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(false) != viewport.alignment.getHeight())
315 hideSelSequences_actionPerformed(null);
318 else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))
319 showAllSeqs_actionPerformed(null);
324 if (viewport.colSel.getSelected().size() > 0)
326 hideSelColumns_actionPerformed(null);
328 viewport.selectionGroup = sg;
331 showAllColumns_actionPerformed(null);
335 case KeyEvent.VK_PAGE_UP:
336 if (viewport.wrapAlignment)
337 alignPanel.scrollUp(true);
339 alignPanel.setScrollValues(viewport.startRes,
341 - viewport.endSeq + viewport.startSeq);
343 case KeyEvent.VK_PAGE_DOWN:
344 if (viewport.wrapAlignment)
345 alignPanel.scrollUp(false);
347 alignPanel.setScrollValues(viewport.startRes,
349 + viewport.endSeq - viewport.startSeq);
357 public void addAlignmentPanel(final AlignmentPanel ap,
360 ap.alignFrame = this;
362 alignPanels.addElement(ap);
364 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
366 int aSize = alignPanels.size();
368 tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
370 if (aSize == 1 && ap.av.viewName==null)
372 this.getContentPane().add(ap, BorderLayout.CENTER);
378 setInitialTabVisible();
381 expandViews.setEnabled(true);
382 gatherViews.setEnabled(true);
383 tabbedPane.addTab(ap.av.viewName, ap);
385 ap.setVisible(false);
391 ap.av.alignment.padGaps();
392 ap.av.updateConservation(ap);
393 ap.av.updateConsensus(ap);
397 public void setInitialTabVisible()
399 expandViews.setEnabled(true);
400 gatherViews.setEnabled(true);
401 tabbedPane.setVisible(true);
402 AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
403 tabbedPane.addTab(first.av.viewName,first);
404 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
408 public AlignViewport getViewport()
413 /* Set up intrinsic listeners for dynamically generated GUI bits. */
414 private void addServiceListeners()
416 final java.beans.PropertyChangeListener thisListener;
417 // Do this once to get current state
418 BuildWebServiceMenu();
419 Desktop.discoverer.addPropertyChangeListener(
420 thisListener = new java.beans.PropertyChangeListener()
422 public void propertyChange(PropertyChangeEvent evt)
424 // System.out.println("Discoverer property change.");
425 if (evt.getPropertyName().equals("services"))
427 // System.out.println("Rebuilding web service menu");
428 BuildWebServiceMenu();
433 addInternalFrameListener(new javax.swing.event.
434 InternalFrameAdapter()
436 public void internalFrameClosed(
437 javax.swing.event.InternalFrameEvent evt)
439 // System.out.println("deregistering discoverer listener");
440 Desktop.discoverer.removePropertyChangeListener(thisListener);
441 closeMenuItem_actionPerformed(true);
447 public void setGUINucleotide(boolean nucleotide)
449 showTranslation.setVisible( nucleotide );
450 conservationMenuItem.setEnabled( !nucleotide );
451 modifyConservation.setEnabled( !nucleotide );
453 //Remember AlignFrame always starts as protein
456 calculateMenu.remove(calculateMenu.getItemCount()-2);
461 * Need to call this method when tabs are selected for multiple views,
462 * or when loading from Jalview2XML.java
463 * @param av AlignViewport
465 void setMenusFromViewport(AlignViewport av)
467 padGapsMenuitem.setSelected(av.padGaps);
468 colourTextMenuItem.setSelected(av.showColourText);
469 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
470 conservationMenuItem.setSelected(av.getConservationSelected());
471 seqLimits.setSelected(av.getShowJVSuffix());
472 idRightAlign.setSelected(av.rightAlignIds);
473 renderGapsMenuItem.setSelected(av.renderGaps);
474 wrapMenuItem.setSelected(av.wrapAlignment);
475 annotationPanelMenuItem.setState(av.showAnnotation);
476 viewBoxesMenuItem.setSelected(av.showBoxes);
477 viewTextMenuItem.setSelected(av.showText);
479 setColourSelected(ColourSchemeProperty.
480 getColourName(av.getGlobalColourScheme()));
482 showSeqFeatures.setSelected(av.showSequenceFeatures);
483 hiddenMarkers.setState(av.showHiddenMarkers);
484 applyToAllGroups.setState(av.colourAppliesToAllGroups);
490 Hashtable progressBars;
491 public void setProgressBar(String message, long id)
493 if(progressBars == null)
494 progressBars = new Hashtable();
496 JPanel progressPanel;
497 GridLayout layout = (GridLayout) statusPanel.getLayout();
498 if(progressBars.get( new Long(id) )!=null)
500 progressPanel = (JPanel)progressBars.get( new Long(id) );
501 statusPanel.remove(progressPanel);
502 progressBars.remove( progressPanel );
503 progressPanel = null;
505 statusBar.setText(message);
507 layout.setRows(layout.getRows() - 1);
511 progressPanel = new JPanel(new BorderLayout(10, 5));
513 JProgressBar progressBar = new JProgressBar();
514 progressBar.setIndeterminate(true);
516 progressPanel.add(new JLabel(message), BorderLayout.WEST);
517 progressPanel.add(progressBar, BorderLayout.CENTER);
519 layout.setRows(layout.getRows() + 1);
520 statusPanel.add(progressPanel);
522 progressBars.put(new Long(id), progressPanel);
532 Added so Castor Mapping file can obtain Jalview Version
534 public String getVersion()
536 return jalview.bin.Cache.getProperty("VERSION");
539 public FeatureRenderer getFeatureRenderer()
541 return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
545 public void fetchSequence_actionPerformed(ActionEvent e)
547 new SequenceFetcher(this);
550 public void addFromFile_actionPerformed(ActionEvent e)
552 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
555 public void reload_actionPerformed(ActionEvent e)
559 if(currentFileFormat.equals("Jalview"))
561 JInternalFrame [] frames = Desktop.desktop.getAllFrames();
562 for(int i=0; i<frames.length; i++)
564 if (frames[i] instanceof AlignFrame
566 && ( (AlignFrame) frames[i]).fileName.equals(fileName))
569 frames[i].setSelected(true);
570 Desktop.instance.closeAssociatedWindows();
571 }catch(java.beans.PropertyVetoException ex){}
575 Desktop.instance.closeAssociatedWindows();
580 viewport.alignment.deleteAllGroups();
581 viewport.sequenceColours=null;
582 while (viewport.alignment.getHeight() > 0)
584 viewport.alignment.deleteSequence(0);
587 viewport.historyList.clear();
588 viewport.redoList.clear();
589 Alignment dset = viewport.alignment.getDataset();
590 while (dset.getHeight() > 0)
592 dset.deleteSequence(0);
595 firePropertyChange("Alignment", null, null);
600 FileLoader loader = new FileLoader();
601 String protocol = fileName.startsWith("http:")? "URL":"File";
602 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
608 public void addFromText_actionPerformed(ActionEvent e)
610 Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
613 public void addFromURL_actionPerformed(ActionEvent e)
615 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
619 public void save_actionPerformed(ActionEvent e)
622 || currentFileFormat==null
623 || fileName.startsWith("http")
625 saveAs_actionPerformed(null);
627 saveAlignment(fileName, currentFileFormat);
633 * @param e DOCUMENT ME!
635 public void saveAs_actionPerformed(ActionEvent e)
637 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
638 getProperty( "LAST_DIRECTORY"),
640 { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" },
642 { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
647 chooser.setFileView(new JalviewFileView());
648 chooser.setDialogTitle("Save Alignment to file");
649 chooser.setToolTipText("Save");
651 int value = chooser.showSaveDialog(this);
653 if (value == JalviewFileChooser.APPROVE_OPTION)
655 currentFileFormat = chooser.getSelectedFormat();
656 if (currentFileFormat == null)
658 JOptionPane.showInternalMessageDialog(Desktop.desktop,
659 "You must select a file format before saving!",
660 "File format not specified",
661 JOptionPane.WARNING_MESSAGE);
662 value = chooser.showSaveDialog(this);
666 fileName = chooser.getSelectedFile().getPath();
668 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
671 jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
673 saveAlignment(fileName, currentFileFormat);
677 public boolean saveAlignment(String file, String format)
679 boolean success = true;
681 if (format.equalsIgnoreCase("Jalview"))
683 String shortName = title;
685 if (shortName.indexOf(java.io.File.separatorChar) > -1)
687 shortName = shortName.substring(shortName.lastIndexOf(
688 java.io.File.separatorChar) + 1);
691 success = new Jalview2XML().SaveAlignment(this, file, shortName);
693 statusBar.setText("Successfully saved to file: "
695 +format +" format.");
701 String[] omitHidden = null;
703 if (viewport.hasHiddenColumns)
705 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
706 "The Alignment contains hidden columns."
707 + "\nDo you want to save only the visible alignment?",
708 "Save / Omit Hidden Columns",
709 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
711 if (reply == JOptionPane.YES_OPTION)
712 omitHidden = viewport.getViewAsString(false);
715 String output = new FormatAdapter().formatSequences(
717 viewport.alignment.getSequencesArray(),
728 java.io.PrintWriter out = new java.io.PrintWriter(
729 new java.io.FileWriter(file));
734 statusBar.setText("Successfully saved to file: "
736 + format + " format.");
741 ex.printStackTrace();
747 JOptionPane.showInternalMessageDialog(
748 this, "Couldn't save file: " + fileName,
750 JOptionPane.WARNING_MESSAGE);
758 * @param e DOCUMENT ME!
760 protected void outputText_actionPerformed(ActionEvent e)
762 String [] omitHidden = null;
764 if(viewport.hasHiddenColumns)
766 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
767 "The Alignment contains hidden columns."
768 +"\nDo you want to output only the visible alignment?",
769 "Save / Omit Hidden Columns",
770 JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
772 if(reply==JOptionPane.YES_OPTION)
774 omitHidden = viewport.getViewAsString(false);
778 CutAndPasteTransfer cap = new CutAndPasteTransfer();
779 cap.setForInput(null);
780 Desktop.addInternalFrame(cap,
781 "Alignment output - " + e.getActionCommand(), 600,
785 cap.setText(new FormatAdapter().formatSequences(
786 e.getActionCommand(),
787 viewport.alignment.getSequencesArray(),
794 * @param e DOCUMENT ME!
796 protected void htmlMenuItem_actionPerformed(ActionEvent e)
798 new HTMLOutput(viewport,
799 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
800 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
803 public void createImageMap(File file, String image)
805 alignPanel.makePNGImageMap(file, image);
811 * @param e DOCUMENT ME!
813 public void createPNG(File f)
815 alignPanel.makePNG(f);
821 * @param e DOCUMENT ME!
823 public void createEPS(File f)
825 alignPanel.makeEPS(f);
831 * @param e DOCUMENT ME!
833 public void printMenuItem_actionPerformed(ActionEvent e)
835 //Putting in a thread avoids Swing painting problems
836 PrintThread thread = new PrintThread();
840 public void exportFeatures_actionPerformed(ActionEvent e)
842 new AnnotationExporter().exportFeatures(alignPanel);
846 public void exportAnnotations_actionPerformed(ActionEvent e)
848 new AnnotationExporter().exportAnnotations(
850 viewport.alignment.getAlignmentAnnotation()
855 public void associatedData_actionPerformed(ActionEvent e)
857 // Pick the tree file
858 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
861 chooser.setFileView(new JalviewFileView());
862 chooser.setDialogTitle("Load Jalview Annotations or Features File");
863 chooser.setToolTipText("Load Jalview Annotations / Features file");
865 int value = chooser.showOpenDialog(null);
867 if (value == JalviewFileChooser.APPROVE_OPTION)
869 String choice = chooser.getSelectedFile().getPath();
870 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
871 loadJalviewDataFile(choice);
880 * @param e DOCUMENT ME!
882 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
884 if(alignPanels!=null && alignPanels.size()<2)
889 if(alignPanels!=null)
892 for (int i = 0; i < alignPanels.size(); i++)
894 AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
895 PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
896 PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
897 PaintRefresher.RemoveComponent(ap);
901 int index = tabbedPane.getSelectedIndex();
903 alignPanels.removeElement(alignPanel);
904 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
905 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
906 PaintRefresher.RemoveComponent(alignPanel);
910 tabbedPane.removeTabAt(index);
911 tabbedPane.validate();
913 if(index==tabbedPane.getTabCount())
916 this.tabSelectionChanged(index);
921 this.setClosed(true);
925 ex.printStackTrace();
933 void updateEditMenuBar()
936 if (viewport.historyList.size() > 0)
938 undoMenuItem.setEnabled(true);
939 CommandI command = (CommandI) viewport.historyList.peek();
940 undoMenuItem.setText("Undo " + command.getDescription());
944 undoMenuItem.setEnabled(false);
945 undoMenuItem.setText("Undo");
948 if (viewport.redoList.size() > 0)
950 redoMenuItem.setEnabled(true);
952 CommandI command = (CommandI) viewport.redoList.peek();
953 redoMenuItem.setText("Redo " + command.getDescription());
957 redoMenuItem.setEnabled(false);
958 redoMenuItem.setText("Redo");
963 public void addHistoryItem(CommandI command)
965 if(command.getSize()>0)
967 viewport.historyList.push(command);
968 viewport.redoList.clear();
970 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
979 * @param e DOCUMENT ME!
981 protected void undoMenuItem_actionPerformed(ActionEvent e)
983 CommandI command = (CommandI)viewport.historyList.pop();
984 viewport.redoList.push(command);
985 command.undoCommand();
987 AlignViewport originalSource = getOriginatingSource(command);
990 if(originalSource!=null)
992 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
993 originalSource.firePropertyChange("alignment", null,null);
1000 * @param e DOCUMENT ME!
1002 protected void redoMenuItem_actionPerformed(ActionEvent e)
1004 if(viewport.redoList.size()<1)
1007 CommandI command = (CommandI) viewport.redoList.pop();
1008 viewport.historyList.push(command);
1009 command.doCommand();
1011 AlignViewport originalSource = getOriginatingSource(command);
1012 updateEditMenuBar();
1014 if(originalSource!=null)
1016 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1017 originalSource.firePropertyChange("alignment", null,null);
1021 AlignViewport getOriginatingSource(CommandI command)
1023 AlignViewport originalSource = null;
1024 //For sequence removal and addition, we need to fire
1025 //the property change event FROM the viewport where the
1026 //original alignment was altered
1028 if (command instanceof EditCommand)
1030 EditCommand editCommand = (EditCommand) command;
1031 al = editCommand.getAlignment();
1032 Vector comps = (Vector) PaintRefresher.components
1033 .get(viewport.getSequenceSetId());
1035 for (int i = 0; i < comps.size(); i++)
1037 if (comps.elementAt(i) instanceof AlignmentPanel)
1039 if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
1041 originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
1048 if (originalSource == null)
1050 //The original view is closed, we must validate
1051 //the current view against the closed view first
1053 PaintRefresher.validateSequences(al, viewport.alignment);
1055 originalSource = viewport;
1058 return originalSource;
1064 * @param up DOCUMENT ME!
1066 public void moveSelectedSequences(boolean up)
1068 SequenceGroup sg = viewport.getSelectionGroup();
1077 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1079 SequenceI seq = viewport.alignment.getSequenceAt(i);
1081 if (!sg.getSequences(false).contains(seq))
1086 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1088 if (sg.getSequences(false).contains(temp))
1093 viewport.alignment.getSequences().setElementAt(temp, i);
1094 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1099 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1101 SequenceI seq = viewport.alignment.getSequenceAt(i);
1103 if (!sg.getSequences(false).contains(seq))
1108 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1110 if (sg.getSequences(false).contains(temp))
1115 viewport.alignment.getSequences().setElementAt(temp, i);
1116 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1120 alignPanel.repaint();
1128 * @param e DOCUMENT ME!
1130 protected void copy_actionPerformed(ActionEvent e)
1133 if (viewport.getSelectionGroup() == null)
1138 SequenceI [] seqs = viewport.getSelectionAsNewSequence();
1139 String[] omitHidden = null;
1141 if (viewport.hasHiddenColumns)
1143 omitHidden = viewport.getViewAsString(true);
1146 String output = new FormatAdapter().formatSequences(
1151 StringSelection ss = new StringSelection(output);
1155 //Its really worth setting the clipboard contents
1156 //to empty before setting the large StringSelection!!
1157 Toolkit.getDefaultToolkit().getSystemClipboard()
1158 .setContents(new StringSelection(""), null);
1160 Toolkit.getDefaultToolkit().getSystemClipboard()
1161 .setContents(ss, Desktop.instance);
1163 catch (OutOfMemoryError er)
1165 er.printStackTrace();
1166 javax.swing.SwingUtilities.invokeLater(new Runnable()
1170 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1171 "Out of memory copying region!!"
1173 "\nSee help files for increasing Java Virtual Machine memory."
1175 javax.swing.JOptionPane.WARNING_MESSAGE);
1182 Vector hiddenColumns = null;
1183 if(viewport.hasHiddenColumns)
1185 hiddenColumns =new Vector();
1186 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1187 for(int i=0; i<viewport.getColumnSelection().getHiddenColumns().size(); i++)
1189 int[] region = (int[])
1190 viewport.getColumnSelection().getHiddenColumns().elementAt(i);
1192 hiddenColumns.addElement(new int[]{region[0]-hiddenOffset,
1193 region[1]-hiddenOffset});
1199 Desktop.jalviewClipboard = new Object[]{ seqs,
1200 viewport.alignment.getDataset(),
1202 statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
1208 * @param e DOCUMENT ME!
1210 protected void pasteNew_actionPerformed(ActionEvent e)
1218 * @param e DOCUMENT ME!
1220 protected void pasteThis_actionPerformed(ActionEvent e)
1228 * @param newAlignment DOCUMENT ME!
1230 void paste(boolean newAlignment)
1234 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1235 Transferable contents = c.getContents(this);
1237 if (contents == null)
1245 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1246 if (str.length() < 1)
1249 format = new IdentifyFile().Identify(str, "Paste");
1252 catch (OutOfMemoryError er)
1254 er.printStackTrace();
1255 javax.swing.SwingUtilities.invokeLater(new Runnable()
1259 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
1260 "Out of memory pasting sequences!!"
1262 "\nSee help files for increasing Java Virtual Machine memory."
1264 javax.swing.JOptionPane.WARNING_MESSAGE);
1271 SequenceI[] sequences;
1274 if(Desktop.jalviewClipboard!=null)
1276 // The clipboard was filled from within Jalview, we must use the sequences
1277 // And dataset from the copied alignment
1278 sequences = (SequenceI[])Desktop.jalviewClipboard[0];
1282 sequences = new FormatAdapter().readFile(str, "Paste", format);
1285 AlignmentI alignment = null;
1289 alignment = new Alignment(sequences);
1291 if (Desktop.jalviewClipboard != null)
1292 alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
1294 alignment.setDataset(null);
1298 alignment = viewport.getAlignment();
1301 SequenceI [] newseqs = new SequenceI[sequences.length];
1302 for (int i = 0; i < sequences.length; i++)
1304 newseqs[i] = new Sequence(sequences[i].getName(),
1305 sequences[i].getSequence(), sequences[i].getStart(),
1306 sequences[i].getEnd());
1308 alignment.addSequence(newseqs[i]);
1314 addHistoryItem(new EditCommand(
1319 alignment.getWidth(),
1324 viewport.setEndSeq(alignment.getHeight());
1325 alignment.getWidth();
1326 viewport.firePropertyChange("alignment", null, alignment.getSequences());
1331 // Add any annotations attached to sequences
1332 for (int i = 0; i < sequences.length; i++)
1334 if (sequences[i].getAnnotation() != null)
1336 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1338 AlignmentAnnotation newAnnot =
1339 new AlignmentAnnotation(
1340 sequences[i].getAnnotation()[a].label,
1341 sequences[i].getAnnotation()[a].description,
1342 sequences[i].getAnnotation()[a].annotations,
1343 sequences[i].getAnnotation()[a].graphMin,
1344 sequences[i].getAnnotation()[a].graphMax,
1345 sequences[i].getAnnotation()[a].graph);
1347 sequences[i].getAnnotation()[a] = newAnnot;
1348 newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].
1350 newAnnot.sequenceRef = sequences[i];
1351 newAnnot.adjustForAlignment();
1352 alignment.addAnnotation(newAnnot);
1353 alignment.setAnnotationIndex(newAnnot, a);
1356 alignPanel.annotationPanel.adjustPanelHeight();
1362 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
1363 String newtitle = new String("Copied sequences");
1365 if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
1367 Vector hc = (Vector)Desktop.jalviewClipboard[2];
1368 for(int i=0; i<hc.size(); i++)
1370 int [] region = (int[]) hc.elementAt(i);
1371 af.viewport.hideColumns(region[0], region[1]);
1376 //>>>This is a fix for the moment, until a better solution is found!!<<<
1377 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
1378 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1381 if (title.startsWith("Copied sequences"))
1387 newtitle = newtitle.concat("- from " + title);
1390 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1397 catch (Exception ex)
1399 ex.printStackTrace();
1400 System.out.println("Exception whilst pasting: "+ex);
1401 // could be anything being pasted in here
1410 * @param e DOCUMENT ME!
1412 protected void cut_actionPerformed(ActionEvent e)
1414 copy_actionPerformed(null);
1415 delete_actionPerformed(null);
1421 * @param e DOCUMENT ME!
1423 protected void delete_actionPerformed(ActionEvent evt)
1426 SequenceGroup sg = viewport.getSelectionGroup();
1432 Vector seqs = new Vector();
1434 for (int i = 0; i < sg.getSize(false); i++)
1436 seq = sg.getSequenceAt(i);
1437 seqs.addElement(seq);
1441 // If the cut affects all sequences, remove highlighted columns
1442 if (sg.getSize(false) == viewport.alignment.getHeight())
1444 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1445 sg.getEndRes() + 1);
1449 SequenceI [] cut = new SequenceI[seqs.size()];
1450 for(int i=0; i<seqs.size(); i++)
1451 cut[i] = (SequenceI)seqs.elementAt(i);
1457 addHistoryItem(new EditCommand("Cut Sequences",
1461 sg.getEndRes()-sg.getStartRes()+1,
1462 viewport.alignment));
1465 viewport.setSelectionGroup(null);
1466 viewport.alignment.deleteGroup(sg);
1468 viewport.firePropertyChange("alignment", null,
1469 viewport.getAlignment().getSequences());
1471 if (viewport.getAlignment().getHeight() < 1)
1475 this.setClosed(true);
1477 catch (Exception ex)
1486 * @param e DOCUMENT ME!
1488 protected void deleteGroups_actionPerformed(ActionEvent e)
1490 viewport.alignment.deleteAllGroups();
1491 viewport.sequenceColours = null;
1492 viewport.setSelectionGroup(null);
1493 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1494 alignPanel.repaint();
1500 * @param e DOCUMENT ME!
1502 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1504 SequenceGroup sg = new SequenceGroup();
1506 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1509 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1512 sg.setEndRes(viewport.alignment.getWidth() - 1);
1513 viewport.setSelectionGroup(sg);
1514 alignPanel.repaint();
1515 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1521 * @param e DOCUMENT ME!
1523 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
1525 if(viewport.cursorMode)
1527 alignPanel.seqPanel.keyboardNo1 = null;
1528 alignPanel.seqPanel.keyboardNo2 = null;
1530 viewport.setSelectionGroup(null);
1531 viewport.getColumnSelection().clear();
1532 viewport.setSelectionGroup(null);
1533 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1534 alignPanel.idPanel.idCanvas.searchResults = null;
1535 alignPanel.repaint();
1536 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1542 * @param e DOCUMENT ME!
1544 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
1546 SequenceGroup sg = viewport.getSelectionGroup();
1550 selectAllSequenceMenuItem_actionPerformed(null);
1555 for (int i = 0; i < viewport.getAlignment().getSequences().size();
1558 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1561 alignPanel.repaint();
1563 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1566 public void invertColSel_actionPerformed(ActionEvent e)
1568 viewport.invertColumnSelection();
1569 alignPanel.repaint();
1576 * @param e DOCUMENT ME!
1578 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
1580 trimAlignment(true);
1586 * @param e DOCUMENT ME!
1588 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
1590 trimAlignment(false);
1593 void trimAlignment(boolean trimLeft)
1595 ColumnSelection colSel = viewport.getColumnSelection();
1598 if (colSel.size() > 0)
1601 column = colSel.getMin();
1603 column = colSel.getMax();
1606 if(viewport.getSelectionGroup()!=null)
1607 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
1609 seqs = viewport.alignment.getSequencesArray();
1612 TrimRegionCommand trimRegion;
1615 trimRegion = new TrimRegionCommand("Remove Left",
1616 TrimRegionCommand.TRIM_LEFT,
1621 viewport.selectionGroup);
1622 viewport.setStartRes(0);
1626 trimRegion = new TrimRegionCommand("Remove Right",
1627 TrimRegionCommand.TRIM_RIGHT,
1632 viewport.selectionGroup);
1635 statusBar.setText("Removed "+trimRegion.getSize()+" columns.");
1638 addHistoryItem(trimRegion);
1640 Vector groups = viewport.alignment.getGroups();
1642 for (int i = 0; i < groups.size(); i++)
1644 SequenceGroup sg = (SequenceGroup) groups.get(i);
1646 if ( (trimLeft && !sg.adjustForRemoveLeft(column))
1647 || (!trimLeft && !sg.adjustForRemoveRight(column)))
1649 viewport.alignment.deleteGroup(sg);
1653 viewport.firePropertyChange("alignment", null,
1654 viewport.getAlignment().getSequences());
1661 * @param e DOCUMENT ME!
1663 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
1665 int start = 0, end = viewport.alignment.getWidth()-1;
1668 if (viewport.getSelectionGroup() != null)
1670 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
1671 start = viewport.getSelectionGroup().getStartRes();
1672 end = viewport.getSelectionGroup().getEndRes();
1675 seqs = viewport.alignment.getSequencesArray();
1678 RemoveGapColCommand removeGapCols =
1679 new RemoveGapColCommand("Remove Gapped Columns",
1682 viewport.getGapCharacter());
1684 addHistoryItem(removeGapCols);
1686 statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");
1688 //This is to maintain viewport position on first residue
1690 SequenceI seq = viewport.alignment.getSequenceAt(0);
1691 int startRes = seq.findPosition(viewport.startRes);
1692 // ShiftList shifts;
1693 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
1694 // edit.alColumnChanges=shifts.getInverse();
1695 // if (viewport.hasHiddenColumns)
1696 // viewport.getColumnSelection().compensateForEdits(shifts);
1697 viewport.setStartRes(seq.findIndex(startRes)-1);
1698 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1705 * @param e DOCUMENT ME!
1707 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
1709 int start = 0, end = viewport.alignment.getWidth()-1;
1712 if (viewport.getSelectionGroup() != null)
1714 seqs = viewport.getSelectionGroup().getSequencesAsArray(true);
1715 start = viewport.getSelectionGroup().getStartRes();
1716 end = viewport.getSelectionGroup().getEndRes();
1719 seqs = viewport.alignment.getSequencesArray();
1721 //This is to maintain viewport position on first residue
1723 SequenceI seq = viewport.alignment.getSequenceAt(0);
1724 int startRes = seq.findPosition(viewport.startRes);
1726 addHistoryItem(new RemoveGapsCommand("Remove Gaps",
1729 viewport.getGapCharacter()));
1731 viewport.setStartRes(seq.findIndex(startRes)-1);
1733 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
1740 * @param e DOCUMENT ME!
1742 public void padGapsMenuitem_actionPerformed(ActionEvent e)
1744 viewport.padGaps = padGapsMenuitem.isSelected();
1746 viewport.firePropertyChange("alignment",
1748 viewport.getAlignment().getSequences());
1754 * @param e DOCUMENT ME!
1756 public void findMenuItem_actionPerformed(ActionEvent e)
1761 public void newView_actionPerformed(ActionEvent e)
1763 AlignmentPanel newap =
1764 new Jalview2XML().copyAlignPanel(alignPanel, true);
1766 if (viewport.viewName == null)
1767 viewport.viewName = "Original";
1769 newap.av.historyList = viewport.historyList;
1770 newap.av.redoList = viewport.redoList;
1772 int index = Desktop.getViewCount(viewport.getSequenceSetId());
1773 String newViewName = "View " +index;
1775 Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
1776 Vector existingNames = new Vector();
1777 for(int i=0; i<comps.size(); i++)
1779 if(comps.elementAt(i) instanceof AlignmentPanel)
1781 AlignmentPanel ap = (AlignmentPanel)comps.elementAt(i);
1782 if(!existingNames.contains(ap.av.viewName))
1783 existingNames.addElement(ap.av.viewName);
1787 while(existingNames.contains(newViewName))
1789 newViewName = "View "+ (++index);
1792 newap.av.viewName = newViewName;
1794 addAlignmentPanel(newap, false);
1796 if(alignPanels.size()==2)
1798 viewport.gatherViewsHere = true;
1800 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
1803 public void expandViews_actionPerformed(ActionEvent e)
1805 Desktop.instance.explodeViews(this);
1808 public void gatherViews_actionPerformed(ActionEvent e)
1810 Desktop.instance.gatherViews(this);
1818 * @param e DOCUMENT ME!
1820 public void font_actionPerformed(ActionEvent e)
1822 new FontChooser(alignPanel);
1829 * @param e DOCUMENT ME!
1831 protected void seqLimit_actionPerformed(ActionEvent e)
1833 viewport.setShowJVSuffix(seqLimits.isSelected());
1835 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
1836 alignPanel.repaint();
1839 public void idRightAlign_actionPerformed(ActionEvent e)
1841 viewport.rightAlignIds = idRightAlign.isSelected();
1842 alignPanel.repaint();
1850 * @param e DOCUMENT ME!
1852 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
1854 viewport.setColourText(colourTextMenuItem.isSelected());
1855 alignPanel.repaint();
1861 * @param e DOCUMENT ME!
1863 public void wrapMenuItem_actionPerformed(ActionEvent e)
1865 scaleAbove.setVisible(wrapMenuItem.isSelected());
1866 scaleLeft.setVisible(wrapMenuItem.isSelected());
1867 scaleRight.setVisible(wrapMenuItem.isSelected());
1868 viewport.setWrapAlignment(wrapMenuItem.isSelected());
1869 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
1872 public void showAllSeqs_actionPerformed(ActionEvent e)
1874 viewport.showAllHiddenSeqs();
1877 public void showAllColumns_actionPerformed(ActionEvent e)
1879 viewport.showAllHiddenColumns();
1883 public void hideSelSequences_actionPerformed(ActionEvent e)
1885 viewport.hideAllSelectedSeqs();
1886 alignPanel.repaint();
1889 public void hideSelColumns_actionPerformed(ActionEvent e)
1891 viewport.hideSelectedColumns();
1892 alignPanel.repaint();
1895 public void hiddenMarkers_actionPerformed(ActionEvent e)
1897 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
1904 * @param e DOCUMENT ME!
1906 protected void scaleAbove_actionPerformed(ActionEvent e)
1908 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
1909 alignPanel.repaint();
1915 * @param e DOCUMENT ME!
1917 protected void scaleLeft_actionPerformed(ActionEvent e)
1919 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
1920 alignPanel.repaint();
1926 * @param e DOCUMENT ME!
1928 protected void scaleRight_actionPerformed(ActionEvent e)
1930 viewport.setScaleRightWrapped(scaleRight.isSelected());
1931 alignPanel.repaint();
1937 * @param e DOCUMENT ME!
1939 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
1941 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
1942 alignPanel.repaint();
1948 * @param e DOCUMENT ME!
1950 public void viewTextMenuItem_actionPerformed(ActionEvent e)
1952 viewport.setShowText(viewTextMenuItem.isSelected());
1953 alignPanel.repaint();
1959 * @param e DOCUMENT ME!
1961 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1963 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
1964 alignPanel.repaint();
1968 public FeatureSettings featureSettings;
1969 public void featureSettings_actionPerformed(ActionEvent e)
1971 if(featureSettings !=null )
1973 featureSettings.close();
1974 featureSettings = null;
1976 featureSettings = new FeatureSettings(this);
1982 * @param evt DOCUMENT ME!
1984 public void showSeqFeatures_actionPerformed(ActionEvent evt)
1986 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
1987 alignPanel.repaint();
1988 if (alignPanel.getOverviewPanel() != null)
1990 alignPanel.getOverviewPanel().updateOverviewImage();
1997 * @param e DOCUMENT ME!
1999 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2001 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2002 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2008 * @param e DOCUMENT ME!
2010 public void overviewMenuItem_actionPerformed(ActionEvent e)
2012 if (alignPanel.overviewPanel != null)
2017 JInternalFrame frame = new JInternalFrame();
2018 OverviewPanel overview = new OverviewPanel(alignPanel);
2019 frame.setContentPane(overview);
2020 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2021 frame.getWidth(), frame.getHeight());
2023 frame.setLayer(JLayeredPane.PALETTE_LAYER);
2024 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2026 public void internalFrameClosed(
2027 javax.swing.event.InternalFrameEvent evt)
2029 alignPanel.setOverviewPanel(null);
2034 alignPanel.setOverviewPanel(overview);
2037 public void textColour_actionPerformed(ActionEvent e)
2039 new TextColourChooser().chooseColour(alignPanel, null);
2045 * @param e DOCUMENT ME!
2047 protected void noColourmenuItem_actionPerformed(ActionEvent e)
2055 * @param e DOCUMENT ME!
2057 public void clustalColour_actionPerformed(ActionEvent e)
2059 changeColour(new ClustalxColourScheme(
2060 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
2066 * @param e DOCUMENT ME!
2068 public void zappoColour_actionPerformed(ActionEvent e)
2070 changeColour(new ZappoColourScheme());
2076 * @param e DOCUMENT ME!
2078 public void taylorColour_actionPerformed(ActionEvent e)
2080 changeColour(new TaylorColourScheme());
2086 * @param e DOCUMENT ME!
2088 public void hydrophobicityColour_actionPerformed(ActionEvent e)
2090 changeColour(new HydrophobicColourScheme());
2096 * @param e DOCUMENT ME!
2098 public void helixColour_actionPerformed(ActionEvent e)
2100 changeColour(new HelixColourScheme());
2106 * @param e DOCUMENT ME!
2108 public void strandColour_actionPerformed(ActionEvent e)
2110 changeColour(new StrandColourScheme());
2116 * @param e DOCUMENT ME!
2118 public void turnColour_actionPerformed(ActionEvent e)
2120 changeColour(new TurnColourScheme());
2126 * @param e DOCUMENT ME!
2128 public void buriedColour_actionPerformed(ActionEvent e)
2130 changeColour(new BuriedColourScheme());
2136 * @param e DOCUMENT ME!
2138 public void nucleotideColour_actionPerformed(ActionEvent e)
2140 changeColour(new NucleotideColourScheme());
2143 public void annotationColour_actionPerformed(ActionEvent e)
2145 new AnnotationColourChooser(viewport, alignPanel);
2152 * @param e DOCUMENT ME!
2154 protected void applyToAllGroups_actionPerformed(ActionEvent e)
2156 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
2162 * @param cs DOCUMENT ME!
2164 public void changeColour(ColourSchemeI cs)
2170 if (viewport.getAbovePIDThreshold())
2172 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2175 cs.setThreshold(threshold,
2176 viewport.getIgnoreGapsConsensus());
2178 viewport.setGlobalColourScheme(cs);
2182 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2185 if (viewport.getConservationSelected())
2188 Alignment al = (Alignment) viewport.alignment;
2189 Conservation c = new Conservation("All",
2190 ResidueProperties.propHash, 3,
2191 al.getSequences(), 0,
2195 c.verdict(false, viewport.ConsPercGaps);
2197 cs.setConservation(c);
2199 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
2204 cs.setConservation(null);
2207 cs.setConsensus(viewport.hconsensus);
2210 viewport.setGlobalColourScheme(cs);
2212 if (viewport.getColourAppliesToAllGroups())
2214 Vector groups = viewport.alignment.getGroups();
2216 for (int i = 0; i < groups.size(); i++)
2218 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2226 if (cs instanceof ClustalxColourScheme)
2228 sg.cs = new ClustalxColourScheme(
2229 sg.getSequences(true), sg.getWidth());
2231 else if (cs instanceof UserColourScheme)
2233 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
2239 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2241 catch (Exception ex)
2246 if (viewport.getAbovePIDThreshold()
2247 || cs instanceof PIDColourScheme
2248 || cs instanceof Blosum62ColourScheme)
2250 sg.cs.setThreshold(threshold,
2251 viewport.getIgnoreGapsConsensus());
2253 sg.cs.setConsensus(AAFrequency.calculate(
2254 sg.getSequences(true), sg.getStartRes(),
2258 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2261 if (viewport.getConservationSelected())
2263 Conservation c = new Conservation("Group",
2264 ResidueProperties.propHash, 3,
2265 sg.getSequences(true),
2269 c.verdict(false, viewport.ConsPercGaps);
2270 sg.cs.setConservation(c);
2273 sg.cs.setConservation(null);
2277 if (alignPanel.getOverviewPanel() != null)
2279 alignPanel.getOverviewPanel().updateOverviewImage();
2282 alignPanel.repaint();
2288 * @param e DOCUMENT ME!
2290 protected void modifyPID_actionPerformed(ActionEvent e)
2292 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
2294 SliderPanel.setPIDSliderSource(alignPanel,
2295 viewport.getGlobalColourScheme(),
2297 SliderPanel.showPIDSlider();
2304 * @param e DOCUMENT ME!
2306 protected void modifyConservation_actionPerformed(ActionEvent e)
2308 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
2310 SliderPanel.setConservationSlider(alignPanel,
2311 viewport.globalColourScheme,
2313 SliderPanel.showConservationSlider();
2320 * @param e DOCUMENT ME!
2322 protected void conservationMenuItem_actionPerformed(ActionEvent e)
2324 viewport.setConservationSelected(conservationMenuItem.isSelected());
2326 viewport.setAbovePIDThreshold(false);
2327 abovePIDThreshold.setSelected(false);
2329 changeColour(viewport.getGlobalColourScheme());
2331 modifyConservation_actionPerformed(null);
2337 * @param e DOCUMENT ME!
2339 public void abovePIDThreshold_actionPerformed(ActionEvent e)
2341 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
2343 conservationMenuItem.setSelected(false);
2344 viewport.setConservationSelected(false);
2346 changeColour(viewport.getGlobalColourScheme());
2348 modifyPID_actionPerformed(null);
2354 * @param e DOCUMENT ME!
2356 public void userDefinedColour_actionPerformed(ActionEvent e)
2358 if (e.getActionCommand().equals("User Defined..."))
2360 new UserDefinedColours(alignPanel, null);
2364 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
2365 getUserColourSchemes().get(e.getActionCommand());
2371 public void updateUserColourMenu()
2374 Component[] menuItems = colourMenu.getMenuComponents();
2375 int i, iSize = menuItems.length;
2376 for (i = 0; i < iSize; i++)
2378 if (menuItems[i].getName() != null &&
2379 menuItems[i].getName().equals("USER_DEFINED"))
2381 colourMenu.remove(menuItems[i]);
2385 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
2387 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
2388 getUserColourSchemes().keys();
2390 while (userColours.hasMoreElements())
2392 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
2393 nextElement().toString());
2394 radioItem.setName("USER_DEFINED");
2395 radioItem.addMouseListener(new MouseAdapter()
2397 public void mousePressed(MouseEvent evt)
2399 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
2401 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
2403 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
2404 "Remove from default list?",
2405 "Remove user defined colour",
2406 JOptionPane.YES_NO_OPTION);
2407 if(option == JOptionPane.YES_OPTION)
2409 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
2410 colourMenu.remove(radioItem);
2413 radioItem.addActionListener(new ActionListener()
2415 public void actionPerformed(ActionEvent evt)
2417 userDefinedColour_actionPerformed(evt);
2423 radioItem.addActionListener(new ActionListener()
2425 public void actionPerformed(ActionEvent evt)
2427 userDefinedColour_actionPerformed(evt);
2431 colourMenu.insert(radioItem, 15);
2432 colours.add(radioItem);
2440 * @param e DOCUMENT ME!
2442 public void PIDColour_actionPerformed(ActionEvent e)
2444 changeColour(new PIDColourScheme());
2450 * @param e DOCUMENT ME!
2452 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
2454 changeColour(new Blosum62ColourScheme());
2460 * @param e DOCUMENT ME!
2462 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
2464 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2465 AlignmentSorter.sortByPID(viewport.getAlignment(),
2466 viewport.getAlignment().getSequenceAt(0));
2467 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));
2468 alignPanel.repaint();
2474 * @param e DOCUMENT ME!
2476 public void sortIDMenuItem_actionPerformed(ActionEvent e)
2478 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2479 AlignmentSorter.sortByID(viewport.getAlignment());
2480 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
2481 alignPanel.repaint();
2487 * @param e DOCUMENT ME!
2489 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
2491 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2492 AlignmentSorter.sortByGroup(viewport.getAlignment());
2493 addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.alignment));
2495 alignPanel.repaint();
2501 * @param e DOCUMENT ME!
2503 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
2505 new RedundancyPanel(alignPanel, this);
2512 * @param e DOCUMENT ME!
2514 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
2516 if ( (viewport.getSelectionGroup() == null) ||
2517 (viewport.getSelectionGroup().getSize(false) < 2))
2519 JOptionPane.showInternalMessageDialog(this,
2520 "You must select at least 2 sequences.",
2521 "Invalid Selection",
2522 JOptionPane.WARNING_MESSAGE);
2526 JInternalFrame frame = new JInternalFrame();
2527 frame.setContentPane(new PairwiseAlignPanel(viewport));
2528 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
2535 * @param e DOCUMENT ME!
2537 public void PCAMenuItem_actionPerformed(ActionEvent e)
2539 if ( ( (viewport.getSelectionGroup() != null) &&
2540 (viewport.getSelectionGroup().getSize(false) < 4) &&
2541 (viewport.getSelectionGroup().getSize(false) > 0)) ||
2542 (viewport.getAlignment().getHeight() < 4))
2544 JOptionPane.showInternalMessageDialog(this,
2545 "Principal component analysis must take\n" +
2546 "at least 4 input sequences.",
2547 "Sequence selection insufficient",
2548 JOptionPane.WARNING_MESSAGE);
2553 new PCAPanel(alignPanel);
2557 public void autoCalculate_actionPerformed(ActionEvent e)
2559 viewport.autoCalculateConsensus = autoCalculate.isSelected();
2560 if(viewport.autoCalculateConsensus)
2562 viewport.firePropertyChange("alignment",
2564 viewport.getAlignment().getSequences());
2572 * @param e DOCUMENT ME!
2574 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
2576 NewTreePanel("AV", "PID", "Average distance tree using PID");
2582 * @param e DOCUMENT ME!
2584 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
2586 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2592 * @param e DOCUMENT ME!
2594 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2596 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2602 * @param e DOCUMENT ME!
2604 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
2606 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2612 * @param type DOCUMENT ME!
2613 * @param pwType DOCUMENT ME!
2614 * @param title DOCUMENT ME!
2616 void NewTreePanel(String type, String pwType, String title)
2620 if (viewport.getSelectionGroup() != null) {
2621 if (viewport.getSelectionGroup().getSize(false) < 3) {
2622 JOptionPane.showMessageDialog(Desktop.desktop,
2623 "You need to have more than two sequences selected to build a tree!",
2624 "Not enough sequences",
2625 JOptionPane.WARNING_MESSAGE);
2630 SequenceGroup sg = viewport.getSelectionGroup();
2632 /* Decide if the selection is a column region */
2633 while (s < sg.getSize(false))
2635 if ( ( (SequenceI) sg.getSequences(false).elementAt(s++)).getLength() <
2638 JOptionPane.showMessageDialog(Desktop.desktop,
2639 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
2640 "Try using the Pad function in the edit menu,\n" +
2641 "or one of the multiple sequence alignment web services.",
2642 "Sequences in selection are not aligned",
2643 JOptionPane.WARNING_MESSAGE);
2649 title = title + " on region";
2650 tp = new TreePanel(alignPanel, type, pwType);
2654 //are the sequences aligned?
2655 if (!viewport.alignment.isAligned())
2657 JOptionPane.showMessageDialog(Desktop.desktop,
2658 "The sequences must be aligned before creating a tree.\n" +
2659 "Try using the Pad function in the edit menu,\n" +
2660 "or one of the multiple sequence alignment web services.",
2661 "Sequences not aligned",
2662 JOptionPane.WARNING_MESSAGE);
2667 if(viewport.alignment.getHeight()<2)
2670 tp = new TreePanel(alignPanel, type, pwType);
2675 if(viewport.viewName!=null)
2676 title+= viewport.viewName+" of ";
2678 title += this.title;
2680 Desktop.addInternalFrame(tp, title, 600, 500);
2686 * @param title DOCUMENT ME!
2687 * @param order DOCUMENT ME!
2689 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
2691 final JMenuItem item = new JMenuItem("by " + title);
2693 item.addActionListener(new java.awt.event.ActionListener()
2695 public void actionPerformed(ActionEvent e)
2697 SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
2699 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
2700 AlignmentSorter.sortBy(viewport.getAlignment(), order);
2702 addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport.alignment));
2704 alignPanel.repaint();
2710 * Maintain the Order by->Displayed Tree menu.
2711 * Creates a new menu item for a TreePanel with an appropriate
2712 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
2713 * to remove the menu item when the treePanel is closed, and adjust
2714 * the tree leaf to sequence mapping when the alignment is modified.
2715 * @param treePanel Displayed tree window.
2716 * @param title SortBy menu item title.
2718 public void buildTreeMenu()
2720 sortByTreeMenu.removeAll();
2722 Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
2723 Vector treePanels = new Vector();
2724 int i, iSize = comps.size();
2725 for(i=0; i<iSize; i++)
2727 if(comps.elementAt(i) instanceof TreePanel)
2729 treePanels.add(comps.elementAt(i));
2733 iSize = treePanels.size();
2737 sortByTreeMenu.setVisible(false);
2741 sortByTreeMenu.setVisible(true);
2743 for(i=0; i<treePanels.size(); i++)
2745 TreePanel tp = (TreePanel)treePanels.elementAt(i);
2746 final JMenuItem item = new JMenuItem(tp.getTitle());
2747 final NJTree tree = ((TreePanel)treePanels.elementAt(i)).getTree();
2748 item.addActionListener(new java.awt.event.ActionListener()
2750 public void actionPerformed(ActionEvent e)
2752 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2753 AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
2755 addHistoryItem(new OrderCommand("Tree Sort",
2757 viewport.alignment));
2759 alignPanel.repaint();
2763 sortByTreeMenu.add(item);
2768 * Work out whether the whole set of sequences
2769 * or just the selected set will be submitted for multiple alignment.
2772 private jalview.datamodel.AlignmentView gatherSequencesForAlignment()
2774 // Now, check we have enough sequences
2775 AlignmentView msa = null;
2777 if ( (viewport.getSelectionGroup() != null) &&
2778 (viewport.getSelectionGroup().getSize(false) > 1))
2780 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
2781 /*SequenceGroup seqs = viewport.getSelectionGroup();
2783 msa = new SequenceI[sz = seqs.getSize(false)];
2785 for (int i = 0; i < sz; i++)
2787 msa[i] = (SequenceI) seqs.getSequenceAt(i);
2789 msa = viewport.getAlignmentView(true);
2793 /*Vector seqs = viewport.getAlignment().getSequences();
2795 if (seqs.size() > 1)
2797 msa = new SequenceI[seqs.size()];
2799 for (int i = 0; i < seqs.size(); i++)
2801 msa[i] = (SequenceI) seqs.elementAt(i);
2804 msa = viewport.getAlignmentView(false);
2810 * Decides what is submitted to a secondary structure prediction service,
2811 * the currently selected sequence, or the currently selected alignment
2812 * (where the first sequence in the set is the one that the prediction
2815 AlignmentView gatherSeqOrMsaForSecStrPrediction()
2817 AlignmentView seqs = null;
2819 if ( (viewport.getSelectionGroup() != null) &&
2820 (viewport.getSelectionGroup().getSize(false) > 0))
2822 seqs = viewport.getAlignmentView(true);
2826 seqs = viewport.getAlignmentView(false);
2828 // limit sequences - JBPNote in future - could spawn multiple prediction jobs
2829 // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment.
2830 if (!viewport.alignment.isAligned())
2832 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] } );
2839 * @param e DOCUMENT ME!
2841 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
2843 // Pick the tree file
2844 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
2847 chooser.setFileView(new JalviewFileView());
2848 chooser.setDialogTitle("Select a newick-like tree file");
2849 chooser.setToolTipText("Load a tree file");
2851 int value = chooser.showOpenDialog(null);
2853 if (value == JalviewFileChooser.APPROVE_OPTION)
2855 String choice = chooser.getSelectedFile().getPath();
2856 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
2860 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
2862 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
2864 catch (Exception ex)
2866 JOptionPane.showMessageDialog(Desktop.desktop,
2867 "Problem reading tree file",
2869 JOptionPane.WARNING_MESSAGE);
2870 ex.printStackTrace();
2876 public TreePanel ShowNewickTree(NewickFile nf, String title)
2878 return ShowNewickTree(nf,title,600,500,4,5);
2880 public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input)
2882 return ShowNewickTree(nf,title, input, 600,500,4,5);
2884 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y) {
2885 return ShowNewickTree(nf, title, null, w, h, x, y);
2888 * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
2890 * @param nf the tree
2891 * @param title tree viewer title
2892 * @param input Associated alignment input data (or null)
2897 * @return TreePanel handle
2899 public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input, int w,int h,int x, int y) {
2900 TreePanel tp = null;
2906 if (nf.getTree() != null)
2908 tp = new TreePanel(alignPanel,
2916 tp.setLocation(x,y);
2919 Desktop.addInternalFrame(tp, title, w, h);
2922 catch (Exception ex)
2924 ex.printStackTrace();
2935 PrinterJob printJob = PrinterJob.getPrinterJob();
2936 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
2937 printJob.setPrintable(alignPanel, pf);
2939 if (printJob.printDialog())
2945 catch (Exception PrintException)
2947 PrintException.printStackTrace();
2954 * Generates menu items and listener event actions for web service clients
2957 public void BuildWebServiceMenu()
2959 if ( (Discoverer.services != null)
2960 && (Discoverer.services.size() > 0))
2962 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
2963 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
2964 Vector wsmenu = new Vector();
2965 final AlignFrame af = this;
2968 // Add any Multiple Sequence Alignment Services
2969 final JMenu msawsmenu = new JMenu("Alignment");
2970 for (int i = 0, j = msaws.size(); i < j; i++)
2972 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
2974 final JMenuItem method = new JMenuItem(sh.getName());
2975 method.addActionListener(new ActionListener()
2977 public void actionPerformed(ActionEvent e)
2979 AlignmentView msa = gatherSequencesForAlignment();
2980 new jalview.ws.MsaWSClient(sh, title, msa,
2981 false, true, viewport.getAlignment().getDataset(), af);
2986 msawsmenu.add(method);
2987 // Deal with services that we know accept partial alignments.
2988 if (sh.getName().indexOf("lustal") > -1)
2990 // We know that ClustalWS can accept partial alignments for refinement.
2991 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
2992 methodR.addActionListener(new ActionListener()
2994 public void actionPerformed(ActionEvent e)
2996 AlignmentView msa = gatherSequencesForAlignment();
2997 new jalview.ws.MsaWSClient(sh, title, msa,
2998 true, true, viewport.getAlignment().getDataset(), af);
3003 msawsmenu.add(methodR);
3007 wsmenu.add(msawsmenu);
3009 if (secstrpr != null)
3011 // Add any secondary structure prediction services
3012 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
3013 for (int i = 0, j = secstrpr.size(); i < j; i++)
3015 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
3017 final JMenuItem method = new JMenuItem(sh.getName());
3018 method.addActionListener(new ActionListener()
3020 public void actionPerformed(ActionEvent e)
3022 AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
3023 if (msa.getSequences().length == 1)
3025 // Single Sequence prediction
3026 new jalview.ws.JPredClient(sh, title, false, msa, af, true);
3030 if (msa.getSequences().length > 1)
3032 // Sequence profile based prediction
3033 new jalview.ws.JPredClient(sh,
3034 title, true, msa, af, true);
3039 secstrmenu.add(method);
3041 wsmenu.add(secstrmenu);
3043 this.webService.removeAll();
3044 for (int i = 0, j = wsmenu.size(); i < j; i++)
3046 webService.add( (JMenu) wsmenu.get(i));
3051 this.webService.removeAll();
3052 this.webService.add(this.webServiceNoServices);
3054 // TODO: add in rediscovery function
3055 // TODO: reduce code redundancy.
3056 // TODO: group services by location as well as function.
3059 /* public void vamsasStore_actionPerformed(ActionEvent e)
3061 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
3062 getProperty("LAST_DIRECTORY"));
3064 chooser.setFileView(new JalviewFileView());
3065 chooser.setDialogTitle("Export to Vamsas file");
3066 chooser.setToolTipText("Export");
3068 int value = chooser.showSaveDialog(this);
3070 if (value == JalviewFileChooser.APPROVE_OPTION)
3072 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
3073 //vs.store(chooser.getSelectedFile().getAbsolutePath() );
3074 vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
3081 public void showTranslation_actionPerformed(ActionEvent e)
3083 SequenceI [] selection = viewport.getSelectionAsNewSequence();
3084 String [] seqstring = viewport.getViewAsString(true);
3086 int s, sSize = selection.length;
3087 SequenceI [] newSeq = new SequenceI[sSize];
3090 StringBuffer protein;
3092 for(s=0; s<sSize; s++)
3094 protein = new StringBuffer();
3095 seq = AlignSeq.extractGaps("-. ", seqstring[s]);
3096 resSize = seq.length();
3097 resSize -= resSize%3;
3099 for(res = 0; res < resSize; res+=3)
3101 String codon = seq.substring(res, res+3);
3102 codon = codon.replace('U', 'T');
3103 String aa = ResidueProperties.codonTranslate(codon);
3105 protein.append(viewport.getGapCharacter());
3106 else if(aa.equals("STOP"))
3107 protein.append("X");
3109 protein.append( aa );
3111 newSeq[s] = new Sequence(selection[s].getName(),
3112 protein.toString());
3116 AlignmentI al = new Alignment(newSeq);
3117 al.setDataset(null);
3120 ////////////////////////////////
3121 // Copy annotations across
3122 jalview.datamodel.AlignmentAnnotation[] annotations
3123 = viewport.alignment.getAlignmentAnnotation();
3125 if(annotations!=null)
3127 for (int i = 0; i < annotations.length; i++)
3129 if (annotations[i].label.equals("Quality") ||
3130 annotations[i].label.equals("Conservation") ||
3131 annotations[i].label.equals("Consensus"))
3136 aSize = viewport.alignment.getWidth() / 3;
3137 jalview.datamodel.Annotation[] anots =
3138 new jalview.datamodel.Annotation[aSize];
3140 for (a = 0; a < viewport.alignment.getWidth(); a++)
3142 if (annotations[i].annotations[a] == null
3143 || annotations[i].annotations[a] == null)
3146 anots[a / 3] = new Annotation(
3147 annotations[i].annotations[a].displayCharacter,
3148 annotations[i].annotations[a].description,
3149 annotations[i].annotations[a].secondaryStructure,
3150 annotations[i].annotations[a].value,
3151 annotations[i].annotations[a].colour);
3154 jalview.datamodel.AlignmentAnnotation aa
3155 = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
3156 annotations[i].description, anots);
3157 al.addAnnotation(aa);
3161 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
3162 Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
3174 * @param String DOCUMENT ME!
3176 public boolean parseFeaturesFile(String file, String type)
3178 boolean featuresFile = false;
3180 featuresFile = new FeaturesFile(file, type).parse(viewport.alignment.getDataset(),
3181 alignPanel.seqPanel.seqCanvas.
3182 getFeatureRenderer().featureColours,
3187 ex.printStackTrace();
3192 viewport.showSequenceFeatures = true;
3193 showSeqFeatures.setSelected(true);
3194 alignPanel.repaint();
3197 return featuresFile;
3200 public void dragEnter(DropTargetDragEvent evt)
3203 public void dragExit(DropTargetEvent evt)
3206 public void dragOver(DropTargetDragEvent evt)
3209 public void dropActionChanged(DropTargetDragEvent evt)
3212 public void drop(DropTargetDropEvent evt)
3214 Transferable t = evt.getTransferable();
3215 java.util.List files = null;
3219 DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
3220 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
3222 //Works on Windows and MacOSX
3223 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3224 files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
3226 else if (t.isDataFlavorSupported(uriListFlavor))
3228 // This is used by Unix drag system
3229 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
3230 String data = (String) t.getTransferData(uriListFlavor);
3231 files = new java.util.ArrayList(1);
3232 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
3235 st.hasMoreTokens(); )
3237 String s = st.nextToken();
3238 if (s.startsWith("#"))
3240 // the line is a comment (as per the RFC 2483)
3244 java.net.URI uri = new java.net.URI(s);
3245 java.io.File file = new java.io.File(uri);
3252 e.printStackTrace();
3259 for (int i = 0; i < files.size(); i++)
3261 loadJalviewDataFile(files.get(i).toString());
3264 catch (Exception ex)
3266 ex.printStackTrace();
3271 // This method will attempt to load a "dropped" file first by testing
3272 // whether its and Annotation file, then features file. If both are
3273 // false then the user may have dropped an alignment file onto this
3275 public void loadJalviewDataFile(String file)
3278 String protocol = "File";
3280 if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
3285 boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
3290 boolean isGroupsFile = parseFeaturesFile(file,protocol);
3293 String format = new IdentifyFile().Identify(file, protocol);
3295 if(format.equalsIgnoreCase("JnetFile"))
3297 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
3299 new JnetAnnotationMaker().add_annotation(predictions,
3300 viewport.getAlignment(),
3302 alignPanel.adjustAnnotationHeight();
3303 alignPanel.repaint();
3306 new FileLoader().LoadFile(viewport, file, protocol, format);
3312 alignPanel.adjustAnnotationHeight();
3315 }catch(Exception ex)
3317 ex.printStackTrace();
3321 public void tabSelectionChanged(int index)
3325 alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
3326 viewport = alignPanel.av;
3327 setMenusFromViewport(viewport);
3331 public void tabbedPane_mousePressed(MouseEvent e)
3333 if(SwingUtilities.isRightMouseButton(e))
3335 String reply = JOptionPane.showInternalInputDialog(this,
3338 JOptionPane.QUESTION_MESSAGE);
3342 viewport.viewName = reply;
3343 tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
3349 public AlignViewport getCurrentView()