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);
\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
192 protected void modifyAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
194 viewport.groupDefiningMode = !modifyAlignmentMenuItem.isSelected();
\r
198 public void groupsMenuItem_actionPerformed(ActionEvent e)
\r
200 GroupEditor geditor = new GroupEditor(viewport, alignPanel);
\r
201 JInternalFrame frame = new JInternalFrame();
\r
202 frame.setContentPane(geditor);
\r
203 Desktop.addInternalFrame(frame, "Group editor", 710, 410);
\r
204 frame.setResizable(false);
\r
207 public void groupEditingMenuItem_actionPerformed(ActionEvent e)
\r
209 viewport.setGroupEdit( groupEditingMenuItem.isSelected() );
\r
212 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
214 Selection sel = viewport.getSelection();
\r
215 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
\r
216 sel.addElement( viewport.getAlignment().getSequenceAt(i));
\r
217 PaintRefresher.Refresh(null);
\r
220 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
222 viewport.getSelection().clear();
\r
223 PaintRefresher.Refresh(null);
\r
226 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
228 Selection sel = viewport.getSelection();
\r
229 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
\r
231 if (sel.contains(viewport.getAlignment().getSequenceAt(i)))
\r
232 sel.removeElement(viewport.getAlignment().getSequenceAt(i));
\r
234 sel.addElement(viewport.getAlignment().getSequenceAt(i));
\r
236 PaintRefresher.Refresh(null);
\r
240 public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
\r
242 viewport.getColumnSelection().clear();
\r
246 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
248 addHistoryItem("delete columns");
\r
249 ColumnSelection colSel = viewport.getColumnSelection();
\r
250 if (colSel.size() > 0)
\r
252 int min = colSel.getMin();
\r
253 viewport.getAlignment().trimLeft(min);
\r
254 colSel.compensateForEdit(0,min);
\r
255 alignPanel.RefreshPanels();
\r
259 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
261 addHistoryItem("delete columns");
\r
262 ColumnSelection colSel = viewport.getColumnSelection();
\r
263 if (colSel.size() > 0)
\r
265 int max = colSel.getMax();
\r
267 viewport.getAlignment().trimRight(max);
\r
269 alignPanel.RefreshPanels();
\r
274 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
276 addHistoryItem("delete gapped columns");
\r
277 viewport.getAlignment().removeGaps();
\r
278 alignPanel.RefreshPanels();
\r
281 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
283 addHistoryItem("delete all gaps");
\r
286 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
\r
288 current = viewport.getAlignment().getSequenceAt(i);
\r
289 jSize = current.getLength();
\r
290 for (int j=0; j < jSize; j++)
\r
291 if (current.getCharAt(j)=='-' || current.getCharAt(j)=='.' || current.getCharAt(j)==' ')
\r
293 current.deleteCharAt(j);
\r
299 alignPanel.RefreshPanels();
\r
302 public void setGapCharMenuItem_actionPerformed(ActionEvent e)
\r
304 char thisChar = '-';
\r
305 char nextChar = '.';
\r
306 if(viewport.getGapCharacter()=='-')
\r
311 setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
\r
312 viewport.setGapCharacter(thisChar);
\r
313 alignPanel.RefreshPanels();
\r
316 public void findMenuItem_actionPerformed(ActionEvent e)
\r
318 JOptionPane op = new JOptionPane();
\r
319 JInternalFrame frame = op.createInternalFrame(this, "Find");
\r
320 Finder finder = new Finder(viewport, alignPanel, frame);
\r
321 frame.setContentPane(finder);
\r
322 frame.setSize(300,110);
\r
323 frame.setVisible(true);
\r
328 public void fontNameMenuItem_actionPerformed(ActionEvent e)
\r
330 String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
\r
333 String selection = JOptionPane.showInternalInputDialog(this,
\r
336 JOptionPane.QUESTION_MESSAGE,
\r
338 ,fontNameMenuItem.getText()).toString();
\r
339 if(selection!=null)
\r
341 fontNameMenuItem.setText(selection);
\r
347 public void fontSizeMenuItem_actionPerformed(ActionEvent e)
\r
349 String selection = JOptionPane.showInternalInputDialog(this,
\r
350 "Select font size",
\r
352 JOptionPane.QUESTION_MESSAGE,
\r
353 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
\r
354 ,fontSizeMenuItem.getText()).toString();
\r
355 if(selection!=null)
\r
357 fontSizeMenuItem.setText(selection);
\r
362 public void fontStyleMenuItem_actionPerformed(ActionEvent e)
\r
364 String selection = JOptionPane.showInternalInputDialog(this,
\r
365 "Select font style",
\r
367 JOptionPane.QUESTION_MESSAGE,
\r
368 null, new String[]{"plain", "bold", "italic"}
\r
369 ,fontStyleMenuItem.getText()).toString();
\r
370 if(selection!=null)
\r
372 fontStyleMenuItem.setText(selection);
\r
378 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
380 viewport.setColourText( colourTextMenuItem.isSelected() );
\r
381 alignPanel.RefreshPanels();
\r
386 int style = java.awt.Font.PLAIN;
\r
387 if(fontStyleMenuItem.getText().equals("bold"))
\r
388 style = java.awt.Font.BOLD;
\r
389 else if(fontStyleMenuItem.getText().equals("italic"))
\r
390 style = java.awt.Font.ITALIC;
\r
392 viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),
\r
394 Integer.parseInt(fontSizeMenuItem.getText())));
\r
395 alignPanel.RefreshPanels();
\r
399 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
401 viewport.setWrapAlignment( wrapMenuItem.isSelected() );
\r
402 alignPanel.RefreshPanels();
\r
406 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
408 viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
\r
409 alignPanel.RefreshPanels();
\r
412 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
414 viewport.setShowText( viewTextMenuItem.isSelected() );
\r
415 alignPanel.RefreshPanels();
\r
419 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
421 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
\r
422 alignPanel.RefreshPanels();
\r
426 public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
\r
428 alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
\r
431 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
434 JInternalFrame frame = new JInternalFrame();
\r
435 OverviewPanel overview = alignPanel.getOverviewPanel();
\r
437 overview = new OverviewPanel(alignPanel, viewport);
\r
438 frame.setContentPane(overview);
\r
439 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
\r
440 frame.getWidth(), frame.getHeight());
\r
442 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
443 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
\r
445 alignPanel.setOverviewPanel(null);
\r
448 alignPanel.setOverviewPanel( overview );
\r
450 }catch(java.lang.OutOfMemoryError ex)
\r
452 JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
\r
453 +"\nTry reducing the font size.",
\r
454 "Out of memory", JOptionPane.WARNING_MESSAGE);
\r
460 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
462 viewport.setGlobalColourScheme( null );
\r
463 alignPanel.setColourScheme();
\r
467 public void clustalColour_actionPerformed(ActionEvent e)
\r
469 // alignPanel.setColourScheme( new ClustalxColourScheme() );
\r
472 public void zappoColour_actionPerformed(ActionEvent e)
\r
474 viewport.setGlobalColourScheme(new ZappoColourScheme() );
\r
475 alignPanel.setColourScheme( );
\r
478 public void taylorColour_actionPerformed(ActionEvent e)
\r
480 viewport.setGlobalColourScheme(new TaylorColourScheme() );
\r
481 alignPanel.setColourScheme( );
\r
485 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
487 viewport.setGlobalColourScheme( new HydrophobicColourScheme() );
\r
488 alignPanel.setColourScheme( );
\r
491 public void helixColour_actionPerformed(ActionEvent e)
\r
493 viewport.setGlobalColourScheme( new HelixColourScheme() );
\r
494 alignPanel.setColourScheme();
\r
498 public void strandColour_actionPerformed(ActionEvent e)
\r
500 viewport.setGlobalColourScheme(new StrandColourScheme() );
\r
501 alignPanel.setColourScheme( );
\r
505 public void turnColour_actionPerformed(ActionEvent e)
\r
507 viewport.setGlobalColourScheme(new TurnColourScheme() );
\r
508 alignPanel.setColourScheme( );
\r
512 public void buriedColour_actionPerformed(ActionEvent e)
\r
514 viewport.setGlobalColourScheme( new BuriedColourScheme() );
\r
515 alignPanel.setColourScheme( );
\r
519 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
521 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
522 conservationColourIncMenuItem.setEnabled( conservationMenuItem.isSelected() );
\r
523 alignPanel.setColourScheme();
\r
526 public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
\r
528 ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);
\r
529 JInternalFrame frame = new JInternalFrame();
\r
530 frame.setContentPane(cip);
\r
531 Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);
\r
532 frame.setMaximizable(false);
\r
536 public void abovePIDColour_actionPerformed(ActionEvent e)
\r
538 viewport.setGlobalColourScheme(new PIDColourScheme());
\r
539 alignPanel.setColourScheme( );
\r
543 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
545 JInternalFrame frame = new JInternalFrame();
\r
546 UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
\r
547 frame.setContentPane(chooser);
\r
548 Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
\r
549 frame.setResizable(false);
\r
550 frame.setIconifiable(false);
\r
551 frame.setMaximizable(false);
\r
554 public void PIDColour_actionPerformed(ActionEvent e)
\r
556 viewport.setGlobalColourScheme(new PIDColourScheme() );
\r
557 alignPanel.setColourScheme( );
\r
561 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
563 viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport) );
\r
564 alignPanel.setColourScheme();
\r
569 protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
\r
571 ColourKey colourKey = new ColourKey( viewport.getGlobalColourScheme() );
\r
572 Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);
\r
576 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
578 addHistoryItem("sort");
\r
579 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
\r
580 alignPanel.RefreshPanels();
\r
583 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
585 addHistoryItem("sort");
\r
586 AlignmentSorter.sortByID( viewport.getAlignment() );
\r
587 alignPanel.RefreshPanels();
\r
590 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
592 addHistoryItem("sort");
\r
593 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
594 AlignmentSorter.sortGroups(viewport.getAlignment());
\r
595 alignPanel.RefreshPanels();
\r
598 public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
\r
600 addHistoryItem("sort");
\r
601 if(viewport.getCurrentTree()==null)
\r
604 AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
\r
605 alignPanel.RefreshPanels();
\r
608 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
613 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
615 if(viewport.getSelection().size()<2)
\r
616 JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
\r
619 JInternalFrame frame = new JInternalFrame();
\r
620 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
621 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
625 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
627 if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)
\r
628 || viewport.getAlignment().getHeight()<4)
\r
630 JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
\r
631 +"at least 4 input sequences.",
\r
632 "Sequence selection insufficient",
\r
633 JOptionPane.WARNING_MESSAGE);
\r
638 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
639 JInternalFrame frame = new JInternalFrame();
\r
640 frame.setContentPane(pcaPanel);
\r
641 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
\r
642 }catch(java.lang.OutOfMemoryError ex)
\r
644 JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
\r
645 "Out of memory", JOptionPane.WARNING_MESSAGE);
\r
651 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
653 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
656 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
658 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
662 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
664 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
667 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
669 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
672 void NewTreePanel(String type, String pwType, String title)
\r
674 JInternalFrame frame = new javax.swing.JInternalFrame();
\r
676 if (viewport.getSelection() != null && viewport.getSelection().size() > 3)
\r
678 tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,
\r
679 viewport.getStartRes(), viewport.getEndRes());
\r
683 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
684 type, pwType, viewport.getStartRes(),
\r
685 viewport.getEndRes());
\r
688 frame.setContentPane(tp);
\r
689 Desktop.addInternalFrame(frame, title, 600, 500);
\r
694 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
696 JOptionPane.showInternalMessageDialog(this, "Jalview is currently being reengineered"
\r
697 +"\nwithin the Barton Group, Dundee University."
\r
698 +"\nThis will be available as a web service 2005",
\r
699 "Web service", JOptionPane.INFORMATION_MESSAGE);
\r
702 public void pdbTest_actionPerformed(ActionEvent e)
\r
704 String reply = JOptionPane.showInternalInputDialog(this, "Enter pdb code", "PDB test viewer", JOptionPane.QUESTION_MESSAGE);
\r
706 String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u";
\r
707 if (reply.length()>1)
\r
708 url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id="+reply;
\r
712 PDBfile pdb = new PDBfile(url,
\r
714 Sequence seq = (Sequence)viewport.getAlignment().getSequenceAt(0);
\r
715 seq.setPDBfile(pdb);
\r
716 ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).isVisible = true;
\r
717 ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).sequence = seq;
\r
718 // ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).colourBySequence();
\r
720 rotCanvas rc = new rotCanvas(pdb);
\r
721 JInternalFrame frame = new JInternalFrame();
\r
722 frame.setContentPane(rc);
\r
723 Desktop.addInternalFrame(frame, url, 400,400);
\r
725 catch (Exception ex)
\r
727 ex.printStackTrace();
\r
733 public void doKeyPressed(KeyEvent evt)
\r
736 System.out.println(evt.getKeyChar());
\r
737 if(evt.isControlDown() && evt.getKeyChar()=='f')
\r
738 findMenuItem_actionPerformed(null);
\r