(ActionEvent e)
559 if(currentFileFormat.equals("Jalview"))
561 JInternalFrame [] frames = Desktop.desktop.getAllFrames();
562 for(int i=0; i<frames.length; i++)
564 if (frames[i] instanceof AlignFrame
566 && ( (AlignFrame) frames[i]).fileName.equals(fileName))
569 frames[i].setSelected(true);
570 Desktop.instance.closeAssociatedWindows();
571 }catch(java.beans.PropertyVetoException ex){}
575 Desktop.instance.closeAssociatedWindows();
580 viewport.alignment.deleteAllGroups();
581 viewport.sequenceColours=null;
582 while (viewport.alignment.getHeight() > 0)
584 viewport.alignment.deleteSequence(0);
587 viewport.historyList.clear();
588 viewport.redoList.clear();
589 Alignment dset = viewport.alignment.getDataset();
590 while (dset.getHeight() > 0)
592 dset.deleteSequence(0);
595 firePropertyChange("Alignment", null, viewport.alignment.getSequences());
600 FileLoader loader = new FileLoader();
601 String protocol = fileName.startsWith("http:")? "URL":"File";
602 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
608 public void addFromText_actionPerformed(ActionEvent e)
610 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
613 public void addFromURL_actionPerformed(ActionEvent e)
615 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
619 public void save_actionPerformed(ActionEvent e)
622 || currentFileFormat==null
623 || fileName.startsWith("http")
625 saveAs_actionPerformed(null);
627 saveAlignment(fileName, currentFileFormat);
633 * @param e DOCUMENT ME!
635 public void saveAs_actionPerformed(ActionEvent e)
637 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
638 getProperty( "LAST_DIRECTORY"),
640 { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" },
642 { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
647 chooser.setFileView(new JalviewFileView());
648 chooser.setDialogTitle("Save Alignment to file");
649 chooser.setToolTipText("Save");
651 int value = chooser.showSaveDialog(this);
653 if (value == JalviewFileChooser.APPROVE_OPTION)
655 currentFileFormat = chooser.getSelectedFormat();
656 if (currentFileFormat == null)
658 JOptionPane.showInternalMessageDialog(Desktop.desktop,
659 "You must select a file format before saving!",
660 "File format not specified",
661 JOptionPane.WARNING_MESSAGE);
662 value = chooser.showSaveDialog(this);
666 fileName = chooser.getSelectedFile().getPath();
668 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
671 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
673 saveAlignment(fileName, currentFileFormat);
677 public boolean saveAlignment(String file, String format)
679 boolean success = true;
681 if (format.equalsIgnoreCase("Jalview"))
683 String shortName = title;
685 if (shortName.indexOf(java.io.File.separatorChar) > -1)
687 shortName = shortName.substring(shortName.lastIndexOf(
688 java.io.File.separatorChar) + 1);
691 success = new Jalview2XML().SaveAlignment(this, file, shortName);
693 statusBar.setText("Successfully saved to file: "
695 +format +" format.");
701 String[] omitHidden = null;
703 if (viewport.hasHiddenColumns)
705 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
706 "The Alignment contains hidden columns."
707 + "\nDo you want to save only the visible alignment?",
708 "Save / Omit Hidden Columns",
709 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
711 if (reply == JOptionPane.YES_OPTION)
712 omitHidden = viewport.getViewAsString(false);
715 String output = new FormatAdapter().formatSequences(
717 viewport.alignment.getSequencesArray(),
728 java.io.PrintWriter out = new java.io.PrintWriter(
729 new java.io.FileWriter(file));
734 statusBar.setText("Successfully saved to file: "
736 + format + " format.");
741 ex.printStackTrace();
747 JOptionPane.showInternalMessageDialog(
748 this, "Couldn't save file: " + fileName,
750 JOptionPane.WARNING_MESSAGE);
758 * @param e DOCUMENT ME!
760 protected void outputText_actionPerformed(ActionEvent e)
762 String [] omitHidden = null;
764 if(viewport.hasHiddenColumns)
766 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
767 "The Alignment contains hidden columns."
768 +"\nDo you want to output only the visible alignment?",
769 "Save / Omit Hidden Columns",
770 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
772 if(reply==JOptionPane.YES_OPTION)
774 omitHidden = viewport.getViewAsString(false);
778 CutAndPasteTransfer cap = new CutAndPasteTransfer();
779 cap.setForInput(null);
780 Desktop.addInternalFrame(cap,
781 "Alignment output - " + e.getActionCommand(), 600,
785 cap.setText(new FormatAdapter().formatSequences(
786 e.getActionCommand(),
787 viewport.alignment.getSequencesArray(),
794 * @param e DOCUMENT ME!
796 protected void htmlMenuItem_actionPerformed(ActionEvent e)
798 new HTMLOutput(viewport,
799 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
800 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
803 public void createImageMap(File file, String image)
805 alignPanel.makePNGImageMap(file, image);
811 * @param e DOCUMENT ME!
813 public void createPNG(File f)
815 alignPanel.makePNG(f);
821 * @param e DOCUMENT ME!
823 public void createEPS(File f)
825 alignPanel.makeEPS(f);
831 * @param e DOCUMENT ME!
833 public void printMenuItem_actionPerformed(ActionEvent e)
835 //Putting in a thread avoids Swing painting problems
836 PrintThread thread = new PrintThread();
840 public void exportFeatures_actionPerformed(ActionEvent e)
842 new AnnotationExporter().exportFeatures(alignPanel);
846 public void exportAnnotations_actionPerformed(ActionEvent e)
848 new AnnotationExporter().exportAnnotations(
850 viewport.alignment.getAlignmentAnnotation()
855 public void associatedData_actionPerformed(ActionEvent e)
857 // Pick the tree file
858 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
861 chooser.setFileView(new JalviewFileView());
862 chooser.setDialogTitle("Load Jalview Annotations or Features File");
863 chooser.setToolTipText("Load Jalview Annotations / Features file");
865 int value = chooser.showOpenDialog(null);
867 if (value == JalviewFileChooser.APPROVE_OPTION)
869 String choice = chooser.getSelectedFile().getPath();
870 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
871 loadJalviewDataFile(choice);
880 * @param e DOCUMENT ME!
882 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
884 if(alignPanels!=null && alignPanels.size()<2)
889 if(alignPanels!=null)
892 for (int i = 0; i < alignPanels.size(); i++)
894 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
895 PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
896 PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
897 PaintRefresher.RemoveComponent(ap);
901 int index = tabbedPane.getSelectedIndex();
903 alignPanels.removeElement(alignPanel);
904 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
905 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
906 PaintRefresher.RemoveComponent(alignPanel);
910 tabbedPane.removeTabAt(index);
911 tabbedPane.validate();
913 if(index==tabbedPane.getTabCount())
916 this.tabSelectionChanged(index);
921 this.setClosed(true);
925 ex.printStackTrace();
933 void updateEditMenuBar()
936 if (viewport.historyList.size() > 0)
938 undoMenuItem.setEnabled(true);
939 CommandI command = (CommandI) viewport.historyList.peek();
940 undoMenuItem.setText("Undo " + command.getDescription());
944 undoMenuItem.setEnabled(false);
945 undoMenuItem.setText("Undo");
948 if (viewport.redoList.size() > 0)
950 redoMenuItem.setEnabled(true);
952 CommandI command = (CommandI) viewport.redoList.peek();
953 redoMenuItem.setText("Redo " + command.getDescription());
957 redoMenuItem.setEnabled(false);
958 redoMenuItem.setText("Redo");
963 public void addHistoryItem(CommandI command)
965 if(command.getSize()>0)
967 viewport.historyList.push(command);
968 viewport.redoList.clear();
970 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
979 * @param e DOCUMENT ME!
981 protected void undoMenuItem_actionPerformed(ActionEvent e)
983 CommandI command = (CommandI)viewport.historyList.pop();
984 viewport.redoList.push(command);
985 command.undoCommand();
987 AlignViewport originalSource = getOriginatingSource(command);
990 if(originalSource!=null)
992 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
993 originalSource.firePropertyChange("alignment",
995 originalSource.alignment.getSequences());
1002 * @param e DOCUMENT ME!
1004 protected void redoMenuItem_actionPerformed(ActionEvent e)
1006 if(viewport.redoList.size()<1)
1009 CommandI command = (CommandI) viewport.redoList.pop();
1010 viewport.historyList.push(command);
1011 command.doCommand();
1013 AlignViewport originalSource = getOriginatingSource(command);
1014 updateEditMenuBar();
1016 if(originalSource!=null)
1018 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1019 originalSource.firePropertyChange("alignment",
1021 originalSource.alignment.getSequences());
1025 AlignViewport getOriginatingSource(CommandI command)
1027 AlignViewport originalSource = null;
1028 //For sequence removal and addition, we need to fire
1029 //the property change event FROM the viewport where the
1030 //original alignment was altered
1032 if (command instanceof EditCommand)
1034 EditCommand editCommand = (EditCommand) command;
1035 al = editCommand.getAlignment();
1036 Vector comps = (Vector) PaintRefresher.components
1037 .get(viewport.getSequenceSetId());
1039 for (int i = 0; i < comps.size(); i++)
1041 if (comps.elementAt(i) instanceof AlignmentPanel)
1043 if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
1045 originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
1052 if (originalSource == null)
1054 //The original view is closed, we must validate
1055 //the current view against the closed view first
1057 PaintRefresher.validateSequences(al, viewport.alignment);
1059 originalSource = viewport;
1062 return originalSource;
1068 * @param up DOCUMENT ME!
1070 public void moveSelectedSequences(boolean up)
1072 SequenceGroup sg = viewport.getSelectionGroup();
1081 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1083 SequenceI seq = viewport.alignment.getSequenceAt(i);
1085 if (!sg.getSequences(null).contains(seq))
1090 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1092 if (sg.getSequences(null).contains(temp))
1097 viewport.alignment.getSequences().setElementAt(temp, i);
1098 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1103 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1105 SequenceI seq = viewport.alignment.getSequenceAt(i);
1107 if (!sg.getSequences(null).contains(seq))
1112 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1114 if (sg.getSequences(null).contains(temp))
1119 viewport.alignment.getSequences().setElementAt(temp, i);
1120 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1124 alignPanel.repaint();
1132 * @param e DOCUMENT ME!
1134 protected void copy_actionPerformed(ActionEvent e)
1137 if (viewport.getSelectionGroup() == null)
1142 SequenceI [] seqs = viewport.getSelectionAsNewSequence();
1143 String[] omitHidden = null;
1145 if (viewport.hasHiddenColumns)
1147 omitHidden = viewport.getViewAsString(true);
1150 String output = new FormatAdapter().formatSequences(
1155 StringSelection ss = new StringSelection(output);
1159 jalview.gui.Desktop.internalCopy = true;
1160 //Its really worth setting the clipboard contents
1161 //to empty before setting the large StringSelection!!
1162 Toolkit.getDefaultToolkit().getSystemClipboard()
1163 .setContents(new StringSelection(""), null);
1165 Toolkit.getDefaultToolkit().getSystemClipboard()
1166 .setContents(ss, Desktop.instance);
1168 catch (OutOfMemoryError er)
1170 er.printStackTrace();
1171 javax.swing.SwingUtilities.invokeLater(new Runnable()
1175 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1176 "Out of memory copying region!!"
1178 "\nSee help files for increasing Java Virtual Machine memory."
1180 javax.swing.JOptionPane.WARNING_MESSAGE);
1187 Vector hiddenColumns = null;
1188 if(viewport.hasHiddenColumns)
1190 hiddenColumns =new Vector();
1191 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1192 for(int i=0; i<viewport.getColumnSelection().getHiddenColumns().size(); i++)
1194 int[] region = (int[])
1195 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
1197 hiddenColumns.addElement(new int[]{region[0]-hiddenOffset,
1198 region[1]-hiddenOffset});
1204 Desktop.jalviewClipboard = new Object[]{ seqs,
1205 viewport.alignment.getDataset(),
1207 statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
1213 * @param e DOCUMENT ME!
1215 protected void pasteNew_actionPerformed(ActionEvent e)
1223 * @param e DOCUMENT ME!
1225 protected void pasteThis_actionPerformed(ActionEvent e)
1233 * @param newAlignment DOCUMENT ME!
1235 void paste(boolean newAlignment)
1239 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1240 Transferable contents = c.getContents(this);
1242 if (contents == null)
1250 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1251 if (str.length() < 1)
1254 format = new IdentifyFile().Identify(str, "Paste");
1257 catch (OutOfMemoryError er)
1259 er.printStackTrace();
1260 javax.swing.SwingUtilities.invokeLater(new Runnable()
1264 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1265 "Out of memory pasting sequences!!"
1267 "\nSee help files for increasing Java Virtual Machine memory."
1269 javax.swing.JOptionPane.WARNING_MESSAGE);
1276 SequenceI[] sequences;
1279 if(Desktop.jalviewClipboard!=null)
1281 // The clipboard was filled from within Jalview, we must use the sequences
1282 // And dataset from the copied alignment
1283 sequences = (SequenceI[])Desktop.jalviewClipboard[0];
1287 sequences = new FormatAdapter().readFile(str, "Paste", format).getSequencesArray();
1290 AlignmentI alignment = null;
1294 alignment = new Alignment(sequences);
1296 if (Desktop.jalviewClipboard != null)
1297 alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
1299 alignment.setDataset(null);
1303 alignment = viewport.getAlignment();
1306 SequenceI [] newseqs = new SequenceI[sequences.length];
1307 for (int i = 0; i < sequences.length; i++)
1309 newseqs[i] = new Sequence(sequences[i].getName(),
1310 sequences[i].getSequence(), sequences[i].getStart(),
1311 sequences[i].getEnd());
1313 alignment.addSequence(newseqs[i]);
1319 addHistoryItem(new EditCommand(
1324 alignment.getWidth(),
1329 viewport.setEndSeq(alignment.getHeight());
1330 alignment.getWidth();
1331 viewport.firePropertyChange("alignment", null, alignment.getSequences());
1336 // Add any annotations attached to sequences
1337 for (int i = 0; i < sequences.length; i++)
1339 if (sequences[i].getAnnotation() != null)
1341 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1343 AlignmentAnnotation newAnnot =
1344 new AlignmentAnnotation(
1345 sequences[i].getAnnotation()[a].label,
1346 sequences[i].getAnnotation()[a].description,
1347 sequences[i].getAnnotation()[a].annotations,
1348 sequences[i].getAnnotation()[a].graphMin,
1349 sequences[i].getAnnotation()[a].graphMax,
1350 sequences[i].getAnnotation()[a].graph);
1352 sequences[i].getAnnotation()[a] = newAnnot;
1353 newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].
1355 newAnnot.sequenceRef = sequences[i];
1356 newAnnot.adjustForAlignment();
1357 alignment.addAnnotation(newAnnot);
1358 alignment.setAnnotationIndex(newAnnot, a);
1361 alignPanel.annotationPanel.adjustPanelHeight();
1367 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
1368 String newtitle = new String("Copied sequences");
1370 if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
1372 Vector hc = (Vector)Desktop.jalviewClipboard[2];
1373 for(int i=0; i<hc.size(); i++)
1375 int [] region = (int[]) hc.elementAt(i);
1376 af.viewport.hideColumns(region[0], region[1]);
1381 //>>>This is a fix for the moment, until a better solution is found!!<<<
1382 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
1383 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1386 if (title.startsWith("Copied sequences"))
1392 newtitle = newtitle.concat("- from " + title);
1395 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1402 catch (Exception ex)
1404 ex.printStackTrace();
1405 System.out.println("Exception whilst pasting: "+ex);
1406 // could be anything being pasted in here
1415 * @param e DOCUMENT ME!
1417 protected void cut_actionPerformed(ActionEvent e)
1419 copy_actionPerformed(null);
1420 delete_actionPerformed(null);
1426 * @param e DOCUMENT ME!
1428 protected void delete_actionPerformed(ActionEvent evt)
1431 SequenceGroup sg = viewport.getSelectionGroup();
1437 Vector seqs = new Vector();
1439 for (int i = 0; i < sg.getSize(); i++)
1441 seq = sg.getSequenceAt(i);
1442 seqs.addElement(seq);
1446 // If the cut affects all sequences, remove highlighted columns
1447 if (sg.getSize() == viewport.alignment.getHeight())
1449 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1450 sg.getEndRes() + 1);
1454 SequenceI [] cut = new SequenceI[seqs.size()];
1455 for(int i=0; i<seqs.size(); i++)
1456 cut[i] = (SequenceI)seqs.elementAt(i);
1462 addHistoryItem(new EditCommand("Cut Sequences",
1466 sg.getEndRes()-sg.getStartRes()+1,
1467 viewport.alignment));
1470 viewport.setSelectionGroup(null);
1471 viewport.alignment.deleteGroup(sg);
1473 viewport.firePropertyChange("alignment", null,
1474 viewport.getAlignment().getSequences());
1476 if (viewport.getAlignment().getHeight() < 1)
1480 this.setClosed(true);
1482 catch (Exception ex)
1491 * @param e DOCUMENT ME!
1493 protected void deleteGroups_actionPerformed(ActionEvent e)
1495 viewport.alignment.deleteAllGroups();
1496 viewport.sequenceColours = null;
1497 viewport.setSelectionGroup(null);
1498 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1499 alignPanel.repaint();
1505 * @param e DOCUMENT ME!
1507 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1509 SequenceGroup sg = new SequenceGroup();
1511 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1514 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1517 sg.setEndRes(viewport.alignment.getWidth() - 1);
1518 viewport.setSelectionGroup(sg);
1519 alignPanel.repaint();
1520 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1526 * @param e DOCUMENT ME!
1528 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1530 if(viewport.cursorMode)
1532 alignPanel.seqPanel.keyboardNo1 = null;
1533 alignPanel.seqPanel.keyboardNo2 = null;
1535 viewport.setSelectionGroup(null);
1536 viewport.getColumnSelection().clear();
1537 viewport.setSelectionGroup(null);
1538 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1539 alignPanel.idPanel.idCanvas.searchResults = null;
1540 alignPanel.repaint();
1541 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1547 * @param e DOCUMENT ME!
1549 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1551 SequenceGroup sg = viewport.getSelectionGroup();
1555 selectAllSequenceMenuItem_actionPerformed(null);
1560 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1563 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1566 alignPanel.repaint();
1568 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1571 public void invertColSel_actionPerformed(ActionEvent e)
1573 viewport.invertColumnSelection();
1574 alignPanel.repaint();
1581 * @param e DOCUMENT ME!
1583 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1585 trimAlignment(true);
1591 * @param e DOCUMENT ME!
1593 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
1595 trimAlignment(false);
1598 void trimAlignment(boolean trimLeft)
1600 ColumnSelection colSel = viewport.getColumnSelection();
1603 if (colSel.size() > 0)
1606 column = colSel.getMin();
1608 column = colSel.getMax();
1611 if(viewport.getSelectionGroup()!=null)
1612 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
1614 seqs = viewport.alignment.getSequencesArray();
1617 TrimRegionCommand trimRegion;
1620 trimRegion = new TrimRegionCommand("Remove Left",
1621 TrimRegionCommand.TRIM_LEFT,
1626 viewport.selectionGroup);
1627 viewport.setStartRes(0);
1631 trimRegion = new TrimRegionCommand("Remove Right",
1632 TrimRegionCommand.TRIM_RIGHT,
1637 viewport.selectionGroup);
1640 statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
1643 addHistoryItem(trimRegion);
1645 Vector groups = viewport.alignment.getGroups();
1647 for (int i = 0; i < groups.size(); i++)
1649 SequenceGroup sg = (SequenceGroup) groups.get(i);
1651 if ( (trimLeft && !sg.adjustForRemoveLeft(column))
1652 || (!trimLeft && !sg.adjustForRemoveRight(column)))
1654 viewport.alignment.deleteGroup(sg);
1658 viewport.firePropertyChange("alignment", null,
1659 viewport.getAlignment().getSequences());
1666 * @param e DOCUMENT ME!
1668 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1670 int start = 0, end = viewport.alignment.getWidth()-1;
1673 if (viewport.getSelectionGroup() != null)
1675 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
1676 start = viewport.getSelectionGroup().getStartRes();
1677 end = viewport.getSelectionGroup().getEndRes();
1680 seqs = viewport.alignment.getSequencesArray();
1683 RemoveGapColCommand removeGapCols =
1684 new RemoveGapColCommand("Remove Gapped Columns",
1687 viewport.getGapCharacter());
1689 addHistoryItem(removeGapCols);
1691 statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
1693 //This is to maintain viewport position on first residue
1695 SequenceI seq = viewport.alignment.getSequenceAt(0);
1696 int startRes = seq.findPosition(viewport.startRes);
1697 // ShiftList shifts;
1698 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
1699 // edit.alColumnChanges=shifts.getInverse();
1700 // if (viewport.hasHiddenColumns)
1701 // viewport.getColumnSelection().compensateForEdits(shifts);
1702 viewport.setStartRes(seq.findIndex(startRes)-1);
1703 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1710 * @param e DOCUMENT ME!
1712 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1714 int start = 0, end = viewport.alignment.getWidth()-1;
1717 if (viewport.getSelectionGroup() != null)
1719 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
1720 start = viewport.getSelectionGroup().getStartRes();
1721 end = viewport.getSelectionGroup().getEndRes();
1724 seqs = viewport.alignment.getSequencesArray();
1726 //This is to maintain viewport position on first residue
1728 SequenceI seq = viewport.alignment.getSequenceAt(0);
1729 int startRes = seq.findPosition(viewport.startRes);
1731 addHistoryItem(new RemoveGapsCommand("Remove Gaps",
1734 viewport.getGapCharacter()));
1736 viewport.setStartRes(seq.findIndex(startRes)-1);
1738 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1745 * @param e DOCUMENT ME!
1747 public void padGapsMenuitem_actionPerformed(ActionEvent e)
1749 viewport.padGaps = padGapsMenuitem.isSelected();
1751 viewport.firePropertyChange("alignment",
1753 viewport.getAlignment().getSequences());
1759 * @param e DOCUMENT ME!
1761 public void findMenuItem_actionPerformed(ActionEvent e)
1766 public void newView_actionPerformed(ActionEvent e)
1768 AlignmentPanel newap =
1769 new Jalview2XML().copyAlignPanel(alignPanel, true);
1771 if (viewport.viewName == null)
1772 viewport.viewName = "Original";
1774 newap.av.historyList = viewport.historyList;
1775 newap.av.redoList = viewport.redoList;
1777 int index = Desktop.getViewCount(viewport.getSequenceSetId());
1778 String newViewName = "View " +index;
1780 Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
1781 Vector existingNames = new Vector();
1782 for(int i=0; i<comps.size(); i++)
1784 if(comps.elementAt(i) instanceof AlignmentPanel)
1786 AlignmentPanel ap = (AlignmentPanel)comps.elementAt(i);
1787 if(!existingNames.contains(ap.av.viewName))
1788 existingNames.addElement(ap.av.viewName);
1792 while(existingNames.contains(newViewName))
1794 newViewName = "View "+ (++index);
1797 newap.av.viewName = newViewName;
1799 addAlignmentPanel(newap, false);
1801 if(alignPanels.size()==2)
1803 viewport.gatherViewsHere = true;
1805 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
1808 public void expandViews_actionPerformed(ActionEvent e)
1810 Desktop.instance.explodeViews(this);
1813 public void gatherViews_actionPerformed(ActionEvent e)
1815 Desktop.instance.gatherViews(this);
1823 * @param e DOCUMENT ME!
1825 public void font_actionPerformed(ActionEvent e)
1827 new FontChooser(alignPanel);
1834 * @param e DOCUMENT ME!
1836 protected void seqLimit_actionPerformed(ActionEvent e)
1838 viewport.setShowJVSuffix(seqLimits.isSelected());
1840 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
1841 alignPanel.repaint();
1844 public void idRightAlign_actionPerformed(ActionEvent e)
1846 viewport.rightAlignIds = idRightAlign.isSelected();
1847 alignPanel.repaint();
1855 * @param e DOCUMENT ME!
1857 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
1859 viewport.setColourText(colourTextMenuItem.isSelected());
1860 alignPanel.repaint();
1866 * @param e DOCUMENT ME!
1868 public void wrapMenuItem_actionPerformed(ActionEvent e)
1870 scaleAbove.setVisible(wrapMenuItem.isSelected());
1871 scaleLeft.setVisible(wrapMenuItem.isSelected());
1872 scaleRight.setVisible(wrapMenuItem.isSelected());
1873 viewport.setWrapAlignment(wrapMenuItem.isSelected());
1874 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
1877 public void showAllSeqs_actionPerformed(ActionEvent e)
1879 viewport.showAllHiddenSeqs();
1882 public void showAllColumns_actionPerformed(ActionEvent e)
1884 viewport.showAllHiddenColumns();
1888 public void hideSelSequences_actionPerformed(ActionEvent e)
1890 viewport.hideAllSelectedSeqs();
1891 alignPanel.repaint();
1894 public void hideSelColumns_actionPerformed(ActionEvent e)
1896 viewport.hideSelectedColumns();
1897 alignPanel.repaint();
1900 public void hiddenMarkers_actionPerformed(ActionEvent e)
1902 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
1909 * @param e DOCUMENT ME!
1911 protected void scaleAbove_actionPerformed(ActionEvent e)
1913 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
1914 alignPanel.repaint();
1920 * @param e DOCUMENT ME!
1922 protected void scaleLeft_actionPerformed(ActionEvent e)
1924 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
1925 alignPanel.repaint();
1931 * @param e DOCUMENT ME!
1933 protected void scaleRight_actionPerformed(ActionEvent e)
1935 viewport.setScaleRightWrapped(scaleRight.isSelected());
1936 alignPanel.repaint();
1942 * @param e DOCUMENT ME!
1944 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1946 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
1947 alignPanel.repaint();
1953 * @param e DOCUMENT ME!
1955 public void viewTextMenuItem_actionPerformed(ActionEvent e)
1957 viewport.setShowText(viewTextMenuItem.isSelected());
1958 alignPanel.repaint();
1964 * @param e DOCUMENT ME!
1966 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1968 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
1969 alignPanel.repaint();
1973 public FeatureSettings featureSettings;
1974 public void featureSettings_actionPerformed(ActionEvent e)
1976 if(featureSettings !=null )
1978 featureSettings.close();
1979 featureSettings = null;
1981 featureSettings = new FeatureSettings(this);
1987 * @param evt DOCUMENT ME!
1989 public void showSeqFeatures_actionPerformed(ActionEvent evt)
1991 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
1992 alignPanel.repaint();
1993 if (alignPanel.getOverviewPanel() != null)
1995 alignPanel.getOverviewPanel().updateOverviewImage();
2002 * @param e DOCUMENT ME!
2004 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2006 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2007 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2013 * @param e DOCUMENT ME!
2015 public void overviewMenuItem_actionPerformed(ActionEvent e)
2017 if (alignPanel.overviewPanel != null)
2022 JInternalFrame frame = new JInternalFrame();
2023 OverviewPanel overview = new OverviewPanel(alignPanel);
2024 frame.setContentPane(overview);
2025 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2026 frame.getWidth(), frame.getHeight());
2028 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2029 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2031 public void internalFrameClosed(
2032 javax.swing.event.InternalFrameEvent evt)
2034 alignPanel.setOverviewPanel(null);
2039 alignPanel.setOverviewPanel(overview);
2042 public void textColour_actionPerformed(ActionEvent e)
2044 new TextColourChooser().chooseColour(alignPanel, null);
2050 * @param e DOCUMENT ME!
2052 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2060 * @param e DOCUMENT ME!
2062 public void clustalColour_actionPerformed(ActionEvent e)
2064 changeColour(new ClustalxColourScheme(
2065 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
2071 * @param e DOCUMENT ME!
2073 public void zappoColour_actionPerformed(ActionEvent e)
2075 changeColour(new ZappoColourScheme());
2081 * @param e DOCUMENT ME!
2083 public void taylorColour_actionPerformed(ActionEvent e)
2085 changeColour(new TaylorColourScheme());
2091 * @param e DOCUMENT ME!
2093 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2095 changeColour(new HydrophobicColourScheme());
2101 * @param e DOCUMENT ME!
2103 public void helixColour_actionPerformed(ActionEvent e)
2105 changeColour(new HelixColourScheme());
2111 * @param e DOCUMENT ME!
2113 public void strandColour_actionPerformed(ActionEvent e)
2115 changeColour(new StrandColourScheme());
2121 * @param e DOCUMENT ME!
2123 public void turnColour_actionPerformed(ActionEvent e)
2125 changeColour(new TurnColourScheme());
2131 * @param e DOCUMENT ME!
2133 public void buriedColour_actionPerformed(ActionEvent e)
2135 changeColour(new BuriedColourScheme());
2141 * @param e DOCUMENT ME!
2143 public void nucleotideColour_actionPerformed(ActionEvent e)
2145 changeColour(new NucleotideColourScheme());
2148 public void annotationColour_actionPerformed(ActionEvent e)
2150 new AnnotationColourChooser(viewport, alignPanel);
2157 * @param e DOCUMENT ME!
2159 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2161 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2167 * @param cs DOCUMENT ME!
2169 public void changeColour(ColourSchemeI cs)
2175 if (viewport.getAbovePIDThreshold())
2177 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2180 cs.setThreshold(threshold,
2181 viewport.getIgnoreGapsConsensus());
2183 viewport.setGlobalColourScheme(cs);
2187 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2190 if (viewport.getConservationSelected())
2193 Alignment al = (Alignment) viewport.alignment;
2194 Conservation c = new Conservation("All",
2195 ResidueProperties.propHash, 3,
2196 al.getSequences(), 0,
2200 c.verdict(false, viewport.ConsPercGaps);
2202 cs.setConservation(c);
2204 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
2209 cs.setConservation(null);
2212 cs.setConsensus(viewport.hconsensus);
2215 viewport.setGlobalColourScheme(cs);
2217 if (viewport.getColourAppliesToAllGroups())
2219 Vector groups = viewport.alignment.getGroups();
2221 for (int i = 0; i < groups.size(); i++)
2223 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2231 if (cs instanceof ClustalxColourScheme)
2233 sg.cs = new ClustalxColourScheme(
2234 sg.getSequences(viewport.hiddenRepSequences), sg.getWidth());
2236 else if (cs instanceof UserColourScheme)
2238 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
2244 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2246 catch (Exception ex)
2251 if (viewport.getAbovePIDThreshold()
2252 || cs instanceof PIDColourScheme
2253 || cs instanceof Blosum62ColourScheme)
2255 sg.cs.setThreshold(threshold,
2256 viewport.getIgnoreGapsConsensus());
2258 sg.cs.setConsensus(AAFrequency.calculate(
2259 sg.getSequences(viewport.hiddenRepSequences), sg.getStartRes(),
2263 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2266 if (viewport.getConservationSelected())
2268 Conservation c = new Conservation("Group",
2269 ResidueProperties.propHash, 3,
2270 sg.getSequences(viewport.hiddenRepSequences),
2274 c.verdict(false, viewport.ConsPercGaps);
2275 sg.cs.setConservation(c);
2278 sg.cs.setConservation(null);
2282 if (alignPanel.getOverviewPanel() != null)
2284 alignPanel.getOverviewPanel().updateOverviewImage();
2287 alignPanel.repaint();
2293 * @param e DOCUMENT ME!
2295 protected void modifyPID_actionPerformed(ActionEvent e)
2297 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
2299 SliderPanel.setPIDSliderSource(alignPanel,
2300 viewport.getGlobalColourScheme(),
2302 SliderPanel.showPIDSlider();
2309 * @param e DOCUMENT ME!
2311 protected void modifyConservation_actionPerformed(ActionEvent e)
2313 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
2315 SliderPanel.setConservationSlider(alignPanel,
2316 viewport.globalColourScheme,
2318 SliderPanel.showConservationSlider();
2325 * @param e DOCUMENT ME!
2327 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2329 viewport.setConservationSelected(conservationMenuItem.isSelected());
2331 viewport.setAbovePIDThreshold(false);
2332 abovePIDThreshold.setSelected(false);
2334 changeColour(viewport.getGlobalColourScheme());
2336 modifyConservation_actionPerformed(null);
2342 * @param e DOCUMENT ME!
2344 public void abovePIDThreshold_actionPerformed(ActionEvent e)
2346 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
2348 conservationMenuItem.setSelected(false);
2349 viewport.setConservationSelected(false);
2351 changeColour(viewport.getGlobalColourScheme());
2353 modifyPID_actionPerformed(null);
2359 * @param e DOCUMENT ME!
2361 public void userDefinedColour_actionPerformed(ActionEvent e)
2363 if (e.getActionCommand().equals("User Defined..."))
2365 new UserDefinedColours(alignPanel, null);
2369 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
2370 getUserColourSchemes().get(e.getActionCommand());
2376 public void updateUserColourMenu()
2379 Component[] menuItems = colourMenu.getMenuComponents();
2380 int i, iSize = menuItems.length;
2381 for (i = 0; i < iSize; i++)
2383 if (menuItems[i].getName() != null &&
2384 menuItems[i].getName().equals("USER_DEFINED"))
2386 colourMenu.remove(menuItems[i]);
2390 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
2392 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
2393 getUserColourSchemes().keys();
2395 while (userColours.hasMoreElements())
2397 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
2398 nextElement().toString());
2399 radioItem.setName("USER_DEFINED");
2400 radioItem.addMouseListener(new MouseAdapter()
2402 public void mousePressed(MouseEvent evt)
2404 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
2406 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
2408 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
2409 "Remove from default list?",
2410 "Remove user defined colour",
2411 JOptionPane.YES_NO_OPTION);
2412 if(option == JOptionPane.YES_OPTION)
2414 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
2415 colourMenu.remove(radioItem);
2418 radioItem.addActionListener(new ActionListener()
2420 public void actionPerformed(ActionEvent evt)
2422 userDefinedColour_actionPerformed(evt);
2428 radioItem.addActionListener(new ActionListener()
2430 public void actionPerformed(ActionEvent evt)
2432 userDefinedColour_actionPerformed(evt);
2436 colourMenu.insert(radioItem, 15);
2437 colours.add(radioItem);
2445 * @param e DOCUMENT ME!
2447 public void PIDColour_actionPerformed(ActionEvent e)
2449 changeColour(new PIDColourScheme());
2455 * @param e DOCUMENT ME!
2457 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
2459 changeColour(new Blosum62ColourScheme());
2465 * @param e DOCUMENT ME!
2467 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2469 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2470 AlignmentSorter.sortByPID(viewport.getAlignment(),
2471 viewport.getAlignment().getSequenceAt(0));
2472 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));
2473 alignPanel.repaint();
2479 * @param e DOCUMENT ME!
2481 public void sortIDMenuItem_actionPerformed(ActionEvent e)
2483 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2484 AlignmentSorter.sortByID(viewport.getAlignment());
2485 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
2486 alignPanel.repaint();
2492 * @param e DOCUMENT ME!
2494 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
2496 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2497 AlignmentSorter.sortByGroup(viewport.getAlignment());
2498 addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
2500 alignPanel.repaint();
2506 * @param e DOCUMENT ME!
2508 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2510 new RedundancyPanel(alignPanel, this);
2517 * @param e DOCUMENT ME!
2519 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2521 if ( (viewport.getSelectionGroup() == null) ||
2522 (viewport.getSelectionGroup().getSize() < 2))
2524 JOptionPane.showInternalMessageDialog(this,
2525 "You must select at least 2 sequences.",
2526 "Invalid Selection",
2527 JOptionPane.WARNING_MESSAGE);
2531 JInternalFrame frame = new JInternalFrame();
2532 frame.setContentPane(new PairwiseAlignPanel(viewport));
2533 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
2540 * @param e DOCUMENT ME!
2542 public void PCAMenuItem_actionPerformed(ActionEvent e)
2544 if ( ( (viewport.getSelectionGroup() != null) &&
2545 (viewport.getSelectionGroup().getSize() < 4) &&
2546 (viewport.getSelectionGroup().getSize() > 0)) ||
2547 (viewport.getAlignment().getHeight() < 4))
2549 JOptionPane.showInternalMessageDialog(this,
2550 "Principal component analysis must take\n" +
2551 "at least 4 input sequences.",
2552 "Sequence selection insufficient",
2553 JOptionPane.WARNING_MESSAGE);
2558 new PCAPanel(alignPanel);
2562 public void autoCalculate_actionPerformed(ActionEvent e)
2564 viewport.autoCalculateConsensus = autoCalculate.isSelected();
2565 if(viewport.autoCalculateConsensus)
2567 viewport.firePropertyChange("alignment",
2569 viewport.getAlignment().getSequences());
2577 * @param e DOCUMENT ME!
2579 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2581 NewTreePanel("AV", "PID", "Average distance tree using PID");
2587 * @param e DOCUMENT ME!
2589 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2591 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2597 * @param e DOCUMENT ME!
2599 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2601 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2607 * @param e DOCUMENT ME!
2609 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2611 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2617 * @param type DOCUMENT ME!
2618 * @param pwType DOCUMENT ME!
2619 * @param title DOCUMENT ME!
2621 void NewTreePanel(String type, String pwType, String title)
2625 if (viewport.getSelectionGroup() != null) {
2626 if (viewport.getSelectionGroup().getSize() < 3) {
2627 JOptionPane.showMessageDialog(Desktop.desktop,
2628 "You need to have more than two sequences selected to build a tree!",
2629 "Not enough sequences",
2630 JOptionPane.WARNING_MESSAGE);
2635 SequenceGroup sg = viewport.getSelectionGroup();
2637 /* Decide if the selection is a column region */
2638 while (s < sg.getSize())
2640 if ( ( (SequenceI) sg.getSequences(null).elementAt(s++)).getLength() <
2643 JOptionPane.showMessageDialog(Desktop.desktop,
2644 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
2645 "Try using the Pad function in the edit menu,\n" +
2646 "or one of the multiple sequence alignment web services.",
2647 "Sequences in selection are not aligned",
2648 JOptionPane.WARNING_MESSAGE);
2654 title = title + " on region";
2655 tp = new TreePanel(alignPanel, type, pwType);
2659 //are the sequences aligned?
2660 if (!viewport.alignment.isAligned())
2662 JOptionPane.showMessageDialog(Desktop.desktop,
2663 "The sequences must be aligned before creating a tree.\n" +
2664 "Try using the Pad function in the edit menu,\n" +
2665 "or one of the multiple sequence alignment web services.",
2666 "Sequences not aligned",
2667 JOptionPane.WARNING_MESSAGE);
2672 if(viewport.alignment.getHeight()<2)
2675 tp = new TreePanel(alignPanel, type, pwType);
2680 if(viewport.viewName!=null)
2681 title+= viewport.viewName+" of ";
2683 title += this.title;
2685 Desktop.addInternalFrame(tp, title, 600, 500);
2691 * @param title DOCUMENT ME!
2692 * @param order DOCUMENT ME!
2694 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
2696 final JMenuItem item = new JMenuItem("by " + title);
2698 item.addActionListener(new java.awt.event.ActionListener()
2700 public void actionPerformed(ActionEvent e)
2702 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2704 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
2705 AlignmentSorter.sortBy(viewport.getAlignment(), order);
2707 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport.alignment));
2709 alignPanel.repaint();
2715 * Maintain the Order by->Displayed Tree menu.
2716 * Creates a new menu item for a TreePanel with an appropriate
2717 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
2718 * to remove the menu item when the treePanel is closed, and adjust
2719 * the tree leaf to sequence mapping when the alignment is modified.
2720 * @param treePanel Displayed tree window.
2721 * @param title SortBy menu item title.
2723 public void buildTreeMenu()
2725 sortByTreeMenu.removeAll();
2727 Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
2728 Vector treePanels = new Vector();
2729 int i, iSize = comps.size();
2730 for(i=0; i<iSize; i++)
2732 if(comps.elementAt(i) instanceof TreePanel)
2734 treePanels.add(comps.elementAt(i));
2738 iSize = treePanels.size();
2742 sortByTreeMenu.setVisible(false);
2746 sortByTreeMenu.setVisible(true);
2748 for(i=0; i<treePanels.size(); i++)
2750 TreePanel tp = (TreePanel)treePanels.elementAt(i);
2751 final JMenuItem item = new JMenuItem(tp.getTitle());
2752 final NJTree tree = ((TreePanel)treePanels.elementAt(i)).getTree();
2753 item.addActionListener(new java.awt.event.ActionListener()
2755 public void actionPerformed(ActionEvent e)
2757 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2758 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
2760 addHistoryItem(new OrderCommand("Tree Sort",
2762 viewport.alignment));
2764 alignPanel.repaint();
2768 sortByTreeMenu.add(item);
2773 * Work out whether the whole set of sequences
2774 * or just the selected set will be submitted for multiple alignment.
2777 private jalview.datamodel.AlignmentView gatherSequencesForAlignment()
2779 // Now, check we have enough sequences
2780 AlignmentView msa = null;
2782 if ( (viewport.getSelectionGroup() != null) &&
2783 (viewport.getSelectionGroup().getSize() > 1))
2785 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
2786 /*SequenceGroup seqs = viewport.getSelectionGroup();
2788 msa = new SequenceI[sz = seqs.getSize(false)];
2790 for (int i = 0; i < sz; i++)
2792 msa[i] = (SequenceI) seqs.getSequenceAt(i);
2794 msa = viewport.getAlignmentView(true);
2798 /*Vector seqs = viewport.getAlignment().getSequences();
2800 if (seqs.size() > 1)
2802 msa = new SequenceI[seqs.size()];
2804 for (int i = 0; i < seqs.size(); i++)
2806 msa[i] = (SequenceI) seqs.elementAt(i);
2809 msa = viewport.getAlignmentView(false);
2815 * Decides what is submitted to a secondary structure prediction service,
2816 * the currently selected sequence, or the currently selected alignment
2817 * (where the first sequence in the set is the one that the prediction
2820 AlignmentView gatherSeqOrMsaForSecStrPrediction()
2822 AlignmentView seqs = null;
2824 if ( (viewport.getSelectionGroup() != null) &&
2825 (viewport.getSelectionGroup().getSize() > 0))
2827 seqs = viewport.getAlignmentView(true);
2831 seqs = viewport.getAlignmentView(false);
2833 // limit sequences - JBPNote in future - could spawn multiple prediction jobs
2834 // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment.
2835 if (!viewport.alignment.isAligned())
2837 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] } );
2844 * @param e DOCUMENT ME!
2846 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2848 // Pick the tree file
2849 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
2852 chooser.setFileView(new JalviewFileView());
2853 chooser.setDialogTitle("Select a newick-like tree file");
2854 chooser.setToolTipText("Load a tree file");
2856 int value = chooser.showOpenDialog(null);
2858 if (value == JalviewFileChooser.APPROVE_OPTION)
2860 String choice = chooser.getSelectedFile().getPath();
2861 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
2865 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
2867 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
2869 catch (Exception ex)
2871 JOptionPane.showMessageDialog(Desktop.desktop,
2872 "Problem reading tree file",
2874 JOptionPane.WARNING_MESSAGE);
2875 ex.printStackTrace();
2881 public TreePanel ShowNewickTree(NewickFile nf, String title)
2883 return ShowNewickTree(nf,title,600,500,4,5);
2885 public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input)
2887 return ShowNewickTree(nf,title, input, 600,500,4,5);
2889 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y) {
2890 return ShowNewickTree(nf, title, null, w, h, x, y);
2893 * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
2895 * @param nf the tree
2896 * @param title tree viewer title
2897 * @param input Associated alignment input data (or null)
2902 * @return TreePanel handle
2904 public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input, int w,int h,int x, int y) {
2905 TreePanel tp = null;
2911 if (nf.getTree() != null)
2913 tp = new TreePanel(alignPanel,
2921 tp.setLocation(x,y);
2924 Desktop.addInternalFrame(tp, title, w, h);
2927 catch (Exception ex)
2929 ex.printStackTrace();
2940 PrinterJob printJob = PrinterJob.getPrinterJob();
2941 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
2942 printJob.setPrintable(alignPanel, pf);
2944 if (printJob.printDialog())
2950 catch (Exception PrintException)
2952 PrintException.printStackTrace();
2959 * Generates menu items and listener event actions for web service clients
2962 public void BuildWebServiceMenu()
2964 if ( (Discoverer.services != null)
2965 && (Discoverer.services.size() > 0))
2967 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
2968 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
2969 Vector wsmenu = new Vector();
2970 final AlignFrame af = this;
2973 // Add any Multiple Sequence Alignment Services
2974 final JMenu msawsmenu = new JMenu("Alignment");
2975 for (int i = 0, j = msaws.size(); i < j; i++)
2977 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
2979 final JMenuItem method = new JMenuItem(sh.getName());
2980 method.addActionListener(new ActionListener()
2982 public void actionPerformed(ActionEvent e)
2984 AlignmentView msa = gatherSequencesForAlignment();
2985 new jalview.ws.MsaWSClient(sh, title, msa,
2986 false, true, viewport.getAlignment().getDataset(), af);
2991 msawsmenu.add(method);
2992 // Deal with services that we know accept partial alignments.
2993 if (sh.getName().indexOf("lustal") > -1)
2995 // We know that ClustalWS can accept partial alignments for refinement.
2996 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
2997 methodR.addActionListener(new ActionListener()
2999 public void actionPerformed(ActionEvent e)
3001 AlignmentView msa = gatherSequencesForAlignment();
3002 new jalview.ws.MsaWSClient(sh, title, msa,
3003 true, true, viewport.getAlignment().getDataset(), af);
3008 msawsmenu.add(methodR);
3012 wsmenu.add(msawsmenu);
3014 if (secstrpr != null)
3016 // Add any secondary structure prediction services
3017 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
3018 for (int i = 0, j = secstrpr.size(); i < j; i++)
3020 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
3022 final JMenuItem method = new JMenuItem(sh.getName());
3023 method.addActionListener(new ActionListener()
3025 public void actionPerformed(ActionEvent e)
3027 AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
3028 if (msa.getSequences().length == 1)
3030 // Single Sequence prediction
3031 new jalview.ws.JPredClient(sh, title, false, msa, af, true);
3035 if (msa.getSequences().length > 1)
3037 // Sequence profile based prediction
3038 new jalview.ws.JPredClient(sh,
3039 title, true, msa, af, true);
3044 secstrmenu.add(method);
3046 wsmenu.add(secstrmenu);
3048 this.webService.removeAll();
3049 for (int i = 0, j = wsmenu.size(); i < j; i++)
3051 webService.add( (JMenu) wsmenu.get(i));
3056 this.webService.removeAll();
3057 this.webService.add(this.webServiceNoServices);
3059 // TODO: add in rediscovery function
3060 // TODO: reduce code redundancy.
3061 // TODO: group services by location as well as function.
3064 /* public void vamsasStore_actionPerformed(ActionEvent e)
3066 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
3067 getProperty("LAST_DIRECTORY"));
3069 chooser.setFileView(new JalviewFileView());
3070 chooser.setDialogTitle("Export to Vamsas file");
3071 chooser.setToolTipText("Export");
3073 int value = chooser.showSaveDialog(this);
3075 if (value == JalviewFileChooser.APPROVE_OPTION)
3077 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
3078 //vs.store(chooser.getSelectedFile().getAbsolutePath() );
3079 vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
3086 public void showTranslation_actionPerformed(ActionEvent e)
3088 SequenceI [] selection = viewport.getSelectionAsNewSequence();
3089 String [] seqstring = viewport.getViewAsString(true);
3091 int s, sSize = selection.length;
3092 SequenceI [] newSeq = new SequenceI[sSize];
3095 StringBuffer protein;
3097 for(s=0; s<sSize; s++)
3099 protein = new StringBuffer();
3100 seq = AlignSeq.extractGaps("-. ", seqstring[s]);
3101 resSize = seq.length();
3102 resSize -= resSize%3;
3104 for(res = 0; res < resSize; res+=3)
3106 String codon = seq.substring(res, res+3);
3107 codon = codon.replace('U', 'T');
3108 String aa = ResidueProperties.codonTranslate(codon);
3110 protein.append(viewport.getGapCharacter());
3111 else if(aa.equals("STOP"))
3112 protein.append("X");
3114 protein.append( aa );
3116 newSeq[s] = new Sequence(selection[s].getName(),
3117 protein.toString());
3121 AlignmentI al = new Alignment(newSeq);
3122 al.setDataset(null);
3125 ////////////////////////////////
3126 // Copy annotations across
3127 jalview.datamodel.AlignmentAnnotation[] annotations
3128 = viewport.alignment.getAlignmentAnnotation();
3130 if(annotations!=null)
3132 for (int i = 0; i < annotations.length; i++)
3134 if (annotations[i].label.equals("Quality") ||
3135 annotations[i].label.equals("Conservation") ||
3136 annotations[i].label.equals("Consensus"))
3141 aSize = viewport.alignment.getWidth() / 3;
3142 jalview.datamodel.Annotation[] anots =
3143 new jalview.datamodel.Annotation[aSize];
3145 for (a = 0; a < viewport.alignment.getWidth(); a++)
3147 if (annotations[i].annotations[a] == null
3148 || annotations[i].annotations[a] == null)
3151 anots[a / 3] = new Annotation(
3152 annotations[i].annotations[a].displayCharacter,
3153 annotations[i].annotations[a].description,
3154 annotations[i].annotations[a].secondaryStructure,
3155 annotations[i].annotations[a].value,
3156 annotations[i].annotations[a].colour);
3159 jalview.datamodel.AlignmentAnnotation aa
3160 = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
3161 annotations[i].description, anots);
3162 al.addAnnotation(aa);
3166 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
3167 Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
3179 * @param String DOCUMENT ME!
3181 public boolean parseFeaturesFile(String file, String type)
3183 boolean featuresFile = false;
3185 featuresFile = new FeaturesFile(file, type).parse(viewport.alignment.getDataset(),
3186 alignPanel.seqPanel.seqCanvas.
3187 getFeatureRenderer().featureColours,
3192 ex.printStackTrace();
3197 viewport.showSequenceFeatures = true;
3198 showSeqFeatures.setSelected(true);
3199 alignPanel.repaint();
3202 return featuresFile;
3205 public void dragEnter(DropTargetDragEvent evt)
3208 public void dragExit(DropTargetEvent evt)
3211 public void dragOver(DropTargetDragEvent evt)
3214 public void dropActionChanged(DropTargetDragEvent evt)
3217 public void drop(DropTargetDropEvent evt)
3219 Transferable t = evt.getTransferable();
3220 java.util.List files = null;
3224 DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
3225 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
3227 //Works on Windows and MacOSX
3228 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3229 files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
3231 else if (t.isDataFlavorSupported(uriListFlavor))
3233 // This is used by Unix drag system
3234 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3235 String data = (String) t.getTransferData(uriListFlavor);
3236 files = new java.util.ArrayList(1);
3237 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
3240 st.hasMoreTokens(); )
3242 String s = st.nextToken();
3243 if (s.startsWith("#"))
3245 // the line is a comment (as per the RFC 2483)
3249 java.net.URI uri = new java.net.URI(s);
3250 java.io.File file = new java.io.File(uri);
3257 e.printStackTrace();
3264 for (int i = 0; i < files.size(); i++)
3266 loadJalviewDataFile(files.get(i).toString());
3269 catch (Exception ex)
3271 ex.printStackTrace();
3276 // This method will attempt to load a "dropped" file first by testing
3277 // whether its and Annotation file, then features file. If both are
3278 // false then the user may have dropped an alignment file onto this
3280 public void loadJalviewDataFile(String file)
3283 String protocol = "File";
3285 if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
3290 boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
3291 alignment, file, protocol);
3295 boolean isGroupsFile = parseFeaturesFile(file,protocol);
3298 String format = new IdentifyFile().Identify(file, protocol);
3300 if(format.equalsIgnoreCase("JnetFile"))
3302 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
3304 new JnetAnnotationMaker().add_annotation(predictions,
3305 viewport.getAlignment(),
3307 alignPanel.adjustAnnotationHeight();
3308 alignPanel.repaint();
3311 new FileLoader().LoadFile(viewport, file, protocol, format);
3317 alignPanel.adjustAnnotationHeight();
3320 }catch(Exception ex)
3322 ex.printStackTrace();
3326 public void tabSelectionChanged(int index)
3330 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
3331 viewport = alignPanel.av;
3332 setMenusFromViewport(viewport);
3336 public void tabbedPane_mousePressed(MouseEvent e)
3338 if(SwingUtilities.isRightMouseButton(e))
3340 String reply = JOptionPane.showInternalInputDialog(this,
3343 JOptionPane.QUESTION_MESSAGE);
3347 viewport.viewName = reply;
3348 tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
3354 public AlignViewport getCurrentView()