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 scaleAbove.setVisible(av.wrapAlignment);
476 scaleLeft.setVisible(av.wrapAlignment);
477 scaleRight.setVisible(av.wrapAlignment);
478 annotationPanelMenuItem.setState(av.showAnnotation);
479 viewBoxesMenuItem.setSelected(av.showBoxes);
480 viewTextMenuItem.setSelected(av.showText);
482 setColourSelected(ColourSchemeProperty.
483 getColourName(av.getGlobalColourScheme()));
485 showSeqFeatures.setSelected(av.showSequenceFeatures);
486 hiddenMarkers.setState(av.showHiddenMarkers);
487 applyToAllGroups.setState(av.colourAppliesToAllGroups);
493 Hashtable progressBars;
494 public void setProgressBar(String message, long id)
496 if(progressBars == null)
497 progressBars = new Hashtable();
499 JPanel progressPanel;
500 GridLayout layout = (GridLayout) statusPanel.getLayout();
501 if(progressBars.get( new Long(id) )!=null)
503 progressPanel = (JPanel)progressBars.get( new Long(id) );
504 statusPanel.remove(progressPanel);
505 progressBars.remove( progressPanel );
506 progressPanel = null;
508 statusBar.setText(message);
510 layout.setRows(layout.getRows() - 1);
514 progressPanel = new JPanel(new BorderLayout(10, 5));
516 JProgressBar progressBar = new JProgressBar();
517 progressBar.setIndeterminate(true);
519 progressPanel.add(new JLabel(message), BorderLayout.WEST);
520 progressPanel.add(progressBar, BorderLayout.CENTER);
522 layout.setRows(layout.getRows() + 1);
523 statusPanel.add(progressPanel);
525 progressBars.put(new Long(id), progressPanel);
535 Added so Castor Mapping file can obtain Jalview Version
537 public String getVersion()
539 return jalview.bin.Cache.getProperty("VERSION");
542 public FeatureRenderer getFeatureRenderer()
544 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
548 public void fetchSequence_actionPerformed(ActionEvent e)
550 new SequenceFetcher(this);
553 public void addFromFile_actionPerformed(ActionEvent e)
555 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
558 public void reload_actionPerformed(ActionEvent e)
562 if(currentFileFormat.equals("Jalview"))
564 JInternalFrame [] frames = Desktop.desktop.getAllFrames();
565 for(int i=0; i<frames.length; i++)
567 if (frames[i] instanceof AlignFrame
569 && ( (AlignFrame) frames[i]).fileName.equals(fileName))
572 frames[i].setSelected(true);
573 Desktop.instance.closeAssociatedWindows();
574 }catch(java.beans.PropertyVetoException ex){}
578 Desktop.instance.closeAssociatedWindows();
583 viewport.alignment.deleteAllGroups();
584 viewport.sequenceColours=null;
585 while (viewport.alignment.getHeight() > 0)
587 viewport.alignment.deleteSequence(0);
590 viewport.historyList.clear();
591 viewport.redoList.clear();
592 Alignment dset = viewport.alignment.getDataset();
593 while (dset.getHeight() > 0)
595 dset.deleteSequence(0);
598 firePropertyChange("Alignment", null, viewport.alignment.getSequences());
603 FileLoader loader = new FileLoader();
604 String protocol = fileName.startsWith("http:")? "URL":"File";
605 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
611 public void addFromText_actionPerformed(ActionEvent e)
613 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
616 public void addFromURL_actionPerformed(ActionEvent e)
618 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
622 public void save_actionPerformed(ActionEvent e)
625 || currentFileFormat==null
626 || fileName.startsWith("http")
628 saveAs_actionPerformed(null);
630 saveAlignment(fileName, currentFileFormat);
636 * @param e DOCUMENT ME!
638 public void saveAs_actionPerformed(ActionEvent e)
640 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
641 getProperty( "LAST_DIRECTORY"),
643 { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" },
645 { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
650 chooser.setFileView(new JalviewFileView());
651 chooser.setDialogTitle("Save Alignment to file");
652 chooser.setToolTipText("Save");
654 int value = chooser.showSaveDialog(this);
656 if (value == JalviewFileChooser.APPROVE_OPTION)
658 currentFileFormat = chooser.getSelectedFormat();
659 if (currentFileFormat == null)
661 JOptionPane.showInternalMessageDialog(Desktop.desktop,
662 "You must select a file format before saving!",
663 "File format not specified",
664 JOptionPane.WARNING_MESSAGE);
665 value = chooser.showSaveDialog(this);
669 fileName = chooser.getSelectedFile().getPath();
671 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
674 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
676 saveAlignment(fileName, currentFileFormat);
680 public boolean saveAlignment(String file, String format)
682 boolean success = true;
684 if (format.equalsIgnoreCase("Jalview"))
686 String shortName = title;
688 if (shortName.indexOf(java.io.File.separatorChar) > -1)
690 shortName = shortName.substring(shortName.lastIndexOf(
691 java.io.File.separatorChar) + 1);
694 success = new Jalview2XML().SaveAlignment(this, file, shortName);
696 statusBar.setText("Successfully saved to file: "
698 +format +" format.");
704 String[] omitHidden = null;
706 if (viewport.hasHiddenColumns)
708 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
709 "The Alignment contains hidden columns."
710 + "\nDo you want to save only the visible alignment?",
711 "Save / Omit Hidden Columns",
712 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
714 if (reply == JOptionPane.YES_OPTION)
715 omitHidden = viewport.getViewAsString(false);
718 String output = new FormatAdapter().formatSequences(
720 viewport.alignment.getSequencesArray(),
731 java.io.PrintWriter out = new java.io.PrintWriter(
732 new java.io.FileWriter(file));
737 statusBar.setText("Successfully saved to file: "
739 + format + " format.");
744 ex.printStackTrace();
750 JOptionPane.showInternalMessageDialog(
751 this, "Couldn't save file: " + fileName,
753 JOptionPane.WARNING_MESSAGE);
761 * @param e DOCUMENT ME!
763 protected void outputText_actionPerformed(ActionEvent e)
765 String [] omitHidden = null;
767 if(viewport.hasHiddenColumns)
769 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
770 "The Alignment contains hidden columns."
771 +"\nDo you want to output only the visible alignment?",
772 "Save / Omit Hidden Columns",
773 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
775 if(reply==JOptionPane.YES_OPTION)
777 omitHidden = viewport.getViewAsString(false);
781 CutAndPasteTransfer cap = new CutAndPasteTransfer();
782 cap.setForInput(null);
783 Desktop.addInternalFrame(cap,
784 "Alignment output - " + e.getActionCommand(), 600,
788 cap.setText(new FormatAdapter().formatSequences(
789 e.getActionCommand(),
790 viewport.alignment.getSequencesArray(),
797 * @param e DOCUMENT ME!
799 protected void htmlMenuItem_actionPerformed(ActionEvent e)
801 new HTMLOutput(viewport,
802 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
803 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
806 public void createImageMap(File file, String image)
808 alignPanel.makePNGImageMap(file, image);
814 * @param e DOCUMENT ME!
816 public void createPNG(File f)
818 alignPanel.makePNG(f);
824 * @param e DOCUMENT ME!
826 public void createEPS(File f)
828 alignPanel.makeEPS(f);
832 public void pageSetup_actionPerformed(ActionEvent e)
834 PrinterJob printJob = PrinterJob.getPrinterJob();
835 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
841 * @param e DOCUMENT ME!
843 public void printMenuItem_actionPerformed(ActionEvent e)
845 //Putting in a thread avoids Swing painting problems
846 PrintThread thread = new PrintThread(alignPanel);
850 public void exportFeatures_actionPerformed(ActionEvent e)
852 new AnnotationExporter().exportFeatures(alignPanel);
856 public void exportAnnotations_actionPerformed(ActionEvent e)
858 new AnnotationExporter().exportAnnotations(
860 viewport.alignment.getAlignmentAnnotation(),
861 viewport.alignment.getGroups()
866 public void associatedData_actionPerformed(ActionEvent e)
868 // Pick the tree file
869 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
872 chooser.setFileView(new JalviewFileView());
873 chooser.setDialogTitle("Load Jalview Annotations or Features File");
874 chooser.setToolTipText("Load Jalview Annotations / Features file");
876 int value = chooser.showOpenDialog(null);
878 if (value == JalviewFileChooser.APPROVE_OPTION)
880 String choice = chooser.getSelectedFile().getPath();
881 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
882 loadJalviewDataFile(choice);
891 * @param e DOCUMENT ME!
893 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
895 if(alignPanels!=null && alignPanels.size()<2)
900 if(alignPanels!=null)
903 for (int i = 0; i < alignPanels.size(); i++)
905 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
906 PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
907 PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
908 PaintRefresher.RemoveComponent(ap);
912 int index = tabbedPane.getSelectedIndex();
914 alignPanels.removeElement(alignPanel);
915 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
916 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
917 PaintRefresher.RemoveComponent(alignPanel);
921 tabbedPane.removeTabAt(index);
922 tabbedPane.validate();
924 if(index==tabbedPane.getTabCount())
927 this.tabSelectionChanged(index);
932 this.setClosed(true);
936 ex.printStackTrace();
944 void updateEditMenuBar()
947 if (viewport.historyList.size() > 0)
949 undoMenuItem.setEnabled(true);
950 CommandI command = (CommandI) viewport.historyList.peek();
951 undoMenuItem.setText("Undo " + command.getDescription());
955 undoMenuItem.setEnabled(false);
956 undoMenuItem.setText("Undo");
959 if (viewport.redoList.size() > 0)
961 redoMenuItem.setEnabled(true);
963 CommandI command = (CommandI) viewport.redoList.peek();
964 redoMenuItem.setText("Redo " + command.getDescription());
968 redoMenuItem.setEnabled(false);
969 redoMenuItem.setText("Redo");
974 public void addHistoryItem(CommandI command)
976 if(command.getSize()>0)
978 viewport.historyList.push(command);
979 viewport.redoList.clear();
981 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
990 * @param e DOCUMENT ME!
992 protected void undoMenuItem_actionPerformed(ActionEvent e)
994 CommandI command = (CommandI)viewport.historyList.pop();
995 viewport.redoList.push(command);
996 command.undoCommand();
998 AlignViewport originalSource = getOriginatingSource(command);
1001 if(originalSource!=null)
1003 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1004 originalSource.firePropertyChange("alignment",
1006 originalSource.alignment.getSequences());
1013 * @param e DOCUMENT ME!
1015 protected void redoMenuItem_actionPerformed(ActionEvent e)
1017 if(viewport.redoList.size()<1)
1020 CommandI command = (CommandI) viewport.redoList.pop();
1021 viewport.historyList.push(command);
1022 command.doCommand();
1024 AlignViewport originalSource = getOriginatingSource(command);
1025 updateEditMenuBar();
1027 if(originalSource!=null)
1029 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1030 originalSource.firePropertyChange("alignment",
1032 originalSource.alignment.getSequences());
1036 AlignViewport getOriginatingSource(CommandI command)
1038 AlignViewport originalSource = null;
1039 //For sequence removal and addition, we need to fire
1040 //the property change event FROM the viewport where the
1041 //original alignment was altered
1043 if (command instanceof EditCommand)
1045 EditCommand editCommand = (EditCommand) command;
1046 al = editCommand.getAlignment();
1047 Vector comps = (Vector) PaintRefresher.components
1048 .get(viewport.getSequenceSetId());
1050 for (int i = 0; i < comps.size(); i++)
1052 if (comps.elementAt(i) instanceof AlignmentPanel)
1054 if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
1056 originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
1063 if (originalSource == null)
1065 //The original view is closed, we must validate
1066 //the current view against the closed view first
1068 PaintRefresher.validateSequences(al, viewport.alignment);
1070 originalSource = viewport;
1073 return originalSource;
1079 * @param up DOCUMENT ME!
1081 public void moveSelectedSequences(boolean up)
1083 SequenceGroup sg = viewport.getSelectionGroup();
1092 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1094 SequenceI seq = viewport.alignment.getSequenceAt(i);
1096 if (!sg.getSequences(null).contains(seq))
1101 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1103 if (sg.getSequences(null).contains(temp))
1108 viewport.alignment.getSequences().setElementAt(temp, i);
1109 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1114 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1116 SequenceI seq = viewport.alignment.getSequenceAt(i);
1118 if (!sg.getSequences(null).contains(seq))
1123 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1125 if (sg.getSequences(null).contains(temp))
1130 viewport.alignment.getSequences().setElementAt(temp, i);
1131 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1135 alignPanel.repaint();
1143 * @param e DOCUMENT ME!
1145 protected void copy_actionPerformed(ActionEvent e)
1148 if (viewport.getSelectionGroup() == null)
1153 SequenceI [] seqs = viewport.getSelectionAsNewSequence();
1154 String[] omitHidden = null;
1156 if (viewport.hasHiddenColumns)
1158 omitHidden = viewport.getViewAsString(true);
1161 String output = new FormatAdapter().formatSequences(
1166 StringSelection ss = new StringSelection(output);
1170 jalview.gui.Desktop.internalCopy = true;
1171 //Its really worth setting the clipboard contents
1172 //to empty before setting the large StringSelection!!
1173 Toolkit.getDefaultToolkit().getSystemClipboard()
1174 .setContents(new StringSelection(""), null);
1176 Toolkit.getDefaultToolkit().getSystemClipboard()
1177 .setContents(ss, Desktop.instance);
1179 catch (OutOfMemoryError er)
1181 er.printStackTrace();
1182 javax.swing.SwingUtilities.invokeLater(new Runnable()
1186 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1187 "Out of memory copying region!!"
1189 "\nSee help files for increasing Java Virtual Machine memory."
1191 javax.swing.JOptionPane.WARNING_MESSAGE);
1198 Vector hiddenColumns = null;
1199 if(viewport.hasHiddenColumns)
1201 hiddenColumns =new Vector();
1202 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1203 for(int i=0; i<viewport.getColumnSelection().getHiddenColumns().size(); i++)
1205 int[] region = (int[])
1206 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
1208 hiddenColumns.addElement(new int[]{region[0]-hiddenOffset,
1209 region[1]-hiddenOffset});
1215 Desktop.jalviewClipboard = new Object[]{ seqs,
1216 viewport.alignment.getDataset(),
1218 statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
1224 * @param e DOCUMENT ME!
1226 protected void pasteNew_actionPerformed(ActionEvent e)
1234 * @param e DOCUMENT ME!
1236 protected void pasteThis_actionPerformed(ActionEvent e)
1244 * @param newAlignment DOCUMENT ME!
1246 void paste(boolean newAlignment)
1250 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1251 Transferable contents = c.getContents(this);
1253 if (contents == null)
1261 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1262 if (str.length() < 1)
1265 format = new IdentifyFile().Identify(str, "Paste");
1268 catch (OutOfMemoryError er)
1270 er.printStackTrace();
1271 javax.swing.SwingUtilities.invokeLater(new Runnable()
1275 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1276 "Out of memory pasting sequences!!"
1278 "\nSee help files for increasing Java Virtual Machine memory."
1280 javax.swing.JOptionPane.WARNING_MESSAGE);
1287 SequenceI[] sequences;
1290 if(Desktop.jalviewClipboard!=null)
1292 // The clipboard was filled from within Jalview, we must use the sequences
1293 // And dataset from the copied alignment
1294 sequences = (SequenceI[])Desktop.jalviewClipboard[0];
1298 sequences = new FormatAdapter().readFile(str, "Paste", format).getSequencesArray();
1301 AlignmentI alignment = null;
1305 alignment = new Alignment(sequences);
1307 if (Desktop.jalviewClipboard != null)
1308 alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
1310 alignment.setDataset(null);
1314 alignment = viewport.getAlignment();
1317 SequenceI [] newseqs = new SequenceI[sequences.length];
1318 for (int i = 0; i < sequences.length; i++)
1320 newseqs[i] = new Sequence(sequences[i].getName(),
1321 sequences[i].getSequence(), sequences[i].getStart(),
1322 sequences[i].getEnd());
1324 alignment.addSequence(newseqs[i]);
1330 addHistoryItem(new EditCommand(
1335 alignment.getWidth(),
1340 viewport.setEndSeq(alignment.getHeight());
1341 alignment.getWidth();
1342 viewport.firePropertyChange("alignment", null, alignment.getSequences());
1347 // Add any annotations attached to sequences
1348 for (int i = 0; i < sequences.length; i++)
1350 if (sequences[i].getAnnotation() != null)
1352 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1354 AlignmentAnnotation newAnnot =
1355 new AlignmentAnnotation(
1356 sequences[i].getAnnotation()[a].label,
1357 sequences[i].getAnnotation()[a].description,
1358 sequences[i].getAnnotation()[a].annotations,
1359 sequences[i].getAnnotation()[a].graphMin,
1360 sequences[i].getAnnotation()[a].graphMax,
1361 sequences[i].getAnnotation()[a].graph);
1363 sequences[i].getAnnotation()[a] = newAnnot;
1364 newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].
1366 newAnnot.sequenceRef = sequences[i];
1367 newAnnot.adjustForAlignment();
1368 alignment.addAnnotation(newAnnot);
1369 alignment.setAnnotationIndex(newAnnot, a);
1372 alignPanel.annotationPanel.adjustPanelHeight();
1378 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
1379 String newtitle = new String("Copied sequences");
1381 if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
1383 Vector hc = (Vector)Desktop.jalviewClipboard[2];
1384 for(int i=0; i<hc.size(); i++)
1386 int [] region = (int[]) hc.elementAt(i);
1387 af.viewport.hideColumns(region[0], region[1]);
1392 //>>>This is a fix for the moment, until a better solution is found!!<<<
1393 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
1394 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1397 if (title.startsWith("Copied sequences"))
1403 newtitle = newtitle.concat("- from " + title);
1406 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1413 catch (Exception ex)
1415 ex.printStackTrace();
1416 System.out.println("Exception whilst pasting: "+ex);
1417 // could be anything being pasted in here
1426 * @param e DOCUMENT ME!
1428 protected void cut_actionPerformed(ActionEvent e)
1430 copy_actionPerformed(null);
1431 delete_actionPerformed(null);
1437 * @param e DOCUMENT ME!
1439 protected void delete_actionPerformed(ActionEvent evt)
1442 SequenceGroup sg = viewport.getSelectionGroup();
1448 Vector seqs = new Vector();
1450 for (int i = 0; i < sg.getSize(); i++)
1452 seq = sg.getSequenceAt(i);
1453 seqs.addElement(seq);
1457 // If the cut affects all sequences, remove highlighted columns
1458 if (sg.getSize() == viewport.alignment.getHeight())
1460 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1461 sg.getEndRes() + 1);
1465 SequenceI [] cut = new SequenceI[seqs.size()];
1466 for(int i=0; i<seqs.size(); i++)
1467 cut[i] = (SequenceI)seqs.elementAt(i);
1473 addHistoryItem(new EditCommand("Cut Sequences",
1477 sg.getEndRes()-sg.getStartRes()+1,
1478 viewport.alignment));
1481 viewport.setSelectionGroup(null);
1482 viewport.alignment.deleteGroup(sg);
1484 viewport.firePropertyChange("alignment", null,
1485 viewport.getAlignment().getSequences());
1487 if (viewport.getAlignment().getHeight() < 1)
1491 this.setClosed(true);
1493 catch (Exception ex)
1502 * @param e DOCUMENT ME!
1504 protected void deleteGroups_actionPerformed(ActionEvent e)
1506 viewport.alignment.deleteAllGroups();
1507 viewport.sequenceColours = null;
1508 viewport.setSelectionGroup(null);
1509 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1510 alignPanel.repaint();
1516 * @param e DOCUMENT ME!
1518 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1520 SequenceGroup sg = new SequenceGroup();
1522 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1525 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1528 sg.setEndRes(viewport.alignment.getWidth() - 1);
1529 viewport.setSelectionGroup(sg);
1530 alignPanel.repaint();
1531 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1537 * @param e DOCUMENT ME!
1539 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1541 if(viewport.cursorMode)
1543 alignPanel.seqPanel.keyboardNo1 = null;
1544 alignPanel.seqPanel.keyboardNo2 = null;
1546 viewport.setSelectionGroup(null);
1547 viewport.getColumnSelection().clear();
1548 viewport.setSelectionGroup(null);
1549 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1550 alignPanel.idPanel.idCanvas.searchResults = null;
1551 alignPanel.repaint();
1552 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1558 * @param e DOCUMENT ME!
1560 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1562 SequenceGroup sg = viewport.getSelectionGroup();
1566 selectAllSequenceMenuItem_actionPerformed(null);
1571 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1574 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1577 alignPanel.repaint();
1579 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1582 public void invertColSel_actionPerformed(ActionEvent e)
1584 viewport.invertColumnSelection();
1585 alignPanel.repaint();
1592 * @param e DOCUMENT ME!
1594 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1596 trimAlignment(true);
1602 * @param e DOCUMENT ME!
1604 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
1606 trimAlignment(false);
1609 void trimAlignment(boolean trimLeft)
1611 ColumnSelection colSel = viewport.getColumnSelection();
1614 if (colSel.size() > 0)
1617 column = colSel.getMin();
1619 column = colSel.getMax();
1622 if(viewport.getSelectionGroup()!=null)
1623 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
1625 seqs = viewport.alignment.getSequencesArray();
1628 TrimRegionCommand trimRegion;
1631 trimRegion = new TrimRegionCommand("Remove Left",
1632 TrimRegionCommand.TRIM_LEFT,
1637 viewport.selectionGroup);
1638 viewport.setStartRes(0);
1642 trimRegion = new TrimRegionCommand("Remove Right",
1643 TrimRegionCommand.TRIM_RIGHT,
1648 viewport.selectionGroup);
1651 statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
1654 addHistoryItem(trimRegion);
1656 Vector groups = viewport.alignment.getGroups();
1658 for (int i = 0; i < groups.size(); i++)
1660 SequenceGroup sg = (SequenceGroup) groups.get(i);
1662 if ( (trimLeft && !sg.adjustForRemoveLeft(column))
1663 || (!trimLeft && !sg.adjustForRemoveRight(column)))
1665 viewport.alignment.deleteGroup(sg);
1669 viewport.firePropertyChange("alignment", null,
1670 viewport.getAlignment().getSequences());
1677 * @param e DOCUMENT ME!
1679 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1681 int start = 0, end = viewport.alignment.getWidth()-1;
1684 if (viewport.getSelectionGroup() != null)
1686 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
1687 start = viewport.getSelectionGroup().getStartRes();
1688 end = viewport.getSelectionGroup().getEndRes();
1691 seqs = viewport.alignment.getSequencesArray();
1694 RemoveGapColCommand removeGapCols =
1695 new RemoveGapColCommand("Remove Gapped Columns",
1698 viewport.alignment);
1700 addHistoryItem(removeGapCols);
1702 statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
1704 //This is to maintain viewport position on first residue
1706 SequenceI seq = viewport.alignment.getSequenceAt(0);
1707 int startRes = seq.findPosition(viewport.startRes);
1708 // ShiftList shifts;
1709 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
1710 // edit.alColumnChanges=shifts.getInverse();
1711 // if (viewport.hasHiddenColumns)
1712 // viewport.getColumnSelection().compensateForEdits(shifts);
1713 viewport.setStartRes(seq.findIndex(startRes)-1);
1714 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1721 * @param e DOCUMENT ME!
1723 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1725 int start = 0, end = viewport.alignment.getWidth()-1;
1728 if (viewport.getSelectionGroup() != null)
1730 seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);
1731 start = viewport.getSelectionGroup().getStartRes();
1732 end = viewport.getSelectionGroup().getEndRes();
1735 seqs = viewport.alignment.getSequencesArray();
1737 //This is to maintain viewport position on first residue
1739 SequenceI seq = viewport.alignment.getSequenceAt(0);
1740 int startRes = seq.findPosition(viewport.startRes);
1742 addHistoryItem(new RemoveGapsCommand("Remove Gaps",
1745 viewport.alignment));
1747 viewport.setStartRes(seq.findIndex(startRes)-1);
1749 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1756 * @param e DOCUMENT ME!
1758 public void padGapsMenuitem_actionPerformed(ActionEvent e)
1760 viewport.padGaps = padGapsMenuitem.isSelected();
1762 viewport.firePropertyChange("alignment",
1764 viewport.getAlignment().getSequences());
1770 * @param e DOCUMENT ME!
1772 public void findMenuItem_actionPerformed(ActionEvent e)
1777 public void newView_actionPerformed(ActionEvent e)
1779 AlignmentPanel newap =
1780 new Jalview2XML().copyAlignPanel(alignPanel, true);
1782 if (viewport.viewName == null)
1783 viewport.viewName = "Original";
1785 newap.av.historyList = viewport.historyList;
1786 newap.av.redoList = viewport.redoList;
1788 int index = Desktop.getViewCount(viewport.getSequenceSetId());
1789 String newViewName = "View " +index;
1791 Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
1792 Vector existingNames = new Vector();
1793 for(int i=0; i<comps.size(); i++)
1795 if(comps.elementAt(i) instanceof AlignmentPanel)
1797 AlignmentPanel ap = (AlignmentPanel)comps.elementAt(i);
1798 if(!existingNames.contains(ap.av.viewName))
1799 existingNames.addElement(ap.av.viewName);
1803 while(existingNames.contains(newViewName))
1805 newViewName = "View "+ (++index);
1808 newap.av.viewName = newViewName;
1810 addAlignmentPanel(newap, false);
1812 if(alignPanels.size()==2)
1814 viewport.gatherViewsHere = true;
1816 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
1819 public void expandViews_actionPerformed(ActionEvent e)
1821 Desktop.instance.explodeViews(this);
1824 public void gatherViews_actionPerformed(ActionEvent e)
1826 Desktop.instance.gatherViews(this);
1834 * @param e DOCUMENT ME!
1836 public void font_actionPerformed(ActionEvent e)
1838 new FontChooser(alignPanel);
1845 * @param e DOCUMENT ME!
1847 protected void seqLimit_actionPerformed(ActionEvent e)
1849 viewport.setShowJVSuffix(seqLimits.isSelected());
1851 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
1852 alignPanel.repaint();
1855 public void idRightAlign_actionPerformed(ActionEvent e)
1857 viewport.rightAlignIds = idRightAlign.isSelected();
1858 alignPanel.repaint();
1866 * @param e DOCUMENT ME!
1868 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
1870 viewport.setColourText(colourTextMenuItem.isSelected());
1871 alignPanel.repaint();
1877 * @param e DOCUMENT ME!
1879 public void wrapMenuItem_actionPerformed(ActionEvent e)
1881 scaleAbove.setVisible(wrapMenuItem.isSelected());
1882 scaleLeft.setVisible(wrapMenuItem.isSelected());
1883 scaleRight.setVisible(wrapMenuItem.isSelected());
1884 viewport.setWrapAlignment(wrapMenuItem.isSelected());
1885 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
1888 public void showAllSeqs_actionPerformed(ActionEvent e)
1890 viewport.showAllHiddenSeqs();
1893 public void showAllColumns_actionPerformed(ActionEvent e)
1895 viewport.showAllHiddenColumns();
1899 public void hideSelSequences_actionPerformed(ActionEvent e)
1901 viewport.hideAllSelectedSeqs();
1902 alignPanel.repaint();
1905 public void hideSelColumns_actionPerformed(ActionEvent e)
1907 viewport.hideSelectedColumns();
1908 alignPanel.repaint();
1911 public void hiddenMarkers_actionPerformed(ActionEvent e)
1913 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
1920 * @param e DOCUMENT ME!
1922 protected void scaleAbove_actionPerformed(ActionEvent e)
1924 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
1925 alignPanel.repaint();
1931 * @param e DOCUMENT ME!
1933 protected void scaleLeft_actionPerformed(ActionEvent e)
1935 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
1936 alignPanel.repaint();
1942 * @param e DOCUMENT ME!
1944 protected void scaleRight_actionPerformed(ActionEvent e)
1946 viewport.setScaleRightWrapped(scaleRight.isSelected());
1947 alignPanel.repaint();
1953 * @param e DOCUMENT ME!
1955 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1957 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
1958 alignPanel.repaint();
1964 * @param e DOCUMENT ME!
1966 public void viewTextMenuItem_actionPerformed(ActionEvent e)
1968 viewport.setShowText(viewTextMenuItem.isSelected());
1969 alignPanel.repaint();
1975 * @param e DOCUMENT ME!
1977 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1979 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
1980 alignPanel.repaint();
1984 public FeatureSettings featureSettings;
1985 public void featureSettings_actionPerformed(ActionEvent e)
1987 if(featureSettings !=null )
1989 featureSettings.close();
1990 featureSettings = null;
1992 featureSettings = new FeatureSettings(this);
1998 * @param evt DOCUMENT ME!
2000 public void showSeqFeatures_actionPerformed(ActionEvent evt)
2002 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2003 alignPanel.repaint();
2004 if (alignPanel.getOverviewPanel() != null)
2006 alignPanel.getOverviewPanel().updateOverviewImage();
2013 * @param e DOCUMENT ME!
2015 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2017 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2018 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2024 * @param e DOCUMENT ME!
2026 public void overviewMenuItem_actionPerformed(ActionEvent e)
2028 if (alignPanel.overviewPanel != null)
2033 JInternalFrame frame = new JInternalFrame();
2034 OverviewPanel overview = new OverviewPanel(alignPanel);
2035 frame.setContentPane(overview);
2036 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2037 frame.getWidth(), frame.getHeight());
2039 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2040 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2042 public void internalFrameClosed(
2043 javax.swing.event.InternalFrameEvent evt)
2045 alignPanel.setOverviewPanel(null);
2050 alignPanel.setOverviewPanel(overview);
2053 public void textColour_actionPerformed(ActionEvent e)
2055 new TextColourChooser().chooseColour(alignPanel, null);
2061 * @param e DOCUMENT ME!
2063 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2071 * @param e DOCUMENT ME!
2073 public void clustalColour_actionPerformed(ActionEvent e)
2075 changeColour(new ClustalxColourScheme(
2076 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
2082 * @param e DOCUMENT ME!
2084 public void zappoColour_actionPerformed(ActionEvent e)
2086 changeColour(new ZappoColourScheme());
2092 * @param e DOCUMENT ME!
2094 public void taylorColour_actionPerformed(ActionEvent e)
2096 changeColour(new TaylorColourScheme());
2102 * @param e DOCUMENT ME!
2104 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2106 changeColour(new HydrophobicColourScheme());
2112 * @param e DOCUMENT ME!
2114 public void helixColour_actionPerformed(ActionEvent e)
2116 changeColour(new HelixColourScheme());
2122 * @param e DOCUMENT ME!
2124 public void strandColour_actionPerformed(ActionEvent e)
2126 changeColour(new StrandColourScheme());
2132 * @param e DOCUMENT ME!
2134 public void turnColour_actionPerformed(ActionEvent e)
2136 changeColour(new TurnColourScheme());
2142 * @param e DOCUMENT ME!
2144 public void buriedColour_actionPerformed(ActionEvent e)
2146 changeColour(new BuriedColourScheme());
2152 * @param e DOCUMENT ME!
2154 public void nucleotideColour_actionPerformed(ActionEvent e)
2156 changeColour(new NucleotideColourScheme());
2159 public void annotationColour_actionPerformed(ActionEvent e)
2161 new AnnotationColourChooser(viewport, alignPanel);
2168 * @param e DOCUMENT ME!
2170 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2172 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2178 * @param cs DOCUMENT ME!
2180 public void changeColour(ColourSchemeI cs)
2186 if (viewport.getAbovePIDThreshold())
2188 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2191 cs.setThreshold(threshold,
2192 viewport.getIgnoreGapsConsensus());
2194 viewport.setGlobalColourScheme(cs);
2198 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2201 if (viewport.getConservationSelected())
2204 Alignment al = (Alignment) viewport.alignment;
2205 Conservation c = new Conservation("All",
2206 ResidueProperties.propHash, 3,
2207 al.getSequences(), 0,
2211 c.verdict(false, viewport.ConsPercGaps);
2213 cs.setConservation(c);
2215 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
2220 cs.setConservation(null);
2223 cs.setConsensus(viewport.hconsensus);
2226 viewport.setGlobalColourScheme(cs);
2228 if (viewport.getColourAppliesToAllGroups())
2230 Vector groups = viewport.alignment.getGroups();
2232 for (int i = 0; i < groups.size(); i++)
2234 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2242 if (cs instanceof ClustalxColourScheme)
2244 sg.cs = new ClustalxColourScheme(
2245 sg.getSequences(viewport.hiddenRepSequences), sg.getWidth());
2247 else if (cs instanceof UserColourScheme)
2249 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
2255 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2257 catch (Exception ex)
2262 if (viewport.getAbovePIDThreshold()
2263 || cs instanceof PIDColourScheme
2264 || cs instanceof Blosum62ColourScheme)
2266 sg.cs.setThreshold(threshold,
2267 viewport.getIgnoreGapsConsensus());
2269 sg.cs.setConsensus(AAFrequency.calculate(
2270 sg.getSequences(viewport.hiddenRepSequences), sg.getStartRes(),
2274 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2277 if (viewport.getConservationSelected())
2279 Conservation c = new Conservation("Group",
2280 ResidueProperties.propHash, 3,
2281 sg.getSequences(viewport.hiddenRepSequences),
2285 c.verdict(false, viewport.ConsPercGaps);
2286 sg.cs.setConservation(c);
2289 sg.cs.setConservation(null);
2293 if (alignPanel.getOverviewPanel() != null)
2295 alignPanel.getOverviewPanel().updateOverviewImage();
2298 alignPanel.repaint();
2304 * @param e DOCUMENT ME!
2306 protected void modifyPID_actionPerformed(ActionEvent e)
2308 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
2310 SliderPanel.setPIDSliderSource(alignPanel,
2311 viewport.getGlobalColourScheme(),
2313 SliderPanel.showPIDSlider();
2320 * @param e DOCUMENT ME!
2322 protected void modifyConservation_actionPerformed(ActionEvent e)
2324 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
2326 SliderPanel.setConservationSlider(alignPanel,
2327 viewport.globalColourScheme,
2329 SliderPanel.showConservationSlider();
2336 * @param e DOCUMENT ME!
2338 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2340 viewport.setConservationSelected(conservationMenuItem.isSelected());
2342 viewport.setAbovePIDThreshold(false);
2343 abovePIDThreshold.setSelected(false);
2345 changeColour(viewport.getGlobalColourScheme());
2347 modifyConservation_actionPerformed(null);
2353 * @param e DOCUMENT ME!
2355 public void abovePIDThreshold_actionPerformed(ActionEvent e)
2357 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
2359 conservationMenuItem.setSelected(false);
2360 viewport.setConservationSelected(false);
2362 changeColour(viewport.getGlobalColourScheme());
2364 modifyPID_actionPerformed(null);
2370 * @param e DOCUMENT ME!
2372 public void userDefinedColour_actionPerformed(ActionEvent e)
2374 if (e.getActionCommand().equals("User Defined..."))
2376 new UserDefinedColours(alignPanel, null);
2380 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
2381 getUserColourSchemes().get(e.getActionCommand());
2387 public void updateUserColourMenu()
2390 Component[] menuItems = colourMenu.getMenuComponents();
2391 int i, iSize = menuItems.length;
2392 for (i = 0; i < iSize; i++)
2394 if (menuItems[i].getName() != null &&
2395 menuItems[i].getName().equals("USER_DEFINED"))
2397 colourMenu.remove(menuItems[i]);
2401 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
2403 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
2404 getUserColourSchemes().keys();
2406 while (userColours.hasMoreElements())
2408 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
2409 nextElement().toString());
2410 radioItem.setName("USER_DEFINED");
2411 radioItem.addMouseListener(new MouseAdapter()
2413 public void mousePressed(MouseEvent evt)
2415 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
2417 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
2419 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
2420 "Remove from default list?",
2421 "Remove user defined colour",
2422 JOptionPane.YES_NO_OPTION);
2423 if(option == JOptionPane.YES_OPTION)
2425 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
2426 colourMenu.remove(radioItem);
2429 radioItem.addActionListener(new ActionListener()
2431 public void actionPerformed(ActionEvent evt)
2433 userDefinedColour_actionPerformed(evt);
2439 radioItem.addActionListener(new ActionListener()
2441 public void actionPerformed(ActionEvent evt)
2443 userDefinedColour_actionPerformed(evt);
2447 colourMenu.insert(radioItem, 15);
2448 colours.add(radioItem);
2456 * @param e DOCUMENT ME!
2458 public void PIDColour_actionPerformed(ActionEvent e)
2460 changeColour(new PIDColourScheme());
2466 * @param e DOCUMENT ME!
2468 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
2470 changeColour(new Blosum62ColourScheme());
2476 * @param e DOCUMENT ME!
2478 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2480 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2481 AlignmentSorter.sortByPID(viewport.getAlignment(),
2482 viewport.getAlignment().getSequenceAt(0));
2483 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));
2484 alignPanel.repaint();
2490 * @param e DOCUMENT ME!
2492 public void sortIDMenuItem_actionPerformed(ActionEvent e)
2494 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2495 AlignmentSorter.sortByID(viewport.getAlignment());
2496 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
2497 alignPanel.repaint();
2503 * @param e DOCUMENT ME!
2505 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
2507 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2508 AlignmentSorter.sortByGroup(viewport.getAlignment());
2509 addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
2511 alignPanel.repaint();
2517 * @param e DOCUMENT ME!
2519 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2521 new RedundancyPanel(alignPanel, this);
2528 * @param e DOCUMENT ME!
2530 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2532 if ( (viewport.getSelectionGroup() == null) ||
2533 (viewport.getSelectionGroup().getSize() < 2))
2535 JOptionPane.showInternalMessageDialog(this,
2536 "You must select at least 2 sequences.",
2537 "Invalid Selection",
2538 JOptionPane.WARNING_MESSAGE);
2542 JInternalFrame frame = new JInternalFrame();
2543 frame.setContentPane(new PairwiseAlignPanel(viewport));
2544 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
2551 * @param e DOCUMENT ME!
2553 public void PCAMenuItem_actionPerformed(ActionEvent e)
2555 if ( ( (viewport.getSelectionGroup() != null) &&
2556 (viewport.getSelectionGroup().getSize() < 4) &&
2557 (viewport.getSelectionGroup().getSize() > 0)) ||
2558 (viewport.getAlignment().getHeight() < 4))
2560 JOptionPane.showInternalMessageDialog(this,
2561 "Principal component analysis must take\n" +
2562 "at least 4 input sequences.",
2563 "Sequence selection insufficient",
2564 JOptionPane.WARNING_MESSAGE);
2569 new PCAPanel(alignPanel);
2573 public void autoCalculate_actionPerformed(ActionEvent e)
2575 viewport.autoCalculateConsensus = autoCalculate.isSelected();
2576 if(viewport.autoCalculateConsensus)
2578 viewport.firePropertyChange("alignment",
2580 viewport.getAlignment().getSequences());
2588 * @param e DOCUMENT ME!
2590 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2592 NewTreePanel("AV", "PID", "Average distance tree using PID");
2598 * @param e DOCUMENT ME!
2600 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2602 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2608 * @param e DOCUMENT ME!
2610 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2612 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2618 * @param e DOCUMENT ME!
2620 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2622 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2628 * @param type DOCUMENT ME!
2629 * @param pwType DOCUMENT ME!
2630 * @param title DOCUMENT ME!
2632 void NewTreePanel(String type, String pwType, String title)
2636 if (viewport.getSelectionGroup() != null) {
2637 if (viewport.getSelectionGroup().getSize() < 3) {
2638 JOptionPane.showMessageDialog(Desktop.desktop,
2639 "You need to have more than two sequences selected to build a tree!",
2640 "Not enough sequences",
2641 JOptionPane.WARNING_MESSAGE);
2646 SequenceGroup sg = viewport.getSelectionGroup();
2648 /* Decide if the selection is a column region */
2649 while (s < sg.getSize())
2651 if ( ( (SequenceI) sg.getSequences(null).elementAt(s++)).getLength() <
2654 JOptionPane.showMessageDialog(Desktop.desktop,
2655 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
2656 "Try using the Pad function in the edit menu,\n" +
2657 "or one of the multiple sequence alignment web services.",
2658 "Sequences in selection are not aligned",
2659 JOptionPane.WARNING_MESSAGE);
2665 title = title + " on region";
2666 tp = new TreePanel(alignPanel, type, pwType);
2670 //are the sequences aligned?
2671 if (!viewport.alignment.isAligned())
2673 JOptionPane.showMessageDialog(Desktop.desktop,
2674 "The sequences must be aligned before creating a tree.\n" +
2675 "Try using the Pad function in the edit menu,\n" +
2676 "or one of the multiple sequence alignment web services.",
2677 "Sequences not aligned",
2678 JOptionPane.WARNING_MESSAGE);
2683 if(viewport.alignment.getHeight()<2)
2686 tp = new TreePanel(alignPanel, type, pwType);
2691 if(viewport.viewName!=null)
2692 title+= viewport.viewName+" of ";
2694 title += this.title;
2696 Desktop.addInternalFrame(tp, title, 600, 500);
2702 * @param title DOCUMENT ME!
2703 * @param order DOCUMENT ME!
2705 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
2707 final JMenuItem item = new JMenuItem("by " + title);
2709 item.addActionListener(new java.awt.event.ActionListener()
2711 public void actionPerformed(ActionEvent e)
2713 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2715 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
2716 AlignmentSorter.sortBy(viewport.getAlignment(), order);
2718 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport.alignment));
2720 alignPanel.repaint();
2726 * Maintain the Order by->Displayed Tree menu.
2727 * Creates a new menu item for a TreePanel with an appropriate
2728 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
2729 * to remove the menu item when the treePanel is closed, and adjust
2730 * the tree leaf to sequence mapping when the alignment is modified.
2731 * @param treePanel Displayed tree window.
2732 * @param title SortBy menu item title.
2734 public void buildTreeMenu()
2736 sortByTreeMenu.removeAll();
2738 Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
2739 Vector treePanels = new Vector();
2740 int i, iSize = comps.size();
2741 for(i=0; i<iSize; i++)
2743 if(comps.elementAt(i) instanceof TreePanel)
2745 treePanels.add(comps.elementAt(i));
2749 iSize = treePanels.size();
2753 sortByTreeMenu.setVisible(false);
2757 sortByTreeMenu.setVisible(true);
2759 for(i=0; i<treePanels.size(); i++)
2761 TreePanel tp = (TreePanel)treePanels.elementAt(i);
2762 final JMenuItem item = new JMenuItem(tp.getTitle());
2763 final NJTree tree = ((TreePanel)treePanels.elementAt(i)).getTree();
2764 item.addActionListener(new java.awt.event.ActionListener()
2766 public void actionPerformed(ActionEvent e)
2768 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2769 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
2771 addHistoryItem(new OrderCommand("Tree Sort",
2773 viewport.alignment));
2775 alignPanel.repaint();
2779 sortByTreeMenu.add(item);
2784 * Work out whether the whole set of sequences
2785 * or just the selected set will be submitted for multiple alignment.
2788 private jalview.datamodel.AlignmentView gatherSequencesForAlignment()
2790 // Now, check we have enough sequences
2791 AlignmentView msa = null;
2793 if ( (viewport.getSelectionGroup() != null) &&
2794 (viewport.getSelectionGroup().getSize() > 1))
2796 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
2797 /*SequenceGroup seqs = viewport.getSelectionGroup();
2799 msa = new SequenceI[sz = seqs.getSize(false)];
2801 for (int i = 0; i < sz; i++)
2803 msa[i] = (SequenceI) seqs.getSequenceAt(i);
2805 msa = viewport.getAlignmentView(true);
2809 /*Vector seqs = viewport.getAlignment().getSequences();
2811 if (seqs.size() > 1)
2813 msa = new SequenceI[seqs.size()];
2815 for (int i = 0; i < seqs.size(); i++)
2817 msa[i] = (SequenceI) seqs.elementAt(i);
2820 msa = viewport.getAlignmentView(false);
2826 * Decides what is submitted to a secondary structure prediction service,
2827 * the currently selected sequence, or the currently selected alignment
2828 * (where the first sequence in the set is the one that the prediction
2831 AlignmentView gatherSeqOrMsaForSecStrPrediction()
2833 AlignmentView seqs = null;
2835 if ( (viewport.getSelectionGroup() != null) &&
2836 (viewport.getSelectionGroup().getSize() > 0))
2838 seqs = viewport.getAlignmentView(true);
2842 seqs = viewport.getAlignmentView(false);
2844 // limit sequences - JBPNote in future - could spawn multiple prediction jobs
2845 // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment.
2846 if (!viewport.alignment.isAligned())
2848 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] } );
2855 * @param e DOCUMENT ME!
2857 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2859 // Pick the tree file
2860 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
2863 chooser.setFileView(new JalviewFileView());
2864 chooser.setDialogTitle("Select a newick-like tree file");
2865 chooser.setToolTipText("Load a tree file");
2867 int value = chooser.showOpenDialog(null);
2869 if (value == JalviewFileChooser.APPROVE_OPTION)
2871 String choice = chooser.getSelectedFile().getPath();
2872 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
2876 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
2878 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
2880 catch (Exception ex)
2882 JOptionPane.showMessageDialog(Desktop.desktop,
2883 "Problem reading tree file",
2885 JOptionPane.WARNING_MESSAGE);
2886 ex.printStackTrace();
2892 public TreePanel ShowNewickTree(NewickFile nf, String title)
2894 return ShowNewickTree(nf,title,600,500,4,5);
2896 public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input)
2898 return ShowNewickTree(nf,title, input, 600,500,4,5);
2900 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y) {
2901 return ShowNewickTree(nf, title, null, w, h, x, y);
2904 * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
2906 * @param nf the tree
2907 * @param title tree viewer title
2908 * @param input Associated alignment input data (or null)
2913 * @return TreePanel handle
2915 public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input, int w,int h,int x, int y) {
2916 TreePanel tp = null;
2922 if (nf.getTree() != null)
2924 tp = new TreePanel(alignPanel,
2932 tp.setLocation(x,y);
2935 Desktop.addInternalFrame(tp, title, w, h);
2938 catch (Exception ex)
2940 ex.printStackTrace();
2948 * Generates menu items and listener event actions for web service clients
2951 public void BuildWebServiceMenu()
2953 if ( (Discoverer.services != null)
2954 && (Discoverer.services.size() > 0))
2956 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
2957 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
2958 Vector wsmenu = new Vector();
2959 final AlignFrame af = this;
2962 // Add any Multiple Sequence Alignment Services
2963 final JMenu msawsmenu = new JMenu("Alignment");
2964 for (int i = 0, j = msaws.size(); i < j; i++)
2966 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
2968 final JMenuItem method = new JMenuItem(sh.getName());
2969 method.addActionListener(new ActionListener()
2971 public void actionPerformed(ActionEvent e)
2973 AlignmentView msa = gatherSequencesForAlignment();
2974 new jalview.ws.MsaWSClient(sh, title, msa,
2975 false, true, viewport.getAlignment().getDataset(), af);
2980 msawsmenu.add(method);
2981 // Deal with services that we know accept partial alignments.
2982 if (sh.getName().indexOf("lustal") > -1)
2984 // We know that ClustalWS can accept partial alignments for refinement.
2985 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
2986 methodR.addActionListener(new ActionListener()
2988 public void actionPerformed(ActionEvent e)
2990 AlignmentView msa = gatherSequencesForAlignment();
2991 new jalview.ws.MsaWSClient(sh, title, msa,
2992 true, true, viewport.getAlignment().getDataset(), af);
2997 msawsmenu.add(methodR);
3001 wsmenu.add(msawsmenu);
3003 if (secstrpr != null)
3005 // Add any secondary structure prediction services
3006 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
3007 for (int i = 0, j = secstrpr.size(); i < j; i++)
3009 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
3011 final JMenuItem method = new JMenuItem(sh.getName());
3012 method.addActionListener(new ActionListener()
3014 public void actionPerformed(ActionEvent e)
3016 AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
3017 if (msa.getSequences().length == 1)
3019 // Single Sequence prediction
3020 new jalview.ws.JPredClient(sh, title, false, msa, af, true);
3024 if (msa.getSequences().length > 1)
3026 // Sequence profile based prediction
3027 new jalview.ws.JPredClient(sh,
3028 title, true, msa, af, true);
3033 secstrmenu.add(method);
3035 wsmenu.add(secstrmenu);
3037 this.webService.removeAll();
3038 for (int i = 0, j = wsmenu.size(); i < j; i++)
3040 webService.add( (JMenu) wsmenu.get(i));
3045 this.webService.removeAll();
3046 this.webService.add(this.webServiceNoServices);
3048 // TODO: add in rediscovery function
3049 // TODO: reduce code redundancy.
3050 // TODO: group services by location as well as function.
3053 /* public void vamsasStore_actionPerformed(ActionEvent e)
3055 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
3056 getProperty("LAST_DIRECTORY"));
3058 chooser.setFileView(new JalviewFileView());
3059 chooser.setDialogTitle("Export to Vamsas file");
3060 chooser.setToolTipText("Export");
3062 int value = chooser.showSaveDialog(this);
3064 if (value == JalviewFileChooser.APPROVE_OPTION)
3066 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
3067 //vs.store(chooser.getSelectedFile().getAbsolutePath() );
3068 vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
3075 public void showTranslation_actionPerformed(ActionEvent e)
3077 SequenceI [] selection = viewport.getSelectionAsNewSequence();
3078 String [] seqstring = viewport.getViewAsString(true);
3080 int s, sSize = selection.length;
3081 SequenceI [] newSeq = new SequenceI[sSize];
3084 StringBuffer protein;
3086 for(s=0; s<sSize; s++)
3088 protein = new StringBuffer();
3089 seq = AlignSeq.extractGaps("-. ", seqstring[s]);
3090 resSize = seq.length();
3091 resSize -= resSize%3;
3093 for(res = 0; res < resSize; res+=3)
3095 String codon = seq.substring(res, res+3);
3096 codon = codon.replace('U', 'T');
3097 String aa = ResidueProperties.codonTranslate(codon);
3099 protein.append(viewport.getGapCharacter());
3100 else if(aa.equals("STOP"))
3101 protein.append("X");
3103 protein.append( aa );
3105 newSeq[s] = new Sequence(selection[s].getName(),
3106 protein.toString());
3110 AlignmentI al = new Alignment(newSeq);
3111 al.setDataset(null);
3114 ////////////////////////////////
3115 // Copy annotations across
3116 jalview.datamodel.AlignmentAnnotation[] annotations
3117 = viewport.alignment.getAlignmentAnnotation();
3119 if(annotations!=null)
3121 for (int i = 0; i < annotations.length; i++)
3123 if (annotations[i].label.equals("Quality") ||
3124 annotations[i].label.equals("Conservation") ||
3125 annotations[i].label.equals("Consensus"))
3130 aSize = viewport.alignment.getWidth() / 3;
3131 jalview.datamodel.Annotation[] anots =
3132 new jalview.datamodel.Annotation[aSize];
3134 for (a = 0; a < viewport.alignment.getWidth(); a++)
3136 if (annotations[i].annotations[a] == null
3137 || annotations[i].annotations[a] == null)
3140 anots[a / 3] = new Annotation(
3141 annotations[i].annotations[a].displayCharacter,
3142 annotations[i].annotations[a].description,
3143 annotations[i].annotations[a].secondaryStructure,
3144 annotations[i].annotations[a].value,
3145 annotations[i].annotations[a].colour);
3148 jalview.datamodel.AlignmentAnnotation aa
3149 = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
3150 annotations[i].description, anots);
3151 al.addAnnotation(aa);
3155 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
3156 Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
3168 * @param String DOCUMENT ME!
3170 public boolean parseFeaturesFile(String file, String type)
3172 boolean featuresFile = false;
3174 featuresFile = new FeaturesFile(file, type).parse(viewport.alignment.getDataset(),
3175 alignPanel.seqPanel.seqCanvas.
3176 getFeatureRenderer().featureColours,
3181 ex.printStackTrace();
3186 viewport.showSequenceFeatures = true;
3187 showSeqFeatures.setSelected(true);
3188 alignPanel.repaint();
3191 return featuresFile;
3194 public void dragEnter(DropTargetDragEvent evt)
3197 public void dragExit(DropTargetEvent evt)
3200 public void dragOver(DropTargetDragEvent evt)
3203 public void dropActionChanged(DropTargetDragEvent evt)
3206 public void drop(DropTargetDropEvent evt)
3208 Transferable t = evt.getTransferable();
3209 java.util.List files = null;
3213 DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
3214 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
3216 //Works on Windows and MacOSX
3217 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3218 files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
3220 else if (t.isDataFlavorSupported(uriListFlavor))
3222 // This is used by Unix drag system
3223 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3224 String data = (String) t.getTransferData(uriListFlavor);
3225 files = new java.util.ArrayList(1);
3226 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
3229 st.hasMoreTokens(); )
3231 String s = st.nextToken();
3232 if (s.startsWith("#"))
3234 // the line is a comment (as per the RFC 2483)
3238 java.net.URI uri = new java.net.URI(s);
3239 java.io.File file = new java.io.File(uri);
3246 e.printStackTrace();
3253 for (int i = 0; i < files.size(); i++)
3255 loadJalviewDataFile(files.get(i).toString());
3258 catch (Exception ex)
3260 ex.printStackTrace();
3265 // This method will attempt to load a "dropped" file first by testing
3266 // whether its and Annotation file, then features file. If both are
3267 // false then the user may have dropped an alignment file onto this
3269 public void loadJalviewDataFile(String file)
3272 String protocol = "File";
3274 if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
3279 boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
3280 alignment, file, protocol);
3284 boolean isGroupsFile = parseFeaturesFile(file,protocol);
3287 String format = new IdentifyFile().Identify(file, protocol);
3289 if(format.equalsIgnoreCase("JnetFile"))
3291 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
3293 new JnetAnnotationMaker().add_annotation(predictions,
3294 viewport.getAlignment(),
3296 alignPanel.adjustAnnotationHeight();
3297 alignPanel.repaint();
3300 new FileLoader().LoadFile(viewport, file, protocol, format);
3306 alignPanel.adjustAnnotationHeight();
3309 }catch(Exception ex)
3311 ex.printStackTrace();
3315 public void tabSelectionChanged(int index)
3319 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
3320 viewport = alignPanel.av;
3321 setMenusFromViewport(viewport);
3325 public void tabbedPane_mousePressed(MouseEvent e)
3327 if(SwingUtilities.isRightMouseButton(e))
3329 String reply = JOptionPane.showInternalInputDialog(this,
3332 JOptionPane.QUESTION_MESSAGE);
3336 viewport.viewName = reply;
3337 tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
3343 public AlignViewport getCurrentView()
3349 class PrintThread extends Thread
3352 public PrintThread(AlignmentPanel ap)
3356 static PageFormat pf;
3359 PrinterJob printJob = PrinterJob.getPrinterJob();
3362 printJob.setPrintable(ap, pf);
3364 printJob.setPrintable(ap);
3366 if (printJob.printDialog())
3372 catch (Exception PrintException)
3374 PrintException.printStackTrace();