1 /********************
\r
2 * 2004 Jalview Reengineered
\r
12 package jalview.gui;
\r
14 import jalview.jbgui.GAlignFrame;
\r
15 import jalview.schemes.*;
\r
16 import jalview.datamodel.*;
\r
17 import jalview.analysis.*;
\r
18 import jalview.io.*;
\r
19 import jalview.ws.*;
\r
21 import java.awt.event.*;
\r
22 import java.awt.print.*;
\r
23 import javax.swing.*;
\r
24 import javax.swing.event.*;
\r
26 import java.awt.datatransfer.*;
\r
29 public class AlignFrame extends GAlignFrame
\r
31 final AlignmentPanel alignPanel;
\r
32 final AlignViewport viewport;
\r
33 public AlignFrame(AlignmentI al)
\r
36 viewport = new AlignViewport(al,true,true,true,false);
\r
37 alignPanel = new AlignmentPanel(this, viewport);
\r
38 getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
\r
39 fontNameMenuItem.setText(viewport.getFont().getName());
\r
40 fontSizeMenuItem.setText(viewport.getFont().getSize()+"");
\r
42 addInternalFrameListener(new InternalFrameAdapter()
\r
44 public void internalFrameActivated(InternalFrameEvent evt)
\r
46 javax.swing.SwingUtilities.invokeLater(new Runnable()
\r
49 { alignPanel.requestFocus(); }
\r
55 AlignmentUtil.fetchSequenceFeatures(al, alignPanel);
\r
58 protected void saveAs_actionPerformed(ActionEvent e)
\r
60 JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
\r
61 chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
\r
62 chooser.setToolTipText("Save");
\r
63 int value = chooser.showSaveDialog(this);
\r
64 if(value == JFileChooser.APPROVE_OPTION)
\r
66 String choice = chooser.getSelectedFile().getPath();
\r
67 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
68 String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
\r
70 java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
\r
71 out.println(output);
\r
74 catch(Exception ex){}
\r
79 protected void outputText_actionPerformed(ActionEvent e)
\r
81 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
\r
82 JInternalFrame frame = new JInternalFrame();
\r
83 cap.formatForOutput();
\r
84 frame.setContentPane(cap);
\r
85 Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
\r
86 cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
\r
89 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
91 HTMLOutput htmlOutput = new HTMLOutput(viewport);
\r
95 public void printMenuItem_actionPerformed(ActionEvent e)
\r
97 //Putting in a thread avoids Swing painting problems
\r
98 PrintThread thread = new PrintThread();
\r
102 class PrintThread extends Thread
\r
106 PrinterJob printJob = PrinterJob.getPrinterJob();
\r
107 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
\r
108 printJob.setPrintable(alignPanel, pf);
\r
109 if (printJob.printDialog())
\r
115 catch (Exception PrintException)
\r
117 PrintException.printStackTrace();
\r
127 public void closeMenuItem_actionPerformed(ActionEvent e)
\r
130 this.setClosed(true);
\r
131 }catch(Exception ex){}
\r
134 ArrayList historyList = new ArrayList();
\r
135 ArrayList redoList = new ArrayList();
\r
137 void updateEditMenuBar()
\r
139 if(historyList.size()>0)
\r
141 undoMenuItem.setEnabled(true);
\r
142 Object [] history = (Object[])historyList.get(0);
\r
143 undoMenuItem.setText("Undo "+history[0]);
\r
147 undoMenuItem.setEnabled(false);
\r
148 undoMenuItem.setText("Undo");
\r
151 if(redoList.size()>0)
\r
153 redoMenuItem.setEnabled(true);
\r
154 Object [] history = (Object[])redoList.get(0);
\r
155 redoMenuItem.setText("Redo "+history[0]);
\r
159 redoMenuItem.setEnabled(false);
\r
160 redoMenuItem.setText("Redo");
\r
164 public void addHistoryItem(String type)
\r
166 // must make sure we add new sequence objects her, not refs to the existing sequences
\r
168 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
\r
169 for(int i=0; i<viewport.getAlignment().getHeight(); i++)
\r
171 seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
\r
172 viewport.getAlignment().getSequenceAt(i).getSequence());
\r
175 historyList.add(0, new Object[]{type, seq} );
\r
176 updateEditMenuBar();
\r
179 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
181 Object [] history = (Object[])historyList.remove(0);
\r
182 // add the redo state before continuing!!
\r
183 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
\r
184 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
\r
186 seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
\r
187 viewport.getAlignment().getSequenceAt(i).
\r
192 redoList.add(0, new Object[] {history[0], seq});
\r
194 seq = (SequenceI[]) history[1];
\r
195 viewport.setAlignment( new Alignment(seq) );
\r
196 updateEditMenuBar();
\r
197 alignPanel.RefreshPanels();
\r
200 public void moveSelectedSequences(boolean up)
\r
202 SequenceGroup sg = viewport.getRubberbandGroup();
\r
208 for (int i = 1; i < viewport.alignment.getHeight(); i++)
\r
210 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
211 if (!sg.sequences.contains(seq))
\r
214 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
\r
215 if (sg.sequences.contains(temp))
\r
218 viewport.alignment.getSequences().setElementAt(temp, i);
\r
219 viewport.alignment.getSequences().setElementAt(seq, i - 1);
\r
224 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
\r
226 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
227 if (!sg.sequences.contains(seq))
\r
230 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
\r
231 if (sg.sequences.contains(temp))
\r
234 viewport.alignment.getSequences().setElementAt(temp, i);
\r
235 viewport.alignment.getSequences().setElementAt(seq, i + 1);
\r
239 alignPanel.RefreshPanels();
\r
244 protected void copy_actionPerformed(ActionEvent e)
\r
246 if(viewport.getRubberbandGroup()==null)
\r
249 SequenceGroup sg = viewport.getRubberbandGroup();
\r
251 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
\r
252 StringBuffer buffer= new StringBuffer();
\r
254 for(int i=0; i<sg.getSize(); i++)
\r
256 SequenceI seq = sg.getSequenceAt(i);
\r
257 buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
\r
258 +seq.findPosition( sg.getEndRes() )+ "\t"
\r
259 +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
\r
261 c.setContents( new StringSelection( buffer.toString()) , null ) ;
\r
266 protected void pasteNew_actionPerformed(ActionEvent e)
\r
271 protected void pasteThis_actionPerformed(ActionEvent e)
\r
276 void paste(boolean newAlignment)
\r
279 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
\r
280 Transferable contents = c.getContents(this);
\r
281 if (contents == null)
\r
284 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
\r
285 StringTokenizer st = new StringTokenizer(str);
\r
286 ArrayList seqs = new ArrayList();
\r
287 while (st.hasMoreElements())
\r
289 String name = st.nextToken();
\r
290 int start = Integer.parseInt(st.nextToken());
\r
291 int end = Integer.parseInt(st.nextToken());
\r
292 Sequence sequence = new Sequence(name,st.nextToken(), start, end);
\r
295 viewport.alignment.addSequence(sequence);
\r
297 seqs.add(sequence);
\r
302 SequenceI[] newSeqs = new SequenceI[seqs.size()];
\r
303 seqs.toArray(newSeqs);
\r
304 AlignFrame af = new AlignFrame(new Alignment(newSeqs));
\r
305 int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;
\r
306 if (newHeight > 500)
\r
308 Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);
\r
312 viewport.setEndSeq(viewport.alignment.getHeight());
\r
313 viewport.alignment.getWidth();
\r
314 alignPanel.RefreshPanels();
\r
317 }catch(Exception ex){}// could be anything being pasted in here
\r
322 protected void cut_actionPerformed(ActionEvent e)
\r
324 copy_actionPerformed(null);
\r
325 delete_actionPerformed(null);
\r
328 protected void delete_actionPerformed(ActionEvent e)
\r
330 if (viewport.getRubberbandGroup() == null)
\r
333 SequenceGroup sg = viewport.getRubberbandGroup();
\r
334 for (int i=0;i < sg.sequences.size(); i++)
\r
335 viewport.getAlignment().deleteSequence(sg.getSequenceAt(i));
\r
337 viewport.alignment.deleteGroup(sg);
\r
338 viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
\r
339 if(viewport.getAlignment().getHeight()<1)
\r
342 this.setClosed(true);
\r
343 }catch(Exception ex){}
\r
344 alignPanel.RefreshPanels();
\r
350 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
352 Object [] history = (Object[])redoList.remove(0);
\r
353 SequenceI[] seq = (SequenceI[]) history[1];
\r
354 viewport.setAlignment( new Alignment(seq) );
\r
355 updateEditMenuBar();
\r
356 alignPanel.RefreshPanels();
\r
360 public void groupsMenuItem_actionPerformed(ActionEvent e)
\r
362 GroupEditor geditor = new GroupEditor(viewport, alignPanel);
\r
363 JInternalFrame frame = new JInternalFrame();
\r
364 frame.setContentPane(geditor);
\r
365 Desktop.addInternalFrame(frame, "Group editor", 710, 410);
\r
366 frame.setResizable(false);
\r
369 protected void deleteGroups_actionPerformed(ActionEvent e)
\r
371 viewport.alignment.deleteAllGroups();
\r
372 viewport.getSelection().clear();
\r
374 alignPanel.RefreshPanels();
\r
379 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
381 Selection sel = viewport.getSelection();
\r
382 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
\r
383 sel.addElement( viewport.getAlignment().getSequenceAt(i));
\r
384 PaintRefresher.Refresh(null);
\r
387 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
389 viewport.setRubberbandGroup(null);
\r
390 viewport.getSelection().clear();
\r
391 PaintRefresher.Refresh(null);
\r
394 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
396 Selection sel = viewport.getSelection();
\r
397 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
\r
399 if (sel.contains(viewport.getAlignment().getSequenceAt(i)))
\r
400 sel.removeElement(viewport.getAlignment().getSequenceAt(i));
\r
402 sel.addElement(viewport.getAlignment().getSequenceAt(i));
\r
404 PaintRefresher.Refresh(null);
\r
408 public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
\r
410 viewport.getColumnSelection().clear();
\r
414 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
416 addHistoryItem("delete columns");
\r
417 ColumnSelection colSel = viewport.getColumnSelection();
\r
418 if (colSel.size() > 0)
\r
420 int min = colSel.getMin();
\r
421 viewport.getAlignment().trimLeft(min);
\r
422 colSel.compensateForEdit(0,min);
\r
423 alignPanel.RefreshPanels();
\r
427 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
429 addHistoryItem("delete columns");
\r
430 ColumnSelection colSel = viewport.getColumnSelection();
\r
431 if (colSel.size() > 0)
\r
433 int max = colSel.getMax();
\r
435 viewport.getAlignment().trimRight(max);
\r
437 alignPanel.RefreshPanels();
\r
442 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
444 addHistoryItem("delete gapped columns");
\r
445 viewport.getAlignment().removeGaps();
\r
446 alignPanel.RefreshPanels();
\r
449 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
451 addHistoryItem("delete all gaps");
\r
454 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
\r
456 current = viewport.getAlignment().getSequenceAt(i);
\r
457 jSize = current.getLength();
\r
458 for (int j=0; j < jSize; j++)
\r
459 if(jalview.util.Comparison.isGap(current.getCharAt(j)))
\r
461 current.deleteCharAt(j);
\r
467 alignPanel.RefreshPanels();
\r
470 public void setGapCharMenuItem_actionPerformed(ActionEvent e)
\r
472 char thisChar = '-';
\r
473 char nextChar = '.';
\r
474 if(viewport.getGapCharacter()=='-')
\r
479 setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
\r
480 viewport.setGapCharacter(thisChar);
\r
481 alignPanel.RefreshPanels();
\r
484 public void findMenuItem_actionPerformed(ActionEvent e)
\r
486 JOptionPane op = new JOptionPane();
\r
487 JInternalFrame frame = op.createInternalFrame(this, "Find");
\r
488 Finder finder = new Finder(viewport, alignPanel, frame);
\r
489 frame.setClosable(true);
\r
490 frame.setContentPane(finder);
\r
491 frame.setSize(340,110);
\r
492 frame.setVisible(true);
\r
497 public void fontNameMenuItem_actionPerformed(ActionEvent e)
\r
499 String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
\r
502 String selection = JOptionPane.showInternalInputDialog(this,
\r
505 JOptionPane.QUESTION_MESSAGE,
\r
507 ,fontNameMenuItem.getText()).toString();
\r
508 if(selection!=null)
\r
510 fontNameMenuItem.setText(selection);
\r
516 public void fontSizeMenuItem_actionPerformed(ActionEvent e)
\r
518 String selection = JOptionPane.showInternalInputDialog(this,
\r
519 "Select font size",
\r
521 JOptionPane.QUESTION_MESSAGE,
\r
522 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
\r
523 ,fontSizeMenuItem.getText()).toString();
\r
524 if(selection!=null)
\r
526 fontSizeMenuItem.setText(selection);
\r
531 public void fontStyleMenuItem_actionPerformed(ActionEvent e)
\r
533 String selection = JOptionPane.showInternalInputDialog(this,
\r
534 "Select font style",
\r
536 JOptionPane.QUESTION_MESSAGE,
\r
537 null, new String[]{"plain", "bold", "italic"}
\r
538 ,fontStyleMenuItem.getText()).toString();
\r
539 if(selection!=null)
\r
541 fontStyleMenuItem.setText(selection);
\r
547 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
549 viewport.setColourText( colourTextMenuItem.isSelected() );
\r
550 alignPanel.RefreshPanels();
\r
555 int style = java.awt.Font.PLAIN;
\r
556 if(fontStyleMenuItem.getText().equals("bold"))
\r
557 style = java.awt.Font.BOLD;
\r
558 else if(fontStyleMenuItem.getText().equals("italic"))
\r
559 style = java.awt.Font.ITALIC;
\r
561 viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),
\r
563 Integer.parseInt(fontSizeMenuItem.getText())));
\r
564 alignPanel.RefreshPanels();
\r
568 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
570 viewport.setWrapAlignment( wrapMenuItem.isSelected() );
\r
571 alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
\r
575 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
577 viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
\r
578 alignPanel.RefreshPanels();
\r
581 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
583 viewport.setShowText( viewTextMenuItem.isSelected() );
\r
584 alignPanel.RefreshPanels();
\r
588 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
590 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
\r
591 alignPanel.RefreshPanels();
\r
594 public void sequenceFeatures_actionPerformed(ActionEvent evt)
\r
596 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
\r
597 alignPanel.RefreshPanels();
\r
600 public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
\r
602 alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
\r
605 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
607 if (alignPanel.overviewPanel != null)
\r
610 JInternalFrame frame = new JInternalFrame();
\r
611 OverviewPanel overview = alignPanel.getOverviewPanel();
\r
613 overview = new OverviewPanel(alignPanel, viewport);
\r
614 frame.setContentPane(overview);
\r
615 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
\r
616 frame.getWidth(), frame.getHeight());
\r
618 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
619 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
\r
621 alignPanel.setOverviewPanel(null);
\r
624 alignPanel.setOverviewPanel( overview );
\r
626 }catch(java.lang.OutOfMemoryError ex)
\r
628 JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
\r
629 +"\nTry reducing the font size.",
\r
630 "Out of memory", JOptionPane.WARNING_MESSAGE);
\r
636 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
638 changeColour( null );
\r
642 public void clustalColour_actionPerformed(ActionEvent e)
\r
644 abovePIDThreshold.setSelected(false);
\r
645 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
\r
648 public void zappoColour_actionPerformed(ActionEvent e)
\r
650 changeColour(new ZappoColourScheme());
\r
653 public void taylorColour_actionPerformed(ActionEvent e)
\r
655 changeColour(new TaylorColourScheme());
\r
659 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
661 changeColour( new HydrophobicColourScheme() );
\r
664 public void helixColour_actionPerformed(ActionEvent e)
\r
666 changeColour(new HelixColourScheme() );
\r
670 public void strandColour_actionPerformed(ActionEvent e)
\r
672 changeColour(new StrandColourScheme());
\r
676 public void turnColour_actionPerformed(ActionEvent e)
\r
678 changeColour(new TurnColourScheme());
\r
682 public void buriedColour_actionPerformed(ActionEvent e)
\r
684 changeColour(new BuriedColourScheme() );
\r
687 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
689 changeColour(new NucleotideColourScheme());
\r
693 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
695 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
\r
700 void changeColour(ColourSchemeI cs)
\r
703 if(viewport.getColourAppliesToAllGroups())
\r
705 Vector groups = viewport.alignment.getGroups();
\r
706 for(int i=0; i<groups.size(); i++)
\r
708 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
\r
711 if(abovePIDThreshold.isSelected())
\r
712 abovePIDThreshold_actionPerformed(null);
\r
713 else if( viewport.getConservationSelected() )
\r
715 Conservation c = new Conservation("Group",
\r
716 ResidueProperties.propHash, 3,
\r
717 sg.sequences, sg.getStartRes(),
\r
720 c.verdict(false, 100);
\r
721 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
\r
730 if ( viewport.getAbovePIDThreshold())
\r
733 threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");
\r
734 Desktop.hideConservationSlider();
\r
736 if (cs instanceof ResidueColourScheme)
\r
737 ( (ResidueColourScheme) cs).setThreshold(threshold);
\r
738 else if (cs instanceof ScoreColourScheme)
\r
739 ( (ScoreColourScheme) cs).setThreshold(threshold);
\r
741 viewport.setGlobalColourScheme(cs);
\r
745 if (cs instanceof ResidueColourScheme)
\r
746 ( (ResidueColourScheme) cs).setThreshold(0);
\r
747 else if (cs instanceof ScoreColourScheme)
\r
748 ( (ScoreColourScheme) cs).setThreshold(0);
\r
753 if ( viewport.getConservationSelected() )
\r
755 ConservationColourScheme ccs = null;
\r
757 Alignment al = (Alignment) viewport.alignment;
\r
758 Conservation c = new Conservation("All",
\r
759 ResidueProperties.propHash, 3,
\r
760 al.getSequences(), 0,
\r
764 c.verdict(false, 100);
\r
766 ccs = new ConservationColourScheme(c, cs);
\r
768 int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,
\r
771 ccs.inc = threshold;
\r
773 viewport.setGlobalColourScheme(ccs);
\r
777 viewport.setGlobalColourScheme( cs );
\r
779 alignPanel.RefreshPanels();
\r
783 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
785 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
787 viewport.setAbovePIDThreshold(false);
\r
788 abovePIDThreshold.setSelected(false);
\r
789 Desktop.hidePIDSlider();
\r
790 if(!viewport.getConservationSelected())
\r
791 Desktop.hideConservationSlider();
\r
793 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
794 if(cs instanceof ConservationColourScheme )
\r
795 changeColour( ((ConservationColourScheme)cs).cs );
\r
797 changeColour( cs );
\r
801 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
803 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
805 conservationMenuItem.setSelected(false);
\r
806 viewport.setConservationSelected(false);
\r
807 Desktop.hideConservationSlider();
\r
809 if(!viewport.getAbovePIDThreshold())
\r
810 Desktop.hidePIDSlider();
\r
813 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
814 if(cs instanceof ConservationColourScheme )
\r
815 changeColour( ((ConservationColourScheme)cs).cs );
\r
817 changeColour( cs );
\r
823 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
825 JInternalFrame frame = new JInternalFrame();
\r
826 UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
\r
827 frame.setContentPane(chooser);
\r
828 Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
\r
829 frame.setResizable(false);
\r
830 frame.setIconifiable(false);
\r
831 frame.setMaximizable(false);
\r
834 public void PIDColour_actionPerformed(ActionEvent e)
\r
836 changeColour( new PIDColourScheme() );
\r
840 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
842 changeColour(new Blosum62ColourScheme(viewport) );
\r
847 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
849 addHistoryItem("sort");
\r
850 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
\r
851 alignPanel.RefreshPanels();
\r
854 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
856 addHistoryItem("sort");
\r
857 AlignmentSorter.sortByID( viewport.getAlignment() );
\r
858 alignPanel.RefreshPanels();
\r
861 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
863 addHistoryItem("sort");
\r
864 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
865 AlignmentSorter.sortGroups(viewport.getAlignment());
\r
866 alignPanel.RefreshPanels();
\r
869 public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
\r
871 addHistoryItem("sort");
\r
872 if(viewport.getCurrentTree()==null)
\r
875 AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
\r
876 alignPanel.RefreshPanels();
\r
879 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
881 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
882 JInternalFrame frame = new JInternalFrame();
\r
883 frame.setContentPane(sp);
\r
884 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);
\r
885 frame.setMaximizable(false);
\r
886 frame.setResizable(false);
\r
890 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
892 if(viewport.getSelection().size()<2)
\r
893 JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
\r
896 JInternalFrame frame = new JInternalFrame();
\r
897 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
898 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
902 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
904 if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)
\r
905 || viewport.getAlignment().getHeight()<4)
\r
907 JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
\r
908 +"at least 4 input sequences.",
\r
909 "Sequence selection insufficient",
\r
910 JOptionPane.WARNING_MESSAGE);
\r
915 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
916 JInternalFrame frame = new JInternalFrame();
\r
917 frame.setContentPane(pcaPanel);
\r
918 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
\r
919 }catch(java.lang.OutOfMemoryError ex)
\r
921 JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
\r
922 "Out of memory", JOptionPane.WARNING_MESSAGE);
\r
928 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
930 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
933 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
935 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
939 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
941 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
944 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
946 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
949 void NewTreePanel(String type, String pwType, String title)
\r
951 //are the sequences aligned?
\r
952 if(!viewport.alignment.isAligned())
\r
954 JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",
\r
955 "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
\r
959 JInternalFrame frame = new javax.swing.JInternalFrame();
\r
961 if (viewport.getSelection() != null && viewport.getSelection().size() > 3)
\r
963 tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,
\r
964 viewport.getStartRes(), viewport.getEndRes());
\r
968 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
969 type, pwType, viewport.getStartRes(),
\r
970 viewport.getEndRes());
\r
973 frame.setContentPane(tp);
\r
974 Desktop.addInternalFrame(frame, title, 600, 500);
\r
980 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
982 JInternalFrame frame = new JInternalFrame();
\r
983 ClustalThread ct = new ClustalThread(frame);
\r
984 Thread t = new Thread(ct);
\r
986 frame.setContentPane(ct);
\r
987 Desktop.addInternalFrame(frame, title, 300, 80);
\r
991 class ClustalThread extends JPanel implements Runnable
\r
994 int imageIndex = 0;
\r
995 boolean webServiceRunning = false;
\r
996 JInternalFrame frame;
\r
997 public ClustalThread(JInternalFrame frame)
\r
999 this.frame = frame;
\r
1000 image = new Image[9];
\r
1001 for(int i=0; i<9; i++)
\r
1003 java.net.URL url = getClass().getResource("/dna" + (i+1) + ".gif");
\r
1006 image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);
\r
1007 MediaTracker mt = new MediaTracker(this);
\r
1008 mt.addImage(image[i], i);
\r
1009 try{mt.waitForID(i);}
\r
1010 catch(Exception ex){}
\r
1013 DNATwirler twirler = new DNATwirler();
\r
1015 webServiceRunning = true;
\r
1018 class DNATwirler extends Thread
\r
1022 while(webServiceRunning)
\r
1025 Thread.sleep(100);
\r
1030 catch(Exception ex){}
\r
1036 // Should check to see if the server settings are valid
\r
1037 // Need visual-delay indication here.
\r
1040 jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
\r
1041 Vector sv = viewport.getAlignment().getSequences();
\r
1042 SequenceI[] seqs = new SequenceI[sv.size()];
\r
1047 seqs[i] = (SequenceI) sv.elementAt(i);
\r
1049 while (++i < sv.size());
\r
1051 SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
\r
1053 if (alignment != null)
\r
1055 AlignFrame af = new AlignFrame(new Alignment(alignment));
\r
1056 af.clustalColour.setSelected(true);
\r
1057 af.clustalColour_actionPerformed(null);
\r
1058 Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),
\r
1059 700, 500); // JBPNote - is there a new window geom. property ?
\r
1062 JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",
\r
1063 JOptionPane.WARNING_MESSAGE);
\r
1065 webServiceRunning = false;
\r
1067 frame.setClosed(true);
\r
1068 }catch(Exception ex){}
\r
1071 public void paintComponent(Graphics g)
\r
1073 g.setColor(Color.white);
\r
1074 g.fillRect(0,0,getWidth(), getHeight());
\r
1077 g.drawImage(image[imageIndex],10,10,this);
\r
1079 g.setFont(new Font("Arial", Font.BOLD, 12));
\r
1080 g.setColor(Color.black);
\r
1081 g.drawString("Clustal Alignment Web Service running", 30,30);
\r