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
21 import java.awt.event.*;
\r
22 import java.awt.print.*;
\r
23 import javax.swing.*;
\r
26 public class AlignFrame extends GAlignFrame
\r
28 final AlignmentPanel alignPanel;
\r
29 final AlignViewport viewport;
\r
30 public AlignFrame(AlignmentI al)
\r
33 viewport = new AlignViewport(al,true,true,true,false);
\r
34 alignPanel = new AlignmentPanel(this, viewport);
\r
35 getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
\r
36 fontNameMenuItem.setText(viewport.getFont().getName());
\r
37 fontSizeMenuItem.setText(viewport.getFont().getSize()+"");
\r
40 protected void saveAs_actionPerformed(ActionEvent e)
\r
42 JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);
\r
43 chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
\r
44 chooser.setToolTipText("Save");
\r
45 int value = chooser.showSaveDialog(this);
\r
46 if(value == JFileChooser.APPROVE_OPTION)
\r
48 String choice = chooser.getSelectedFile().getPath();
\r
49 jalview.bin.Cache.LAST_DIRECTORY = choice;
\r
50 String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
\r
52 java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
\r
53 out.println(output);
\r
56 catch(Exception ex){}
\r
61 protected void outputText_actionPerformed(ActionEvent e)
\r
63 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
\r
64 JInternalFrame frame = new JInternalFrame();
\r
65 cap.formatForOutput();
\r
66 frame.setContentPane(cap);
\r
67 Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
\r
68 cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
\r
71 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
73 HTMLOutput htmlOutput = new HTMLOutput(viewport.getAlignment(), alignPanel.seqPanel.getColourScheme());
\r
77 public void printMenuItem_actionPerformed(ActionEvent e)
\r
79 //Putting in a thread avoids Swing painting problems
\r
80 PrintThread thread = new PrintThread();
\r
84 class PrintThread extends Thread
\r
88 PrinterJob printJob = PrinterJob.getPrinterJob();
\r
89 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
\r
90 printJob.setPrintable(alignPanel, pf);
\r
91 if (printJob.printDialog())
\r
97 catch (Exception PrintException)
\r
99 PrintException.printStackTrace();
\r
109 public void closeMenuItem_actionPerformed(ActionEvent e)
\r
112 this.setClosed(true);
\r
113 }catch(Exception ex){}
\r
116 ArrayList historyList = new ArrayList();
\r
117 ArrayList redoList = new ArrayList();
\r
119 void updateEditMenuBar()
\r
121 if(historyList.size()>0)
\r
123 undoMenuItem.setEnabled(true);
\r
124 Object [] history = (Object[])historyList.get(0);
\r
125 undoMenuItem.setText("Undo "+history[0]);
\r
129 undoMenuItem.setEnabled(false);
\r
130 undoMenuItem.setText("Undo");
\r
133 if(redoList.size()>0)
\r
135 redoMenuItem.setEnabled(true);
\r
136 Object [] history = (Object[])redoList.get(0);
\r
137 redoMenuItem.setText("Redo "+history[0]);
\r
141 redoMenuItem.setEnabled(false);
\r
142 redoMenuItem.setText("Redo");
\r
146 public void addHistoryItem(String type)
\r
148 // must make sure we add new sequence objects her, not refs to the existing sequences
\r
150 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
\r
151 for(int i=0; i<viewport.getAlignment().getHeight(); i++)
\r
153 seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
\r
154 viewport.getAlignment().getSequenceAt(i).getSequence());
\r
157 historyList.add(0, new Object[]{type, seq} );
\r
158 updateEditMenuBar();
\r
161 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
163 Object [] history = (Object[])historyList.remove(0);
\r
164 // add the redo state before continuing!!
\r
165 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
\r
166 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
\r
168 seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
\r
169 viewport.getAlignment().getSequenceAt(i).
\r
174 redoList.add(0, new Object[] {history[0], seq});
\r
176 seq = (SequenceI[]) history[1];
\r
177 viewport.setAlignment( new Alignment(seq) );
\r
178 updateEditMenuBar();
\r
179 alignPanel.RefreshPanels();
\r
183 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
185 Object [] history = (Object[])redoList.remove(0);
\r
186 SequenceI[] seq = (SequenceI[]) history[1];
\r
187 viewport.setAlignment( new Alignment(seq) );
\r
188 updateEditMenuBar();
\r
189 alignPanel.RefreshPanels();
\r
194 public void groupsMenuItem_actionPerformed(ActionEvent e)
\r
196 GroupEditor geditor = new GroupEditor(viewport, alignPanel);
\r
197 JInternalFrame frame = new JInternalFrame();
\r
198 frame.setContentPane(geditor);
\r
199 Desktop.addInternalFrame(frame, "Group editor", 710, 410);
\r
200 frame.setResizable(false);
\r
203 public void groupEditingMenuItem_actionPerformed(ActionEvent e)
\r
205 viewport.setGroupEdit( groupEditingMenuItem.isSelected() );
\r
208 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
210 Selection sel = viewport.getSelection();
\r
211 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
\r
212 sel.addElement( viewport.getAlignment().getSequenceAt(i));
\r
213 PaintRefresher.Refresh(null);
\r
216 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
218 viewport.getSelection().clear();
\r
219 PaintRefresher.Refresh(null);
\r
222 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
224 Selection sel = viewport.getSelection();
\r
225 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
\r
227 if (sel.contains(viewport.getAlignment().getSequenceAt(i)))
\r
228 sel.removeElement(viewport.getAlignment().getSequenceAt(i));
\r
230 sel.addElement(viewport.getAlignment().getSequenceAt(i));
\r
232 PaintRefresher.Refresh(null);
\r
235 public void deleteSelectedMenuItem_actionPerformed(ActionEvent e)
\r
237 addHistoryItem("delete selection");
\r
239 for (int i=0;i < viewport.getSelection().size(); i++)
\r
240 viewport.getAlignment().deleteSequence(viewport.getSelection().sequenceAt(i));
\r
242 viewport.getSelection().clear();
\r
243 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
\r
244 alignPanel.RefreshPanels();
\r
247 public void moveSelectedMenuItem_actionPerformed(ActionEvent e)
\r
249 copySelectedMenuItem_actionPerformed(null);
\r
250 deleteSelectedMenuItem_actionPerformed(null);
\r
251 alignPanel.repaint();
\r
254 public void copySelectedMenuItem_actionPerformed(ActionEvent e)
\r
256 if(viewport.getSelection().size()==0)
\r
259 SequenceI[] s = new Sequence[viewport.getSelection().size()];
\r
260 for (int i=0; i < viewport.getSelection().size(); i++) {
\r
261 s[i] = new Sequence(viewport.getSelection().sequenceAt(i));
\r
263 AlignFrame af = new AlignFrame(new Alignment(s));
\r
264 int newHeight = s.length * af.viewport.getCharHeight() + 200;
\r
267 Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);
\r
270 public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
\r
272 viewport.getColumnSelection().clear();
\r
276 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
278 addHistoryItem("delete columns");
\r
279 ColumnSelection colSel = viewport.getColumnSelection();
\r
280 if (colSel.size() > 0)
\r
282 int min = colSel.getMin();
\r
283 viewport.getAlignment().trimLeft(min);
\r
284 colSel.compensateForEdit(0,min);
\r
285 alignPanel.RefreshPanels();
\r
289 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
291 addHistoryItem("delete columns");
\r
292 ColumnSelection colSel = viewport.getColumnSelection();
\r
293 if (colSel.size() > 0)
\r
295 int max = colSel.getMax();
\r
297 viewport.getAlignment().trimRight(max);
\r
299 alignPanel.RefreshPanels();
\r
304 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
306 addHistoryItem("delete gapped columns");
\r
307 viewport.getAlignment().removeGaps();
\r
308 alignPanel.RefreshPanels();
\r
311 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
313 addHistoryItem("delete all gaps");
\r
316 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
\r
318 current = viewport.getAlignment().getSequenceAt(i);
\r
319 jSize = current.getLength();
\r
320 for (int j=0; j < jSize; j++)
\r
321 if (current.getCharAt(j)=='-' || current.getCharAt(j)=='.' || current.getCharAt(j)==' ')
\r
323 current.deleteCharAt(j);
\r
329 alignPanel.RefreshPanels();
\r
332 public void setGapCharMenuItem_actionPerformed(ActionEvent e)
\r
334 String thisChar = "-";
\r
335 String nextChar = ".";
\r
336 if(viewport.getGapCharacter().equals("-"))
\r
341 setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
\r
342 viewport.setGapCharacter(thisChar);
\r
346 public void fontNameMenuItem_actionPerformed(ActionEvent e)
\r
348 String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
\r
351 String selection = JOptionPane.showInputDialog(this,
\r
354 JOptionPane.QUESTION_MESSAGE,
\r
356 ,fontNameMenuItem.getText()).toString();
\r
357 if(selection!=null)
\r
359 fontNameMenuItem.setText(selection);
\r
365 public void fontSizeMenuItem_actionPerformed(ActionEvent e)
\r
367 String selection = JOptionPane.showInputDialog(this,
\r
368 "Select font size",
\r
370 JOptionPane.QUESTION_MESSAGE,
\r
371 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
\r
372 ,fontSizeMenuItem.getText()).toString();
\r
373 if(selection!=null)
\r
375 fontSizeMenuItem.setText(selection);
\r
380 public void fontStyleMenuItem_actionPerformed(ActionEvent e)
\r
382 String selection = JOptionPane.showInputDialog(this,
\r
383 "Select font style",
\r
385 JOptionPane.QUESTION_MESSAGE,
\r
386 null, new String[]{"plain", "bold", "italic"}
\r
387 ,fontStyleMenuItem.getText()).toString();
\r
388 if(selection!=null)
\r
390 fontStyleMenuItem.setText(selection);
\r
396 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
398 viewport.setColourText( colourTextMenuItem.isSelected() );
\r
399 alignPanel.RefreshPanels();
\r
404 int style = java.awt.Font.PLAIN;
\r
405 if(fontStyleMenuItem.getText().equals("bold"))
\r
406 style = java.awt.Font.BOLD;
\r
407 else if(fontStyleMenuItem.getText().equals("italic"))
\r
408 style = java.awt.Font.ITALIC;
\r
410 viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),
\r
412 Integer.parseInt(fontSizeMenuItem.getText())));
\r
413 alignPanel.RefreshPanels();
\r
417 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
419 viewport.setWrapAlignment( wrapMenuItem.isSelected() );
\r
420 alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );
\r
424 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
426 viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
\r
427 alignPanel.RefreshPanels();
\r
430 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
432 viewport.setShowText( viewTextMenuItem.isSelected() );
\r
433 alignPanel.RefreshPanels();
\r
437 public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
\r
439 alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
\r
442 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
445 JInternalFrame frame = new JInternalFrame();
\r
446 OverviewPanel overview = alignPanel.getOverviewPanel();
\r
448 overview = new OverviewPanel(alignPanel, viewport);
\r
449 frame.setContentPane(overview);
\r
450 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
\r
451 frame.getWidth(), frame.getHeight());
\r
453 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
454 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
\r
456 alignPanel.setOverviewPanel(null);
\r
459 alignPanel.setOverviewPanel( overview );
\r
461 }catch(java.lang.OutOfMemoryError ex)
\r
463 JOptionPane.showMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
\r
464 +"\nTry reducing the font size.",
\r
465 "Out of memory", JOptionPane.WARNING_MESSAGE);
\r
471 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
473 alignPanel.setColourScheme(null, false);
\r
477 public void clustalColour_actionPerformed(ActionEvent e)
\r
479 // alignPanel.setColourScheme( new ClustalxColourScheme() );
\r
482 public void zappoColour_actionPerformed(ActionEvent e)
\r
484 alignPanel.setColourScheme( new ZappoColourScheme(), conservationMenuItem.isSelected() );
\r
487 public void taylorColour_actionPerformed(ActionEvent e)
\r
489 alignPanel.setColourScheme( new TaylorColourScheme(),conservationMenuItem.isSelected() );
\r
493 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
495 alignPanel.setColourScheme( new HydrophobicColourScheme(),conservationMenuItem.isSelected() );
\r
498 public void helixColour_actionPerformed(ActionEvent e)
\r
500 alignPanel.setColourScheme( new HelixColourScheme(),conservationMenuItem.isSelected() );
\r
504 public void strandColour_actionPerformed(ActionEvent e)
\r
506 alignPanel.setColourScheme( new StrandColourScheme() ,conservationMenuItem.isSelected() );
\r
510 public void turnColour_actionPerformed(ActionEvent e)
\r
512 alignPanel.setColourScheme( new TurnColourScheme() ,conservationMenuItem.isSelected() );
\r
516 public void buriedColour_actionPerformed(ActionEvent e)
\r
518 alignPanel.setColourScheme( new BuriedColourScheme() ,conservationMenuItem.isSelected() );
\r
522 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
524 alignPanel.setColourScheme ( alignPanel.seqPanel.getColourScheme(),conservationMenuItem.isSelected() );
\r
525 conservationColourIncMenuItem.setEnabled( conservationMenuItem.isSelected() );
\r
530 public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
\r
532 ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);
\r
533 JInternalFrame frame = new JInternalFrame();
\r
534 frame.setContentPane(cip);
\r
535 Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);
\r
536 frame.setMaximizable(false);
\r
540 public void abovePIDColour_actionPerformed(ActionEvent e)
\r
542 alignPanel.setColourScheme( new PIDColourScheme() ,conservationMenuItem.isSelected() );
\r
546 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
548 JInternalFrame frame = new JInternalFrame();
\r
549 UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel.seqPanel );
\r
550 frame.setContentPane(chooser);
\r
551 Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
\r
552 frame.setResizable(false);
\r
553 frame.setIconifiable(false);
\r
554 frame.setMaximizable(false);
\r
557 public void PIDColour_actionPerformed(ActionEvent e)
\r
559 alignPanel.setColourScheme( new PIDColourScheme(),conservationMenuItem.isSelected() );
\r
563 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
565 alignPanel.setColourScheme( new Blosum62ColourScheme(viewport) ,conservationMenuItem.isSelected() );
\r
570 protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
\r
572 ColourKey colourKey = new ColourKey( alignPanel.seqPanel.getColourScheme() );
\r
573 Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);
\r
577 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
579 addHistoryItem("sort");
\r
580 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
\r
581 alignPanel.RefreshPanels();
\r
584 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
586 addHistoryItem("sort");
\r
587 AlignmentSorter.sortByID( viewport.getAlignment() );
\r
588 alignPanel.RefreshPanels();
\r
591 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
593 addHistoryItem("sort");
\r
594 AlignmentSorter.sortGroups(viewport.getAlignment());
\r
595 AlignmentSorter.sortGroups(viewport.getAlignment());
\r
596 alignPanel.RefreshPanels();
\r
599 public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
\r
601 addHistoryItem("sort");
\r
602 if(viewport.getCurrentTree()==null)
\r
605 AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
\r
606 alignPanel.RefreshPanels();
\r
609 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
614 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
616 if(viewport.getSelection().size()<2)
\r
617 JOptionPane.showMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
\r
620 JInternalFrame frame = new JInternalFrame();
\r
621 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
622 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
626 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
628 if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)
\r
629 || viewport.getAlignment().getHeight()<4)
\r
631 JOptionPane.showMessageDialog(this, "Principal component analysis must take\n"
\r
632 +"at least 4 input sequences.",
\r
633 "Sequence selection insufficient",
\r
634 JOptionPane.WARNING_MESSAGE);
\r
639 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
640 JInternalFrame frame = new JInternalFrame();
\r
641 frame.setContentPane(pcaPanel);
\r
642 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
\r
643 }catch(java.lang.OutOfMemoryError ex)
\r
645 JOptionPane.showMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
\r
646 "Out of memory", JOptionPane.WARNING_MESSAGE);
\r
652 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
654 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
657 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
659 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
663 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
665 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
668 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
670 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
673 void NewTreePanel(String type, String pwType, String title)
\r
675 JInternalFrame frame = new javax.swing.JInternalFrame();
\r
677 if (viewport.getSelection() != null && viewport.getSelection().size() > 3)
\r
679 tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,
\r
680 viewport.getStartRes(), viewport.getEndRes());
\r
684 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
685 type, pwType, viewport.getStartRes(),
\r
686 viewport.getEndRes());
\r
689 frame.setContentPane(tp);
\r
690 Desktop.addInternalFrame(frame, title, 600, 500);
\r
695 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
697 JOptionPane.showMessageDialog(this, "Jalview is currently being reengineered"
\r
698 +"\nwithin the Barton Group, Dundee University."
\r
699 +"\nThis will be available as a web service 2005",
\r
700 "Web service", JOptionPane.INFORMATION_MESSAGE);
\r
703 public void pdbTest_actionPerformed(ActionEvent e)
\r
705 String reply = JOptionPane.showInputDialog(this, "Enter pdb code", "PDB test viewer", JOptionPane.QUESTION_MESSAGE);
\r
707 String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u";
\r
708 if (reply.length()>1)
\r
709 url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id="+reply;
\r
713 PDBfile pdb = new PDBfile(url,
\r
715 Sequence seq = (Sequence)viewport.getAlignment().getSequenceAt(0);
\r
716 seq.setPDBfile(pdb);
\r
717 ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).isVisible = true;
\r
718 ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).sequence = seq;
\r
719 // ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).colourBySequence();
\r
721 rotCanvas rc = new rotCanvas(pdb);
\r
722 JInternalFrame frame = new JInternalFrame();
\r
723 frame.setContentPane(rc);
\r
724 Desktop.addInternalFrame(frame, url, 400,400);
\r
726 catch (Exception ex)
\r
728 ex.printStackTrace();
\r