2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Softwarechang
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
26 import java.awt.datatransfer.*;
27 import java.awt.event.*;
28 import java.awt.print.*;
31 import jalview.analysis.*;
32 import jalview.datamodel.*;
34 import jalview.jbgui.*;
35 import jalview.schemes.*;
36 import jalview.commands.*;
38 import java.awt.dnd.*;
39 import javax.swing.event.ChangeListener;
40 import javax.swing.event.ChangeEvent;
48 public class AlignFrame extends GAlignFrame implements DropTargetListener
51 public static final int DEFAULT_WIDTH = 700;
54 public static final int DEFAULT_HEIGHT = 500;
55 public AlignmentPanel alignPanel;
57 AlignViewport viewport;
59 Vector alignPanels = new Vector();
63 String currentFileFormat = null;
65 String fileName = null;
67 private int treeCount = 0;
70 * Creates a new AlignFrame object.
72 * @param al DOCUMENT ME!
74 public AlignFrame(AlignmentI al, int width, int height)
76 this(al, null, width, height);
81 * new alignment window with hidden columns
82 * @param al AlignmentI
83 * @param hiddenColumns ColumnSelection or null
85 public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
86 int width, int height)
88 this.setSize(width, height);
89 viewport = new AlignViewport(al, hiddenColumns);
91 alignPanel = new AlignmentPanel(this, viewport);
93 if(al.getDataset()==null)
98 addAlignmentPanel(alignPanel, true);
103 * Make a new AlignFrame from exisiting alignmentPanels
104 * @param ap AlignmentPanel
105 * @param av AlignViewport
107 public AlignFrame(AlignmentPanel ap)
111 addAlignmentPanel(ap, false);
117 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
119 if (viewport.conservation == null)
121 BLOSUM62Colour.setEnabled(false);
122 conservationMenuItem.setEnabled(false);
123 modifyConservation.setEnabled(false);
124 // PIDColour.setEnabled(false);
125 // abovePIDThreshold.setEnabled(false);
126 // modifyPID.setEnabled(false);
129 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
131 if (sortby.equals("Id"))
132 sortIDMenuItem_actionPerformed(null);
133 else if (sortby.equals("Pairwise Identity"))
134 sortPairwiseMenuItem_actionPerformed(null);
136 if (Desktop.desktop != null)
138 addServiceListeners();
139 setGUINucleotide(viewport.alignment.isNucleotide());
142 setMenusFromViewport(viewport);
144 if (viewport.wrapAlignment)
146 wrapMenuItem_actionPerformed(null);
153 public void setFileName(String file, String format)
156 currentFileFormat = format;
157 reload.setEnabled(true);
160 void addKeyListener()
162 addKeyListener(new KeyAdapter()
164 public void keyPressed(KeyEvent evt)
166 if (viewport.cursorMode
167 && evt.getKeyCode() >= KeyEvent.VK_0
168 && evt.getKeyCode() <= KeyEvent.VK_9)
170 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
173 switch (evt.getKeyCode())
176 case 27: // escape key
177 deselectAllSequenceMenuItem_actionPerformed(null);
181 case KeyEvent.VK_DOWN:
182 if (viewport.cursorMode)
184 alignPanel.seqPanel.moveCursor(0, 1);
187 moveSelectedSequences(false);
191 if (viewport.cursorMode)
193 alignPanel.seqPanel.moveCursor(0, -1);
196 moveSelectedSequences(true);
199 case KeyEvent.VK_LEFT:
200 if (viewport.cursorMode)
202 alignPanel.seqPanel.moveCursor( -1, 0);
206 case KeyEvent.VK_RIGHT:
207 if (viewport.cursorMode)
209 alignPanel.seqPanel.moveCursor(1, 0);
213 case KeyEvent.VK_SPACE:
214 if (viewport.cursorMode)
216 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
222 case KeyEvent.VK_DELETE:
223 case KeyEvent.VK_BACK_SPACE:
224 if (!viewport.cursorMode)
226 cut_actionPerformed(null);
229 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
236 if (viewport.cursorMode)
238 alignPanel.seqPanel.setCursorRow();
242 if (viewport.cursorMode && !evt.isControlDown())
244 alignPanel.seqPanel.setCursorColumn();
248 if (viewport.cursorMode)
250 alignPanel.seqPanel.setCursorPosition();
254 case KeyEvent.VK_ENTER:
255 case KeyEvent.VK_COMMA:
256 if (viewport.cursorMode)
258 alignPanel.seqPanel.setCursorRowAndColumn();
263 if (viewport.cursorMode)
265 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
269 if (viewport.cursorMode)
271 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
276 viewport.cursorMode = !viewport.cursorMode;
277 statusBar.setText("Keyboard editing mode is " +
278 (viewport.cursorMode ? "on" : "off"));
279 if (viewport.cursorMode)
281 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
282 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
284 alignPanel.seqPanel.seqCanvas.repaint();
290 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
291 java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
292 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
294 javax.help.HelpBroker hb = hs.createHelpBroker();
295 hb.setCurrentID("home");
296 hb.setDisplayed(true);
300 ex.printStackTrace();
306 boolean toggleSeqs = !evt.isControlDown();
307 boolean toggleCols = !evt.isShiftDown();
309 boolean hide = false;
311 SequenceGroup sg = viewport.getSelectionGroup();
314 if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
316 hideSelSequences_actionPerformed(null);
319 else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))
320 showAllSeqs_actionPerformed(null);
325 if (viewport.colSel.getSelected().size() > 0)
327 hideSelColumns_actionPerformed(null);
329 viewport.selectionGroup = sg;
332 showAllColumns_actionPerformed(null);
336 case KeyEvent.VK_PAGE_UP:
337 if (viewport.wrapAlignment)
338 alignPanel.scrollUp(true);
340 alignPanel.setScrollValues(viewport.startRes,
342 - viewport.endSeq + viewport.startSeq);
344 case KeyEvent.VK_PAGE_DOWN:
345 if (viewport.wrapAlignment)
346 alignPanel.scrollUp(false);
348 alignPanel.setScrollValues(viewport.startRes,
350 + viewport.endSeq - viewport.startSeq);
358 public void addAlignmentPanel(final AlignmentPanel ap,
361 ap.alignFrame = this;
363 alignPanels.addElement(ap);
365 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
367 int aSize = alignPanels.size();
369 tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
371 if (aSize == 1 && ap.av.viewName==null)
373 this.getContentPane().add(ap, BorderLayout.CENTER);
379 setInitialTabVisible();
382 expandViews.setEnabled(true);
383 gatherViews.setEnabled(true);
384 tabbedPane.addTab(ap.av.viewName==null?"Original":ap.av.viewName, ap);
386 ap.setVisible(false);
392 ap.av.alignment.padGaps();
393 ap.av.updateConservation(ap);
394 ap.av.updateConsensus(ap);
398 public void setInitialTabVisible()
400 expandViews.setEnabled(true);
401 gatherViews.setEnabled(true);
402 tabbedPane.setVisible(true);
403 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
404 tabbedPane.addTab(first.av.viewName==null?"Original":first.av.viewName,first);
405 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
409 public AlignViewport getViewport()
414 /* Set up intrinsic listeners for dynamically generated GUI bits. */
415 private void addServiceListeners()
417 final java.beans.PropertyChangeListener thisListener;
418 // Do this once to get current state
419 BuildWebServiceMenu();
420 Desktop.discoverer.addPropertyChangeListener(
421 thisListener = new java.beans.PropertyChangeListener()
423 public void propertyChange(PropertyChangeEvent evt)
425 // System.out.println("Discoverer property change.");
426 if (evt.getPropertyName().equals("services"))
428 // System.out.println("Rebuilding web service menu");
429 BuildWebServiceMenu();
434 addInternalFrameListener(new javax.swing.event.
435 InternalFrameAdapter()
437 public void internalFrameClosed(
438 javax.swing.event.InternalFrameEvent evt)
440 // System.out.println("deregistering discoverer listener");
441 Desktop.discoverer.removePropertyChangeListener(thisListener);
442 closeMenuItem_actionPerformed(true);
448 public void setGUINucleotide(boolean nucleotide)
450 showTranslation.setVisible( nucleotide );
451 conservationMenuItem.setEnabled( !nucleotide );
452 modifyConservation.setEnabled( !nucleotide );
454 //Remember AlignFrame always starts as protein
457 calculateMenu.remove(calculateMenu.getItemCount()-2);
462 * Need to call this method when tabs are selected for multiple views,
463 * or when loading from Jalview2XML.java
464 * @param av AlignViewport
466 void setMenusFromViewport(AlignViewport av)
468 padGapsMenuitem.setSelected(av.padGaps);
469 colourTextMenuItem.setSelected(av.showColourText);
470 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
471 conservationMenuItem.setSelected(av.getConservationSelected());
472 seqLimits.setSelected(av.getShowJVSuffix());
473 idRightAlign.setSelected(av.rightAlignIds);
474 renderGapsMenuItem.setSelected(av.renderGaps);
475 wrapMenuItem.setSelected(av.wrapAlignment);
476 annotationPanelMenuItem.setState(av.showAnnotation);
477 viewBoxesMenuItem.setSelected(av.showBoxes);
478 viewTextMenuItem.setSelected(av.showText);
480 setColourSelected(ColourSchemeProperty.
481 getColourName(av.getGlobalColourScheme()));
483 showSeqFeatures.setSelected(av.showSequenceFeatures);
484 hiddenMarkers.setState(av.showHiddenMarkers);
485 applyToAllGroups.setState(av.colourAppliesToAllGroups);
491 Hashtable progressBars;
492 public void setProgressBar(String message, long id)
494 if(progressBars == null)
495 progressBars = new Hashtable();
497 JPanel progressPanel;
498 GridLayout layout = (GridLayout) statusPanel.getLayout();
499 if(progressBars.get( new Long(id) )!=null)
501 progressPanel = (JPanel)progressBars.get( new Long(id) );
502 statusPanel.remove(progressPanel);
503 progressBars.remove( progressPanel );
504 progressPanel = null;
506 statusBar.setText(message);
508 layout.setRows(layout.getRows() - 1);
512 progressPanel = new JPanel(new BorderLayout(10, 5));
514 JProgressBar progressBar = new JProgressBar();
515 progressBar.setIndeterminate(true);
517 progressPanel.add(new JLabel(message), BorderLayout.WEST);
518 progressPanel.add(progressBar, BorderLayout.CENTER);
520 layout.setRows(layout.getRows() + 1);
521 statusPanel.add(progressPanel);
523 progressBars.put(new Long(id), progressPanel);
533 Added so Castor Mapping file can obtain Jalview Version
535 public String getVersion()
537 return jalview.bin.Cache.getProperty("VERSION");
540 public FeatureRenderer getFeatureRenderer()
542 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
546 public void fetchSequence_actionPerformed(ActionEvent e)
548 new SequenceFetcher(this);
551 public void addFromFile_actionPerformed(ActionEvent e)
553 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
556 public void reload_actionPerformed(ActionEvent e)
560 if(currentFileFormat.equals("Jalview"))
562 JInternalFrame [] frames = Desktop.desktop.getAllFrames();
563 for(int i=0; i<frames.length; i++)
565 if (frames[i] instanceof AlignFrame
567 && ( (AlignFrame) frames[i]).fileName.equals(fileName))
570 frames[i].setSelected(true);
571 Desktop.instance.closeAssociatedWindows();
572 }catch(java.beans.PropertyVetoException ex){}
576 Desktop.instance.closeAssociatedWindows();
581 viewport.alignment.deleteAllGroups();
582 viewport.sequenceColours=null;
583 while (viewport.alignment.getHeight() > 0)
585 viewport.alignment.deleteSequence(0);
588 viewport.historyList.clear();
589 viewport.redoList.clear();
590 Alignment dset = viewport.alignment.getDataset();
591 while (dset.getHeight() > 0)
593 dset.deleteSequence(0);
596 firePropertyChange("Alignment", null, null);
601 FileLoader loader = new FileLoader();
602 String protocol = fileName.startsWith("http:")? "URL":"File";
603 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
609 public void addFromText_actionPerformed(ActionEvent e)
611 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
614 public void addFromURL_actionPerformed(ActionEvent e)
616 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
620 public void save_actionPerformed(ActionEvent e)
622 if(fileName==null || currentFileFormat==null)
623 saveAs_actionPerformed(null);
625 saveAlignment(fileName, currentFileFormat);
631 * @param e DOCUMENT ME!
633 public void saveAs_actionPerformed(ActionEvent e)
635 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
636 getProperty( "LAST_DIRECTORY"),
638 { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" },
640 { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
645 chooser.setFileView(new JalviewFileView());
646 chooser.setDialogTitle("Save Alignment to file");
647 chooser.setToolTipText("Save");
649 int value = chooser.showSaveDialog(this);
651 if (value == JalviewFileChooser.APPROVE_OPTION)
653 currentFileFormat = chooser.getSelectedFormat();
654 if (currentFileFormat == null)
656 JOptionPane.showInternalMessageDialog(Desktop.desktop,
657 "You must select a file format before saving!",
658 "File format not specified",
659 JOptionPane.WARNING_MESSAGE);
660 value = chooser.showSaveDialog(this);
664 fileName = chooser.getSelectedFile().getPath();
666 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
669 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
671 saveAlignment(fileName, currentFileFormat);
675 public boolean saveAlignment(String file, String format)
677 if (format.equalsIgnoreCase("Jalview"))
679 String shortName = title;
681 if (shortName.indexOf(java.io.File.separatorChar) > -1)
683 shortName = shortName.substring(shortName.lastIndexOf(
684 java.io.File.separatorChar) + 1);
687 new Jalview2XML().SaveAlignment(this, file, shortName);
689 statusBar.setText("Successfully saved to file: "
691 +format +" format.");
694 // USE Jalview2XML to save this file
700 String[] omitHidden = null;
702 if (viewport.hasHiddenColumns)
704 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
705 "The Alignment contains hidden columns."
706 + "\nDo you want to save only the visible alignment?",
707 "Save / Omit Hidden Columns",
708 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
710 if (reply == JOptionPane.YES_OPTION)
711 omitHidden = viewport.getViewAsString(false);
714 String output = new FormatAdapter().formatSequences(
716 viewport.alignment.getSequencesArray(),
726 java.io.PrintWriter out = new java.io.PrintWriter(
727 new java.io.FileWriter(file));
732 statusBar.setText("Successfully saved to file: "
734 +format +" format.");
739 ex.printStackTrace();
748 * @param e DOCUMENT ME!
750 protected void outputText_actionPerformed(ActionEvent e)
752 String [] omitHidden = null;
754 if(viewport.hasHiddenColumns)
756 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
757 "The Alignment contains hidden columns."
758 +"\nDo you want to output only the visible alignment?",
759 "Save / Omit Hidden Columns",
760 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
762 if(reply==JOptionPane.YES_OPTION)
764 omitHidden = viewport.getViewAsString(false);
768 CutAndPasteTransfer cap = new CutAndPasteTransfer();
769 cap.setForInput(null);
770 Desktop.addInternalFrame(cap,
771 "Alignment output - " + e.getActionCommand(), 600,
775 cap.setText(new FormatAdapter().formatSequences(
776 e.getActionCommand(),
777 viewport.alignment.getSequencesArray(),
784 * @param e DOCUMENT ME!
786 protected void htmlMenuItem_actionPerformed(ActionEvent e)
788 new HTMLOutput(viewport,
789 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
790 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
793 public void createImageMap(File file, String image)
795 alignPanel.makePNGImageMap(file, image);
801 * @param e DOCUMENT ME!
803 public void createPNG(File f)
805 alignPanel.makePNG(f);
811 * @param e DOCUMENT ME!
813 public void createEPS(File f)
815 alignPanel.makeEPS(f);
821 * @param e DOCUMENT ME!
823 public void printMenuItem_actionPerformed(ActionEvent e)
825 //Putting in a thread avoids Swing painting problems
826 PrintThread thread = new PrintThread();
830 public void exportFeatures_actionPerformed(ActionEvent e)
832 new AnnotationExporter().exportFeatures(alignPanel);
836 public void exportAnnotations_actionPerformed(ActionEvent e)
838 new AnnotationExporter().exportAnnotations(
840 viewport.alignment.getAlignmentAnnotation()
845 public void associatedData_actionPerformed(ActionEvent e)
847 // Pick the tree file
848 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
851 chooser.setFileView(new JalviewFileView());
852 chooser.setDialogTitle("Load Jalview Annotations or Features File");
853 chooser.setToolTipText("Load Jalview Annotations / Features file");
855 int value = chooser.showOpenDialog(null);
857 if (value == JalviewFileChooser.APPROVE_OPTION)
859 String choice = chooser.getSelectedFile().getPath();
860 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
861 loadJalviewDataFile(choice);
870 * @param e DOCUMENT ME!
872 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
874 if(alignPanels!=null && alignPanels.size()<2)
879 if(alignPanels!=null)
882 for (int i = 0; i < alignPanels.size(); i++)
884 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
885 PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
886 PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
887 PaintRefresher.RemoveComponent(ap);
891 int index = tabbedPane.getSelectedIndex();
893 tabbedPane.removeTabAt(index);
894 alignPanels.removeElement(alignPanel);
895 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
896 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
897 PaintRefresher.RemoveComponent(alignPanel);
900 tabbedPane.validate();
902 if(index==tabbedPane.getTabCount())
905 this.tabSelectionChanged(index);
910 this.setClosed(true);
914 ex.printStackTrace();
922 void updateEditMenuBar()
925 if (viewport.historyList.size() > 0)
927 undoMenuItem.setEnabled(true);
928 CommandI command = (CommandI) viewport.historyList.peek();
929 undoMenuItem.setText("Undo " + command.getDescription());
933 undoMenuItem.setEnabled(false);
934 undoMenuItem.setText("Undo");
937 if (viewport.redoList.size() > 0)
939 redoMenuItem.setEnabled(true);
941 CommandI command = (CommandI) viewport.redoList.peek();
942 redoMenuItem.setText("Redo " + command.getDescription());
946 redoMenuItem.setEnabled(false);
947 redoMenuItem.setText("Redo");
952 public void addHistoryItem(CommandI command)
954 if(command.getSize()>0)
956 viewport.historyList.push(command);
957 viewport.redoList.clear();
959 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
968 * @param e DOCUMENT ME!
970 protected void undoMenuItem_actionPerformed(ActionEvent e)
972 CommandI command = (CommandI)viewport.historyList.pop();
973 viewport.redoList.push(command);
974 command.undoCommand();
976 AlignViewport originalSource = getOriginatingSource(command);
978 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
980 originalSource.firePropertyChange("alignment", null,viewport.getAlignment().getSequences());
986 * @param e DOCUMENT ME!
988 protected void redoMenuItem_actionPerformed(ActionEvent e)
990 CommandI command = (CommandI) viewport.redoList.pop();
991 viewport.historyList.push(command);
994 AlignViewport originalSource = getOriginatingSource(command);
995 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
998 originalSource.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1001 AlignViewport getOriginatingSource(CommandI command)
1003 AlignViewport originalSource = viewport;
1004 //For sequence removal and addition, we need to fire
1005 //the property change event FROM the viewport where the
1006 //original alignment was altered
1007 if (command instanceof EditCommand)
1009 EditCommand editCommand = (EditCommand) command;
1010 AlignmentI al = editCommand.getAlignment();
1011 Vector comps = (Vector) PaintRefresher.components
1012 .get(viewport.getSequenceSetId());
1013 for (int i = 0; i < comps.size(); i++)
1015 if (comps.elementAt(i) instanceof AlignmentPanel)
1017 if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
1019 originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
1025 return originalSource;
1031 * @param up DOCUMENT ME!
1033 public void moveSelectedSequences(boolean up)
1035 SequenceGroup sg = viewport.getSelectionGroup();
1044 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1046 SequenceI seq = viewport.alignment.getSequenceAt(i);
1048 if (!sg.getSequences(false).contains(seq))
1053 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1055 if (sg.getSequences(false).contains(temp))
1060 viewport.alignment.getSequences().setElementAt(temp, i);
1061 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1066 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1068 SequenceI seq = viewport.alignment.getSequenceAt(i);
1070 if (!sg.getSequences(false).contains(seq))
1075 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1077 if (sg.getSequences(false).contains(temp))
1082 viewport.alignment.getSequences().setElementAt(temp, i);
1083 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1087 alignPanel.repaint();
1095 * @param e DOCUMENT ME!
1097 protected void copy_actionPerformed(ActionEvent e)
1100 if (viewport.getSelectionGroup() == null)
1105 SequenceI [] seqs = viewport.getSelectionAsNewSequence();
1106 String[] omitHidden = null;
1108 if (viewport.hasHiddenColumns)
1110 omitHidden = viewport.getViewAsString(true);
1113 String output = new FormatAdapter().formatSequences(
1118 StringSelection ss = new StringSelection(output);
1122 //Its really worth setting the clipboard contents
1123 //to empty before setting the large StringSelection!!
1124 Toolkit.getDefaultToolkit().getSystemClipboard()
1125 .setContents(new StringSelection(""), null);
1127 Toolkit.getDefaultToolkit().getSystemClipboard()
1128 .setContents(ss, Desktop.instance);
1130 catch (OutOfMemoryError er)
1132 er.printStackTrace();
1133 javax.swing.SwingUtilities.invokeLater(new Runnable()
1137 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1138 "Out of memory copying region!!"
1140 "\nSee help files for increasing Java Virtual Machine memory."
1142 javax.swing.JOptionPane.WARNING_MESSAGE);
1149 Vector hiddenColumns = null;
1150 if(viewport.hasHiddenColumns)
1152 hiddenColumns =new Vector();
1153 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1154 for(int i=0; i<viewport.getColumnSelection().getHiddenColumns().size(); i++)
1156 int[] region = (int[])
1157 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
1159 hiddenColumns.addElement(new int[]{region[0]-hiddenOffset,
1160 region[1]-hiddenOffset});
1166 Desktop.jalviewClipboard = new Object[]{ seqs,
1167 viewport.alignment.getDataset(),
1169 statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
1175 * @param e DOCUMENT ME!
1177 protected void pasteNew_actionPerformed(ActionEvent e)
1185 * @param e DOCUMENT ME!
1187 protected void pasteThis_actionPerformed(ActionEvent e)
1195 * @param newAlignment DOCUMENT ME!
1197 void paste(boolean newAlignment)
1201 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1202 Transferable contents = c.getContents(this);
1204 if (contents == null)
1212 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1213 if (str.length() < 1)
1216 format = new IdentifyFile().Identify(str, "Paste");
1219 catch (OutOfMemoryError er)
1221 er.printStackTrace();
1222 javax.swing.SwingUtilities.invokeLater(new Runnable()
1226 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1227 "Out of memory pasting sequences!!"
1229 "\nSee help files for increasing Java Virtual Machine memory."
1231 javax.swing.JOptionPane.WARNING_MESSAGE);
1238 SequenceI[] sequences;
1241 if(Desktop.jalviewClipboard!=null)
1243 // The clipboard was filled from within Jalview, we must use the sequences
1244 // And dataset from the copied alignment
1245 sequences = (SequenceI[])Desktop.jalviewClipboard[0];
1249 sequences = new FormatAdapter().readFile(str, "Paste", format);
1252 AlignmentI alignment = null;
1256 alignment = new Alignment(sequences);
1258 if (Desktop.jalviewClipboard != null)
1259 alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
1261 alignment.setDataset(null);
1265 alignment = viewport.getAlignment();
1268 SequenceI [] newseqs = new SequenceI[sequences.length];
1269 for (int i = 0; i < sequences.length; i++)
1271 newseqs[i] = new Sequence(sequences[i].getName(),
1272 sequences[i].getSequence(), sequences[i].getStart(),
1273 sequences[i].getEnd());
1275 alignment.addSequence(newseqs[i]);
1281 addHistoryItem(new EditCommand(
1286 alignment.getWidth(),
1291 viewport.setEndSeq(alignment.getHeight());
1292 alignment.getWidth();
1293 viewport.firePropertyChange("alignment", null, alignment.getSequences());
1298 // Add any annotations attached to sequences
1299 for (int i = 0; i < sequences.length; i++)
1301 if (sequences[i].getAnnotation() != null)
1303 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1305 AlignmentAnnotation newAnnot =
1306 new AlignmentAnnotation(
1307 sequences[i].getAnnotation()[a].label,
1308 sequences[i].getAnnotation()[a].description,
1309 sequences[i].getAnnotation()[a].annotations,
1310 sequences[i].getAnnotation()[a].graphMin,
1311 sequences[i].getAnnotation()[a].graphMax,
1312 sequences[i].getAnnotation()[a].graph);
1314 sequences[i].getAnnotation()[a] = newAnnot;
1315 newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].
1317 newAnnot.sequenceRef = sequences[i];
1318 newAnnot.adjustForAlignment();
1319 alignment.addAnnotation(newAnnot);
1320 alignment.setAnnotationIndex(newAnnot, a);
1323 alignPanel.annotationPanel.adjustPanelHeight();
1329 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
1330 String newtitle = new String("Copied sequences");
1332 if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
1334 Vector hc = (Vector)Desktop.jalviewClipboard[2];
1335 for(int i=0; i<hc.size(); i++)
1337 int [] region = (int[]) hc.elementAt(i);
1338 af.viewport.hideColumns(region[0], region[1]);
1343 //>>>This is a fix for the moment, until a better solution is found!!<<<
1344 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
1345 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1348 if (title.startsWith("Copied sequences"))
1354 newtitle = newtitle.concat("- from " + title);
1357 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1364 catch (Exception ex)
1366 ex.printStackTrace();
1367 System.out.println("Exception whilst pasting: "+ex);
1368 // could be anything being pasted in here
1377 * @param e DOCUMENT ME!
1379 protected void cut_actionPerformed(ActionEvent e)
1381 copy_actionPerformed(null);
1382 delete_actionPerformed(null);
1388 * @param e DOCUMENT ME!
1390 protected void delete_actionPerformed(ActionEvent evt)
1393 SequenceGroup sg = viewport.getSelectionGroup();
1399 Vector seqs = new Vector();
1401 for (int i = 0; i < sg.getSize(false); i++)
1403 seq = sg.getSequenceAt(i);
1404 seqs.addElement(seq);
1408 // If the cut affects all sequences, remove highlighted columns
1409 if (sg.getSize(false) == viewport.alignment.getHeight())
1411 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1412 sg.getEndRes() + 1);
1416 SequenceI [] cut = new SequenceI[seqs.size()];
1417 for(int i=0; i<seqs.size(); i++)
1418 cut[i] = (SequenceI)seqs.elementAt(i);
1424 addHistoryItem(new EditCommand("Cut Sequences",
1428 sg.getEndRes()-sg.getStartRes()+1,
1429 viewport.alignment));
1432 viewport.setSelectionGroup(null);
1433 viewport.alignment.deleteGroup(sg);
1435 viewport.firePropertyChange("alignment", null,
1436 viewport.getAlignment().getSequences());
1438 if (viewport.getAlignment().getHeight() < 1)
1442 this.setClosed(true);
1444 catch (Exception ex)
1453 * @param e DOCUMENT ME!
1455 protected void deleteGroups_actionPerformed(ActionEvent e)
1457 viewport.alignment.deleteAllGroups();
1458 viewport.sequenceColours.clear();
1459 viewport.setSelectionGroup(null);
1460 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1461 alignPanel.repaint();
1467 * @param e DOCUMENT ME!
1469 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1471 SequenceGroup sg = new SequenceGroup();
1473 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1476 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1479 sg.setEndRes(viewport.alignment.getWidth() - 1);
1480 viewport.setSelectionGroup(sg);
1481 alignPanel.repaint();
1482 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1488 * @param e DOCUMENT ME!
1490 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1492 if(viewport.cursorMode)
1494 alignPanel.seqPanel.keyboardNo1 = null;
1495 alignPanel.seqPanel.keyboardNo2 = null;
1497 viewport.setSelectionGroup(null);
1498 viewport.getColumnSelection().clear();
1499 viewport.setSelectionGroup(null);
1500 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1501 alignPanel.idPanel.idCanvas.searchResults = null;
1502 alignPanel.repaint();
1503 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1509 * @param e DOCUMENT ME!
1511 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1513 SequenceGroup sg = viewport.getSelectionGroup();
1517 selectAllSequenceMenuItem_actionPerformed(null);
1522 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1525 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1528 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1531 public void invertColSel_actionPerformed(ActionEvent e)
1533 viewport.invertColumnSelection();
1534 alignPanel.repaint();
1541 * @param e DOCUMENT ME!
1543 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1545 trimAlignment(true);
1551 * @param e DOCUMENT ME!
1553 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
1555 trimAlignment(false);
1558 void trimAlignment(boolean trimLeft)
1560 ColumnSelection colSel = viewport.getColumnSelection();
1563 if (colSel.size() > 0)
1566 column = colSel.getMin();
1568 column = colSel.getMax();
1571 if(viewport.getSelectionGroup()!=null)
1572 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
1574 seqs = viewport.alignment.getSequencesArray();
1577 TrimRegionCommand trimRegion;
1580 trimRegion = new TrimRegionCommand("Remove Left",
1581 TrimRegionCommand.TRIM_LEFT,
1586 viewport.selectionGroup);
1587 viewport.setStartRes(0);
1591 trimRegion = new TrimRegionCommand("Remove Right",
1592 TrimRegionCommand.TRIM_RIGHT,
1597 viewport.selectionGroup);
1600 statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
1603 addHistoryItem(trimRegion);
1605 Vector groups = viewport.alignment.getGroups();
1607 for (int i = 0; i < groups.size(); i++)
1609 SequenceGroup sg = (SequenceGroup) groups.get(i);
1611 if ( (trimLeft && !sg.adjustForRemoveLeft(column))
1612 || (!trimLeft && !sg.adjustForRemoveRight(column)))
1614 viewport.alignment.deleteGroup(sg);
1618 viewport.firePropertyChange("alignment", null,
1619 viewport.getAlignment().getSequences());
1626 * @param e DOCUMENT ME!
1628 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1630 int start = 0, end = viewport.alignment.getWidth()-1;
1633 if (viewport.getSelectionGroup() != null)
1635 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
1636 start = viewport.getSelectionGroup().getStartRes();
1637 end = viewport.getSelectionGroup().getEndRes();
1640 seqs = viewport.alignment.getSequencesArray();
1643 RemoveGapColCommand removeGapCols =
1644 new RemoveGapColCommand("Remove Gapped Columns",
1647 viewport.getGapCharacter());
1649 addHistoryItem(removeGapCols);
1651 statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
1653 //This is to maintain viewport position on first residue
1655 SequenceI seq = viewport.alignment.getSequenceAt(0);
1656 int startRes = seq.findPosition(viewport.startRes);
1657 // ShiftList shifts;
1658 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
1659 // edit.alColumnChanges=shifts.getInverse();
1660 // if (viewport.hasHiddenColumns)
1661 // viewport.getColumnSelection().compensateForEdits(shifts);
1662 viewport.setStartRes(seq.findIndex(startRes)-1);
1663 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1670 * @param e DOCUMENT ME!
1672 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1674 int start = 0, end = viewport.alignment.getWidth()-1;
1677 if (viewport.getSelectionGroup() != null)
1679 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
1680 start = viewport.getSelectionGroup().getStartRes();
1681 end = viewport.getSelectionGroup().getEndRes();
1684 seqs = viewport.alignment.getSequencesArray();
1686 //This is to maintain viewport position on first residue
1688 SequenceI seq = viewport.alignment.getSequenceAt(0);
1689 int startRes = seq.findPosition(viewport.startRes);
1691 addHistoryItem(new RemoveGapsCommand("Remove Gaps",
1694 viewport.getGapCharacter()));
1696 viewport.setStartRes(seq.findIndex(startRes)-1);
1698 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1705 * @param e DOCUMENT ME!
1707 public void padGapsMenuitem_actionPerformed(ActionEvent e)
1709 viewport.padGaps = padGapsMenuitem.isSelected();
1711 viewport.firePropertyChange("alignment",
1713 viewport.getAlignment().getSequences());
1719 * @param e DOCUMENT ME!
1721 public void findMenuItem_actionPerformed(ActionEvent e)
1726 public void newView_actionPerformed(ActionEvent e)
1728 AlignmentPanel newap =
1729 new Jalview2XML().copyAlignPanel(alignPanel, true);
1731 if (viewport.viewName == null)
1732 viewport.viewName = "View 1";
1734 newap.av.historyList = viewport.historyList;
1735 newap.av.redoList = viewport.redoList;
1736 newap.av.viewName = "View " +
1737 (Desktop.getViewCount(viewport.getSequenceSetId()) + 1);
1739 addAlignmentPanel(newap, false);
1741 if(alignPanels.size()==2)
1743 viewport.gatherViewsHere = true;
1745 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
1748 public void expandViews_actionPerformed(ActionEvent e)
1750 Desktop.instance.explodeViews(this);
1753 public void gatherViews_actionPerformed(ActionEvent e)
1755 Desktop.instance.gatherViews(this);
1763 * @param e DOCUMENT ME!
1765 public void font_actionPerformed(ActionEvent e)
1767 new FontChooser(alignPanel);
1774 * @param e DOCUMENT ME!
1776 protected void seqLimit_actionPerformed(ActionEvent e)
1778 viewport.setShowJVSuffix(seqLimits.isSelected());
1780 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
1781 alignPanel.repaint();
1784 public void idRightAlign_actionPerformed(ActionEvent e)
1786 viewport.rightAlignIds = idRightAlign.isSelected();
1787 alignPanel.repaint();
1795 * @param e DOCUMENT ME!
1797 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
1799 viewport.setColourText(colourTextMenuItem.isSelected());
1800 alignPanel.repaint();
1806 * @param e DOCUMENT ME!
1808 public void wrapMenuItem_actionPerformed(ActionEvent e)
1810 scaleAbove.setVisible(wrapMenuItem.isSelected());
1811 scaleLeft.setVisible(wrapMenuItem.isSelected());
1812 scaleRight.setVisible(wrapMenuItem.isSelected());
1813 viewport.setWrapAlignment(wrapMenuItem.isSelected());
1814 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
1817 public void showAllSeqs_actionPerformed(ActionEvent e)
1819 viewport.showAllHiddenSeqs();
1822 public void showAllColumns_actionPerformed(ActionEvent e)
1824 viewport.showAllHiddenColumns();
1828 public void hideSelSequences_actionPerformed(ActionEvent e)
1830 viewport.hideAllSelectedSeqs();
1831 alignPanel.repaint();
1834 public void hideSelColumns_actionPerformed(ActionEvent e)
1836 viewport.hideSelectedColumns();
1837 alignPanel.repaint();
1840 public void hiddenMarkers_actionPerformed(ActionEvent e)
1842 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
1849 * @param e DOCUMENT ME!
1851 protected void scaleAbove_actionPerformed(ActionEvent e)
1853 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
1854 alignPanel.repaint();
1860 * @param e DOCUMENT ME!
1862 protected void scaleLeft_actionPerformed(ActionEvent e)
1864 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
1865 alignPanel.repaint();
1871 * @param e DOCUMENT ME!
1873 protected void scaleRight_actionPerformed(ActionEvent e)
1875 viewport.setScaleRightWrapped(scaleRight.isSelected());
1876 alignPanel.repaint();
1882 * @param e DOCUMENT ME!
1884 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1886 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
1887 alignPanel.repaint();
1893 * @param e DOCUMENT ME!
1895 public void viewTextMenuItem_actionPerformed(ActionEvent e)
1897 viewport.setShowText(viewTextMenuItem.isSelected());
1898 alignPanel.repaint();
1904 * @param e DOCUMENT ME!
1906 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1908 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
1909 alignPanel.repaint();
1913 public FeatureSettings featureSettings;
1914 public void featureSettings_actionPerformed(ActionEvent e)
1916 if(featureSettings !=null )
1918 featureSettings.close();
1919 featureSettings = null;
1921 featureSettings = new FeatureSettings(this);
1927 * @param evt DOCUMENT ME!
1929 public void showSeqFeatures_actionPerformed(ActionEvent evt)
1931 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
1932 alignPanel.repaint();
1933 if (alignPanel.getOverviewPanel() != null)
1935 alignPanel.getOverviewPanel().updateOverviewImage();
1942 * @param e DOCUMENT ME!
1944 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
1946 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
1947 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
1953 * @param e DOCUMENT ME!
1955 public void overviewMenuItem_actionPerformed(ActionEvent e)
1957 if (alignPanel.overviewPanel != null)
1962 JInternalFrame frame = new JInternalFrame();
1963 OverviewPanel overview = new OverviewPanel(alignPanel);
1964 frame.setContentPane(overview);
1965 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
1966 frame.getWidth(), frame.getHeight());
1968 frame.setLayer(JLayeredPane.PALETTE_LAYER);
1969 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
1971 public void internalFrameClosed(
1972 javax.swing.event.InternalFrameEvent evt)
1974 alignPanel.setOverviewPanel(null);
1979 alignPanel.setOverviewPanel(overview);
1982 public void textColour_actionPerformed(ActionEvent e)
1984 new TextColourChooser().chooseColour(alignPanel, null);
1990 * @param e DOCUMENT ME!
1992 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2000 * @param e DOCUMENT ME!
2002 public void clustalColour_actionPerformed(ActionEvent e)
2004 changeColour(new ClustalxColourScheme(
2005 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
2011 * @param e DOCUMENT ME!
2013 public void zappoColour_actionPerformed(ActionEvent e)
2015 changeColour(new ZappoColourScheme());
2021 * @param e DOCUMENT ME!
2023 public void taylorColour_actionPerformed(ActionEvent e)
2025 changeColour(new TaylorColourScheme());
2031 * @param e DOCUMENT ME!
2033 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2035 changeColour(new HydrophobicColourScheme());
2041 * @param e DOCUMENT ME!
2043 public void helixColour_actionPerformed(ActionEvent e)
2045 changeColour(new HelixColourScheme());
2051 * @param e DOCUMENT ME!
2053 public void strandColour_actionPerformed(ActionEvent e)
2055 changeColour(new StrandColourScheme());
2061 * @param e DOCUMENT ME!
2063 public void turnColour_actionPerformed(ActionEvent e)
2065 changeColour(new TurnColourScheme());
2071 * @param e DOCUMENT ME!
2073 public void buriedColour_actionPerformed(ActionEvent e)
2075 changeColour(new BuriedColourScheme());
2081 * @param e DOCUMENT ME!
2083 public void nucleotideColour_actionPerformed(ActionEvent e)
2085 changeColour(new NucleotideColourScheme());
2088 public void annotationColour_actionPerformed(ActionEvent e)
2090 new AnnotationColourChooser(viewport, alignPanel);
2097 * @param e DOCUMENT ME!
2099 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2101 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2107 * @param cs DOCUMENT ME!
2109 public void changeColour(ColourSchemeI cs)
2115 if (viewport.getAbovePIDThreshold())
2117 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2120 cs.setThreshold(threshold,
2121 viewport.getIgnoreGapsConsensus());
2123 viewport.setGlobalColourScheme(cs);
2127 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2130 if (viewport.getConservationSelected())
2133 Alignment al = (Alignment) viewport.alignment;
2134 Conservation c = new Conservation("All",
2135 ResidueProperties.propHash, 3,
2136 al.getSequences(), 0,
2140 c.verdict(false, viewport.ConsPercGaps);
2142 cs.setConservation(c);
2144 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
2149 cs.setConservation(null);
2152 cs.setConsensus(viewport.hconsensus);
2155 viewport.setGlobalColourScheme(cs);
2157 if (viewport.getColourAppliesToAllGroups())
2159 Vector groups = viewport.alignment.getGroups();
2161 for (int i = 0; i < groups.size(); i++)
2163 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2171 if (cs instanceof ClustalxColourScheme)
2173 sg.cs = new ClustalxColourScheme(
2174 sg.getSequences(true), sg.getWidth());
2176 else if (cs instanceof UserColourScheme)
2178 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
2184 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2186 catch (Exception ex)
2191 if (viewport.getAbovePIDThreshold()
2192 || cs instanceof PIDColourScheme
2193 || cs instanceof Blosum62ColourScheme)
2195 sg.cs.setThreshold(threshold,
2196 viewport.getIgnoreGapsConsensus());
2198 sg.cs.setConsensus(AAFrequency.calculate(
2199 sg.getSequences(true), sg.getStartRes(),
2203 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2206 if (viewport.getConservationSelected())
2208 Conservation c = new Conservation("Group",
2209 ResidueProperties.propHash, 3,
2210 sg.getSequences(true),
2214 c.verdict(false, viewport.ConsPercGaps);
2215 sg.cs.setConservation(c);
2218 sg.cs.setConservation(null);
2222 if (alignPanel.getOverviewPanel() != null)
2224 alignPanel.getOverviewPanel().updateOverviewImage();
2227 alignPanel.repaint();
2233 * @param e DOCUMENT ME!
2235 protected void modifyPID_actionPerformed(ActionEvent e)
2237 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
2239 SliderPanel.setPIDSliderSource(alignPanel,
2240 viewport.getGlobalColourScheme(),
2242 SliderPanel.showPIDSlider();
2249 * @param e DOCUMENT ME!
2251 protected void modifyConservation_actionPerformed(ActionEvent e)
2253 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
2255 SliderPanel.setConservationSlider(alignPanel,
2256 viewport.globalColourScheme,
2258 SliderPanel.showConservationSlider();
2265 * @param e DOCUMENT ME!
2267 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2269 viewport.setConservationSelected(conservationMenuItem.isSelected());
2271 viewport.setAbovePIDThreshold(false);
2272 abovePIDThreshold.setSelected(false);
2274 changeColour(viewport.getGlobalColourScheme());
2276 modifyConservation_actionPerformed(null);
2282 * @param e DOCUMENT ME!
2284 public void abovePIDThreshold_actionPerformed(ActionEvent e)
2286 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
2288 conservationMenuItem.setSelected(false);
2289 viewport.setConservationSelected(false);
2291 changeColour(viewport.getGlobalColourScheme());
2293 modifyPID_actionPerformed(null);
2299 * @param e DOCUMENT ME!
2301 public void userDefinedColour_actionPerformed(ActionEvent e)
2303 if (e.getActionCommand().equals("User Defined..."))
2305 new UserDefinedColours(alignPanel, null);
2309 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
2310 getUserColourSchemes().get(e.getActionCommand());
2316 public void updateUserColourMenu()
2319 Component[] menuItems = colourMenu.getMenuComponents();
2320 int i, iSize = menuItems.length;
2321 for (i = 0; i < iSize; i++)
2323 if (menuItems[i].getName() != null &&
2324 menuItems[i].getName().equals("USER_DEFINED"))
2326 colourMenu.remove(menuItems[i]);
2330 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
2332 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
2333 getUserColourSchemes().keys();
2335 while (userColours.hasMoreElements())
2337 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
2338 nextElement().toString());
2339 radioItem.setName("USER_DEFINED");
2340 radioItem.addMouseListener(new MouseAdapter()
2342 public void mousePressed(MouseEvent evt)
2344 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
2346 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
2348 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
2349 "Remove from default list?",
2350 "Remove user defined colour",
2351 JOptionPane.YES_NO_OPTION);
2352 if(option == JOptionPane.YES_OPTION)
2354 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
2355 colourMenu.remove(radioItem);
2358 radioItem.addActionListener(new ActionListener()
2360 public void actionPerformed(ActionEvent evt)
2362 userDefinedColour_actionPerformed(evt);
2368 radioItem.addActionListener(new ActionListener()
2370 public void actionPerformed(ActionEvent evt)
2372 userDefinedColour_actionPerformed(evt);
2376 colourMenu.insert(radioItem, 15);
2377 colours.add(radioItem);
2385 * @param e DOCUMENT ME!
2387 public void PIDColour_actionPerformed(ActionEvent e)
2389 changeColour(new PIDColourScheme());
2395 * @param e DOCUMENT ME!
2397 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
2399 changeColour(new Blosum62ColourScheme());
2405 * @param e DOCUMENT ME!
2407 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2409 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2410 AlignmentSorter.sortByPID(viewport.getAlignment(),
2411 viewport.getAlignment().getSequenceAt(0));
2412 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));
2413 alignPanel.repaint();
2419 * @param e DOCUMENT ME!
2421 public void sortIDMenuItem_actionPerformed(ActionEvent e)
2423 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2424 AlignmentSorter.sortByID(viewport.getAlignment());
2425 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
2426 alignPanel.repaint();
2432 * @param e DOCUMENT ME!
2434 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
2436 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2437 AlignmentSorter.sortByGroup(viewport.getAlignment());
2438 addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
2440 alignPanel.repaint();
2446 * @param e DOCUMENT ME!
2448 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2450 new RedundancyPanel(alignPanel, this);
2457 * @param e DOCUMENT ME!
2459 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2461 if ( (viewport.getSelectionGroup() == null) ||
2462 (viewport.getSelectionGroup().getSize(false) < 2))
2464 JOptionPane.showInternalMessageDialog(this,
2465 "You must select at least 2 sequences.",
2466 "Invalid Selection",
2467 JOptionPane.WARNING_MESSAGE);
2471 JInternalFrame frame = new JInternalFrame();
2472 frame.setContentPane(new PairwiseAlignPanel(viewport));
2473 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
2480 * @param e DOCUMENT ME!
2482 public void PCAMenuItem_actionPerformed(ActionEvent e)
2484 if ( ( (viewport.getSelectionGroup() != null) &&
2485 (viewport.getSelectionGroup().getSize(false) < 4) &&
2486 (viewport.getSelectionGroup().getSize(false) > 0)) ||
2487 (viewport.getAlignment().getHeight() < 4))
2489 JOptionPane.showInternalMessageDialog(this,
2490 "Principal component analysis must take\n" +
2491 "at least 4 input sequences.",
2492 "Sequence selection insufficient",
2493 JOptionPane.WARNING_MESSAGE);
2498 new PCAPanel(viewport);
2502 public void autoCalculate_actionPerformed(ActionEvent e)
2504 viewport.autoCalculateConsensus = autoCalculate.isSelected();
2505 if(viewport.autoCalculateConsensus)
2507 viewport.firePropertyChange("alignment",
2509 viewport.getAlignment().getSequences());
2517 * @param e DOCUMENT ME!
2519 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2521 NewTreePanel("AV", "PID", "Average distance tree using PID");
2527 * @param e DOCUMENT ME!
2529 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2531 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2537 * @param e DOCUMENT ME!
2539 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2541 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2547 * @param e DOCUMENT ME!
2549 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2551 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2557 * @param type DOCUMENT ME!
2558 * @param pwType DOCUMENT ME!
2559 * @param title DOCUMENT ME!
2561 void NewTreePanel(String type, String pwType, String title)
2565 if (viewport.getSelectionGroup() != null) {
2566 if (viewport.getSelectionGroup().getSize(false) < 3) {
2567 JOptionPane.showMessageDialog(Desktop.desktop,
2568 "You need to have more than two sequences selected to build a tree!",
2569 "Not enough sequences",
2570 JOptionPane.WARNING_MESSAGE);
2575 SequenceGroup sg = viewport.getSelectionGroup();
2577 /* Decide if the selection is a column region */
2578 while (s < sg.getSize(false))
2580 if ( ( (SequenceI) sg.getSequences(false).elementAt(s++)).getLength() <
2583 JOptionPane.showMessageDialog(Desktop.desktop,
2584 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
2585 "Try using the Pad function in the edit menu,\n" +
2586 "or one of the multiple sequence alignment web services.",
2587 "Sequences in selection are not aligned",
2588 JOptionPane.WARNING_MESSAGE);
2594 title = title + " on region";
2595 tp = new TreePanel(alignPanel, type, pwType);
2599 //are the sequences aligned?
2600 if (!viewport.alignment.isAligned())
2602 JOptionPane.showMessageDialog(Desktop.desktop,
2603 "The sequences must be aligned before creating a tree.\n" +
2604 "Try using the Pad function in the edit menu,\n" +
2605 "or one of the multiple sequence alignment web services.",
2606 "Sequences not aligned",
2607 JOptionPane.WARNING_MESSAGE);
2612 if(viewport.alignment.getHeight()<2)
2615 tp = new TreePanel(alignPanel, type, pwType);
2618 addTreeMenuItem(tp, title);
2620 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
2626 * @param title DOCUMENT ME!
2627 * @param order DOCUMENT ME!
2629 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
2631 final JMenuItem item = new JMenuItem("by " + title);
2633 item.addActionListener(new java.awt.event.ActionListener()
2635 public void actionPerformed(ActionEvent e)
2637 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2639 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
2640 AlignmentSorter.sortBy(viewport.getAlignment(), order);
2642 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport.alignment));
2644 alignPanel.repaint();
2650 * Maintain the Order by->Displayed Tree menu.
2651 * Creates a new menu item for a TreePanel with an appropriate
2652 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
2653 * to remove the menu item when the treePanel is closed, and adjust
2654 * the tree leaf to sequence mapping when the alignment is modified.
2655 * @param treePanel Displayed tree window.
2656 * @param title SortBy menu item title.
2658 void addTreeMenuItem(final TreePanel treePanel, String title)
2660 final JMenuItem item = new JMenuItem(title);
2666 sort.add(sortByTreeMenu);
2669 sortByTreeMenu.add(item);
2670 item.addActionListener(new java.awt.event.ActionListener()
2672 public void actionPerformed(ActionEvent e)
2674 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2675 AlignmentSorter.sortByTree(viewport.getAlignment(),
2676 treePanel.getTree());
2678 addHistoryItem(new OrderCommand("Tree Sort",
2680 viewport.alignment));
2683 alignPanel.repaint();
2687 treePanel.addInternalFrameListener(new javax.swing.event.
2688 InternalFrameAdapter()
2690 public void internalFrameClosed(
2691 javax.swing.event.InternalFrameEvent evt)
2694 sortByTreeMenu.remove(item);
2698 sort.remove(sortByTreeMenu);
2706 * Work out whether the whole set of sequences
2707 * or just the selected set will be submitted for multiple alignment.
2710 private jalview.datamodel.AlignmentView gatherSequencesForAlignment()
2712 // Now, check we have enough sequences
2713 AlignmentView msa = null;
2715 if ( (viewport.getSelectionGroup() != null) &&
2716 (viewport.getSelectionGroup().getSize(false) > 1))
2718 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
2719 /*SequenceGroup seqs = viewport.getSelectionGroup();
2721 msa = new SequenceI[sz = seqs.getSize(false)];
2723 for (int i = 0; i < sz; i++)
2725 msa[i] = (SequenceI) seqs.getSequenceAt(i);
2727 msa = viewport.getAlignmentView(true);
2731 /*Vector seqs = viewport.getAlignment().getSequences();
2733 if (seqs.size() > 1)
2735 msa = new SequenceI[seqs.size()];
2737 for (int i = 0; i < seqs.size(); i++)
2739 msa[i] = (SequenceI) seqs.elementAt(i);
2742 msa = viewport.getAlignmentView(false);
2748 * Decides what is submitted to a secondary structure prediction service,
2749 * the currently selected sequence, or the currently selected alignment
2750 * (where the first sequence in the set is the one that the prediction
2753 AlignmentView gatherSeqOrMsaForSecStrPrediction()
2755 AlignmentView seqs = null;
2757 if ( (viewport.getSelectionGroup() != null) &&
2758 (viewport.getSelectionGroup().getSize(false) > 0))
2760 seqs = viewport.getAlignmentView(true);
2764 seqs = viewport.getAlignmentView(false);
2766 // limit sequences - JBPNote in future - could spawn multiple prediction jobs
2767 // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment.
2768 if (!viewport.alignment.isAligned())
2770 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] } );
2777 * @param e DOCUMENT ME!
2779 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2781 // Pick the tree file
2782 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
2785 chooser.setFileView(new JalviewFileView());
2786 chooser.setDialogTitle("Select a newick-like tree file");
2787 chooser.setToolTipText("Load a tree file");
2789 int value = chooser.showOpenDialog(null);
2791 if (value == JalviewFileChooser.APPROVE_OPTION)
2793 String choice = chooser.getSelectedFile().getPath();
2794 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
2798 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
2800 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
2802 catch (Exception ex)
2804 JOptionPane.showMessageDialog(Desktop.desktop,
2805 "Problem reading tree file",
2807 JOptionPane.WARNING_MESSAGE);
2808 ex.printStackTrace();
2814 public TreePanel ShowNewickTree(NewickFile nf, String title)
2816 return ShowNewickTree(nf,title,600,500,4,5);
2818 public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input)
2820 return ShowNewickTree(nf,title, input, 600,500,4,5);
2822 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y) {
2823 return ShowNewickTree(nf, title, null, w, h, x, y);
2826 * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
2828 * @param nf the tree
2829 * @param title tree viewer title
2830 * @param input Associated alignment input data (or null)
2835 * @return TreePanel handle
2837 public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input, int w,int h,int x, int y) {
2838 TreePanel tp = null;
2844 if (nf.getTree() != null)
2846 tp = new TreePanel(alignPanel,
2854 tp.setLocation(x,y);
2857 Desktop.addInternalFrame(tp, title, w, h);
2858 addTreeMenuItem(tp, title);
2861 catch (Exception ex)
2863 ex.printStackTrace();
2874 PrinterJob printJob = PrinterJob.getPrinterJob();
2875 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
2876 printJob.setPrintable(alignPanel, pf);
2878 if (printJob.printDialog())
2884 catch (Exception PrintException)
2886 PrintException.printStackTrace();
2893 * Generates menu items and listener event actions for web service clients
2896 public void BuildWebServiceMenu()
2898 if ( (Discoverer.services != null)
2899 && (Discoverer.services.size() > 0))
2901 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
2902 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
2903 Vector wsmenu = new Vector();
2904 final AlignFrame af = this;
2907 // Add any Multiple Sequence Alignment Services
2908 final JMenu msawsmenu = new JMenu("Alignment");
2909 for (int i = 0, j = msaws.size(); i < j; i++)
2911 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
2913 final JMenuItem method = new JMenuItem(sh.getName());
2914 method.addActionListener(new ActionListener()
2916 public void actionPerformed(ActionEvent e)
2918 AlignmentView msa = gatherSequencesForAlignment();
2919 new jalview.ws.MsaWSClient(sh, title, msa,
2920 false, true, viewport.getAlignment().getDataset(), af);
2925 msawsmenu.add(method);
2926 // Deal with services that we know accept partial alignments.
2927 if (sh.getName().indexOf("lustal") > -1)
2929 // We know that ClustalWS can accept partial alignments for refinement.
2930 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
2931 methodR.addActionListener(new ActionListener()
2933 public void actionPerformed(ActionEvent e)
2935 AlignmentView msa = gatherSequencesForAlignment();
2936 new jalview.ws.MsaWSClient(sh, title, msa,
2937 true, true, viewport.getAlignment().getDataset(), af);
2942 msawsmenu.add(methodR);
2946 wsmenu.add(msawsmenu);
2948 if (secstrpr != null)
2950 // Add any secondary structure prediction services
2951 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
2952 for (int i = 0, j = secstrpr.size(); i < j; i++)
2954 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
2956 final JMenuItem method = new JMenuItem(sh.getName());
2957 method.addActionListener(new ActionListener()
2959 public void actionPerformed(ActionEvent e)
2961 AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
2962 if (msa.getSequences().length == 1)
2964 // Single Sequence prediction
2965 new jalview.ws.JPredClient(sh, title, false, msa, af, true);
2969 if (msa.getSequences().length > 1)
2971 // Sequence profile based prediction
2972 new jalview.ws.JPredClient(sh,
2973 title, true, msa, af, true);
2978 secstrmenu.add(method);
2980 wsmenu.add(secstrmenu);
2982 this.webService.removeAll();
2983 for (int i = 0, j = wsmenu.size(); i < j; i++)
2985 webService.add( (JMenu) wsmenu.get(i));
2990 this.webService.removeAll();
2991 this.webService.add(this.webServiceNoServices);
2993 // TODO: add in rediscovery function
2994 // TODO: reduce code redundancy.
2995 // TODO: group services by location as well as function.
2998 /* public void vamsasStore_actionPerformed(ActionEvent e)
3000 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
3001 getProperty("LAST_DIRECTORY"));
3003 chooser.setFileView(new JalviewFileView());
3004 chooser.setDialogTitle("Export to Vamsas file");
3005 chooser.setToolTipText("Export");
3007 int value = chooser.showSaveDialog(this);
3009 if (value == JalviewFileChooser.APPROVE_OPTION)
3011 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
3012 //vs.store(chooser.getSelectedFile().getAbsolutePath() );
3013 vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
3020 public void showTranslation_actionPerformed(ActionEvent e)
3022 SequenceI [] selection = viewport.getSelectionAsNewSequence();
3023 String [] seqstring = viewport.getViewAsString(true);
3025 int s, sSize = selection.length;
3026 SequenceI [] newSeq = new SequenceI[sSize];
3029 StringBuffer protein;
3031 for(s=0; s<sSize; s++)
3033 protein = new StringBuffer();
3034 seq = AlignSeq.extractGaps("-. ", seqstring[s]);
3035 resSize = seq.length();
3036 resSize -= resSize%3;
3038 for(res = 0; res < resSize; res+=3)
3040 String codon = seq.substring(res, res+3);
3041 codon = codon.replace('U', 'T');
3042 String aa = ResidueProperties.codonTranslate(codon);
3044 protein.append(viewport.getGapCharacter());
3045 else if(aa.equals("STOP"))
3046 protein.append("X");
3048 protein.append( aa );
3050 newSeq[s] = new Sequence(selection[s].getName(),
3051 protein.toString());
3055 AlignmentI al = new Alignment(newSeq);
3056 al.setDataset(null);
3059 ////////////////////////////////
3060 // Copy annotations across
3061 jalview.datamodel.AlignmentAnnotation[] annotations
3062 = viewport.alignment.getAlignmentAnnotation();
3064 if(annotations!=null)
3066 for (int i = 0; i < annotations.length; i++)
3068 if (annotations[i].label.equals("Quality") ||
3069 annotations[i].label.equals("Conservation") ||
3070 annotations[i].label.equals("Consensus"))
3075 aSize = viewport.alignment.getWidth() / 3;
3076 jalview.datamodel.Annotation[] anots =
3077 new jalview.datamodel.Annotation[aSize];
3079 for (a = 0; a < viewport.alignment.getWidth(); a++)
3081 if (annotations[i].annotations[a] == null
3082 || annotations[i].annotations[a] == null)
3085 anots[a / 3] = new Annotation(
3086 annotations[i].annotations[a].displayCharacter,
3087 annotations[i].annotations[a].description,
3088 annotations[i].annotations[a].secondaryStructure,
3089 annotations[i].annotations[a].value,
3090 annotations[i].annotations[a].colour);
3093 jalview.datamodel.AlignmentAnnotation aa
3094 = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
3095 annotations[i].description, anots);
3096 al.addAnnotation(aa);
3100 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
3101 Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
3113 * @param String DOCUMENT ME!
3115 public boolean parseFeaturesFile(String file, String type)
3117 boolean featuresFile = false;
3119 featuresFile = new FeaturesFile(file, type).parse(viewport.alignment.getDataset(),
3120 alignPanel.seqPanel.seqCanvas.
3121 getFeatureRenderer().featureColours,
3126 ex.printStackTrace();
3131 viewport.showSequenceFeatures = true;
3132 showSeqFeatures.setSelected(true);
3133 alignPanel.repaint();
3136 return featuresFile;
3139 public void dragEnter(DropTargetDragEvent evt)
3142 public void dragExit(DropTargetEvent evt)
3145 public void dragOver(DropTargetDragEvent evt)
3148 public void dropActionChanged(DropTargetDragEvent evt)
3151 public void drop(DropTargetDropEvent evt)
3153 Transferable t = evt.getTransferable();
3154 java.util.List files = null;
3158 DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
3159 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
3161 //Works on Windows and MacOSX
3162 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3163 files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
3165 else if (t.isDataFlavorSupported(uriListFlavor))
3167 // This is used by Unix drag system
3168 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3169 String data = (String) t.getTransferData(uriListFlavor);
3170 files = new java.util.ArrayList(1);
3171 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
3174 st.hasMoreTokens(); )
3176 String s = st.nextToken();
3177 if (s.startsWith("#"))
3179 // the line is a comment (as per the RFC 2483)
3183 java.net.URI uri = new java.net.URI(s);
3184 java.io.File file = new java.io.File(uri);
3191 e.printStackTrace();
3198 for (int i = 0; i < files.size(); i++)
3200 loadJalviewDataFile(files.get(i).toString());
3203 catch (Exception ex)
3205 ex.printStackTrace();
3210 // This method will attempt to load a "dropped" file first by testing
3211 // whether its and Annotation file, then features file. If both are
3212 // false then the user may have dropped an alignment file onto this
3214 public void loadJalviewDataFile(String file)
3217 String protocol = "File";
3219 if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
3224 boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
3229 boolean isGroupsFile = parseFeaturesFile(file,protocol);
3232 String format = new IdentifyFile().Identify(file, protocol);
3234 if(format.equalsIgnoreCase("JnetFile"))
3236 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
3238 new JnetAnnotationMaker().add_annotation(predictions,
3239 viewport.getAlignment(),
3241 alignPanel.adjustAnnotationHeight();
3242 alignPanel.repaint();
3245 new FileLoader().LoadFile(viewport, file, protocol, format);
3251 alignPanel.adjustAnnotationHeight();
3254 }catch(Exception ex)
3256 ex.printStackTrace();
3260 public void tabSelectionChanged(int index)
3264 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
3265 viewport = alignPanel.av;
3266 setMenusFromViewport(viewport);
3270 public void tabbedPane_mousePressed(MouseEvent e)
3272 if(SwingUtilities.isRightMouseButton(e))
3274 String reply = JOptionPane.showInternalInputDialog(this,
3277 JOptionPane.QUESTION_MESSAGE);
3281 viewport.viewName = reply;
3282 tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
3288 public AlignViewport getCurrentView()