3 import jalview.jbgui.GAlignmentPanel;
\r
4 import jalview.schemes.*;
\r
5 import jalview.analysis.*;
\r
6 import jalview.datamodel.*;
\r
8 import java.awt.event.*;
\r
9 import java.awt.print.*;
\r
11 import java.awt.image.*;
\r
12 import org.jibble.epsgraphics.*;
\r
13 import javax.imageio.*;
\r
17 public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable
\r
21 OverviewPanel overviewPanel;
\r
24 IdwidthAdjuster idwidthAdjuster;
\r
25 SecondaryStructurePanel ssPanel;
\r
26 public AlignFrame alignFrame;
\r
27 ScalePanel scalePanel;
\r
28 ScorePanel scorePanel;
\r
30 public AlignmentPanel(AlignFrame af, final AlignViewport av)
\r
34 seqPanel = new SeqPanel (av, this);
\r
35 idPanel = new IdPanel (av, this);
\r
37 scalePanel = new ScalePanel(av, this);
\r
38 scorePanel = new ScorePanel(av);
\r
39 ssPanel = new SecondaryStructurePanel(av);
\r
41 secondaryPanelHolder.add(ssPanel, BorderLayout.CENTER);
\r
43 idPanelHolder.add(idPanel, BorderLayout.CENTER);
\r
44 idwidthAdjuster = new IdwidthAdjuster(this);
\r
45 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
\r
47 Dimension d = calculateIdWidth();
\r
48 d.setSize( d.width+4, d.height);
\r
49 idPanel.idCanvas.setPreferredSize( d );
\r
50 hscrollFillerPanel.setPreferredSize( d );
\r
52 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
\r
53 scorePanelHolder.add(scorePanel, BorderLayout.CENTER);
\r
54 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
\r
57 if(seqPanel.seqCanvas.getWidth()==0)
\r
58 javax.swing.SwingUtilities.invokeLater(new Runnable()
\r
62 setScrollValues(0,0);
\r
63 Dimension d = calculateIdWidth();
\r
64 d.setSize( d.width+4, d.height);
\r
65 idPanel.idCanvas.setPreferredSize( d );
\r
66 hscrollFillerPanel.setPreferredSize( d );
\r
72 hscroll.addAdjustmentListener(this);
\r
73 vscroll.addAdjustmentListener(this);
\r
75 addComponentListener(new ComponentAdapter()
\r
77 public void componentResized(ComponentEvent evt)
\r
84 addKeyListener(new KeyAdapter()
\r
86 public void keyPressed(KeyEvent evt)
\r
88 switch(evt.getKeyCode())
\r
90 case 27: // escape key
\r
91 av.setSelectionGroup(null);
\r
95 alignFrame.cut_actionPerformed(null);
\r
98 alignFrame.copy_actionPerformed(null);
\r
100 case KeyEvent.VK_V:
\r
101 alignFrame.paste(true);
\r
103 case KeyEvent.VK_A:
\r
104 alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
\r
106 case KeyEvent.VK_DOWN:
\r
107 alignFrame.moveSelectedSequences(false);
\r
109 case KeyEvent.VK_UP:
\r
110 alignFrame.moveSelectedSequences(true);
\r
112 case KeyEvent.VK_F:
\r
113 alignFrame.findMenuItem_actionPerformed(null);
\r
120 Dimension calculateIdWidth()
\r
122 Graphics g = this.getGraphics();
\r
125 javax.swing.JFrame f = new javax.swing.JFrame();
\r
127 g = f.getGraphics();
\r
130 FontMetrics fm = g.getFontMetrics(av.font);
\r
131 AlignmentI al = av.getAlignment();
\r
136 while (i < al.getHeight() && al.getSequenceAt(i) != null)
\r
138 SequenceI s = al.getSequenceAt(i);
\r
139 if(av.getShowFullId())
\r
140 id = s.getDisplayId();
\r
144 if (fm.stringWidth(id) > idWidth)
\r
145 idWidth = fm.stringWidth(id);
\r
149 return new Dimension(idWidth, 12);
\r
153 public void highlightSearchResults(int [] results)
\r
155 seqPanel.seqCanvas.highlightSearchResults( results );
\r
157 // do we need to scroll the panel?
\r
158 if(results!=null && (av.getStartSeq()>results[0]
\r
159 || av.getEndSeq()<results[0]
\r
160 || av.getStartRes()>results[1]
\r
161 || av.getEndRes()<results[2]))
\r
162 setScrollValues(results[1], results[0]);
\r
168 public OverviewPanel getOverviewPanel()
\r
170 return overviewPanel;
\r
173 public void setOverviewPanel(OverviewPanel op)
\r
175 overviewPanel = op;
\r
179 public void setGraphPanelVisible(boolean b)
\r
181 idSpaceFillerPanel.setVisible(b);
\r
182 scorePanelHolder.setVisible(b);
\r
185 // bit annoying to call this twice, can you do better?
\r
189 public void setSecondaryStructureVisible(boolean b)
\r
191 secondaryPanelHolder.setVisible(b);
\r
195 public void setWrapAlignment(boolean wrap)
\r
197 scorePanelHolder.setVisible(!wrap);
\r
198 scalePanelHolder.setVisible(!wrap);
\r
199 secondaryPanelHolder.setVisible(!wrap);
\r
201 hscroll.setVisible(!wrap);
\r
203 idwidthAdjuster.setVisible(!wrap);
\r
204 idSpaceFillerPanel.setVisible(!wrap);
\r
205 idSpaceFillerPanel1.setVisible(!wrap);
\r
212 public void setColourScheme()
\r
214 ColourSchemeI cs = av.getGlobalColourScheme();
\r
216 if(av.getConservationSelected())
\r
219 Alignment al = (Alignment)av.getAlignment();
\r
220 Conservation c = new Conservation("All",
\r
221 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
225 c.verdict(false, 100);
\r
226 ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
\r
228 av.setGlobalColourScheme( ccs );
\r
235 public void RefreshPanels()
\r
240 idPanelHolder.setPreferredSize(idPanel.idCanvas.getPreferredSize());
\r
241 if(idPanel.idCanvas.getPreferredSize()!=null)
\r
242 hscrollFillerPanel.setPreferredSize(new Dimension(idPanel.idCanvas.getPreferredSize().width, 12));
\r
243 idSpaceFillerPanel1.setPreferredSize(new Dimension(500,
\r
244 av.charHeight / 2 + 12));
\r
245 scalePanelHolder.setPreferredSize(new Dimension(500,
\r
246 av.charHeight / 2 + 12));
\r
247 if (av.getWrapAlignment())
\r
249 int max = av.alignment.getWidth() /
\r
250 (seqPanel.seqCanvas.getWidth() / av.charWidth) + 1;
\r
252 int h = (av.alignment.getHeight() + 2) * av.charHeight;
\r
253 vextent = seqPanel.seqCanvas.getHeight() / h;
\r
254 vscroll.setValues(0, vextent, 0, max);
\r
258 av.getConsensus(true);
\r
259 if (overviewPanel != null)
\r
260 overviewPanel.updateOverviewImage();
\r
263 setScrollValues(av.getStartRes(), av.getStartSeq());
\r
270 // return value is true if the scroll is valid
\r
271 public boolean scrollUp(boolean up)
\r
275 if(vscroll.getValue()<1)
\r
277 vscroll.setValue(vscroll.getValue() - 1);
\r
281 if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
\r
283 vscroll.setValue(vscroll.getValue() + 1);
\r
289 public boolean scrollRight(boolean right)
\r
293 if(hscroll.getValue()<1)
\r
295 hscroll.setValue(hscroll.getValue() - 1);
\r
299 if(hextent+hscroll.getValue() >= av.getAlignment().getWidth())
\r
301 hscroll.setValue(hscroll.getValue() + 1);
\r
308 public void setScrollValues(int x, int y)
\r
310 hextent = seqPanel.seqCanvas.getWidth()/av.charWidth;
\r
311 vextent = seqPanel.seqCanvas.getHeight()/av.charHeight;
\r
313 if(hextent > av.alignment.getWidth())
\r
314 hextent = av.alignment.getWidth();
\r
315 if(vextent > av.alignment.getHeight())
\r
316 vextent = av.alignment.getHeight();
\r
318 if(hextent+x > av.getAlignment().getWidth())
\r
319 x = av.getAlignment().getWidth()- hextent;
\r
321 if(vextent+y > av.getAlignment().getHeight())
\r
322 y = av.getAlignment().getHeight() - vextent;
\r
330 hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
\r
331 vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
\r
338 public void adjustmentValueChanged(AdjustmentEvent evt)
\r
341 if (evt.getSource() == hscroll)
\r
343 int x = hscroll.getValue();
\r
345 av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
\r
348 if (evt.getSource() == vscroll)
\r
350 int offy = vscroll.getValue();
\r
351 if (av.getWrapAlignment())
\r
353 av.setStartRes( vscroll.getValue() * av.getChunkWidth());
\r
357 av.setStartSeq(offy);
\r
358 av.setEndSeq(offy + seqPanel.seqCanvas.getHeight() / av.getCharHeight());
\r
363 if(overviewPanel!=null)
\r
364 overviewPanel.setBoxPosition();
\r
369 public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
\r
371 pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
\r
373 int pwidth = (int) pf.getImageableWidth();
\r
374 int pheight = (int) pf.getImageableHeight();
\r
376 if (av.getWrapAlignment())
\r
377 return printWrappedAlignment(pg, pwidth,pheight, pi);
\r
379 return printUnwrapped(pg,pwidth, pheight,pi);
\r
382 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
\r
385 int idWidth = calculateIdWidth().width;
\r
388 pg.setColor(Color.white);
\r
389 pg.fillRect(0,0,pwidth, pheight);
\r
390 pg.setFont( av.getFont() );
\r
392 ////////////////////////////////////
\r
393 /// How many sequences and residues can we fit on a printable page?
\r
394 int totalRes = (pwidth - idWidth)/av.getCharWidth();
\r
395 int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1;
\r
396 int pagesWide = av.getAlignment().getWidth() / totalRes +1;
\r
397 int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;
\r
399 if (pi >= pagesWide*pagesHigh)
\r
400 return Printable.NO_SUCH_PAGE;
\r
402 /////////////////////////////
\r
403 /// Only print these sequences and residues on this page
\r
404 int startRes, endRes, startSeq, endSeq;
\r
405 startRes = (pi % pagesWide) * totalRes;
\r
406 endRes = startRes + totalRes-1;
\r
407 if(endRes>av.getAlignment().getWidth())
\r
408 endRes = av.getAlignment().getWidth();
\r
410 startSeq = (pi / pagesWide) * totalSeq;
\r
411 endSeq = startSeq + totalSeq;
\r
412 if(endSeq > av.getAlignment().getHeight())
\r
413 endSeq = av.getAlignment().getHeight();
\r
418 pg.translate(30,0);
\r
419 scalePanel.drawScale(pg, startRes, endRes, pwidth-idWidth);
\r
421 pg.translate(-30, 30);
\r
424 Color currentColor=null;
\r
425 Color currentTextColor=null;
\r
426 for(int i=startSeq; i<endSeq; i++)
\r
428 if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(av.getAlignment().getSequenceAt(i)))
\r
430 currentColor = Color.gray;
\r
431 currentTextColor = Color.black;
\r
435 currentColor = av.getAlignment().getSequenceAt(i).getColor();
\r
436 currentTextColor = Color.black;
\r
439 pg.setColor(currentColor);
\r
440 pg.fillRect(0, jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),
\r
442 av.getCharHeight());
\r
444 pg.setColor(currentTextColor);
\r
446 String string = av.getAlignment().getSequenceAt(i).getName();
\r
447 if(av.getShowFullId())
\r
448 string = av.getAlignment().getSequenceAt(i).getDisplayId();
\r
450 pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight
\r
451 (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));
\r
454 // draw main sequence panel
\r
455 pg.translate(idWidth+4,0);
\r
456 pg.setClip(0,0,pwidth-idWidth, pheight);
\r
457 seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);
\r
459 return Printable.PAGE_EXISTS;
\r
463 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
\r
466 int idWidth = calculateIdWidth().width;
\r
468 if( seqPanel.seqCanvas.getWidth() < pwidth-idWidth)
\r
469 pwidth = seqPanel.seqCanvas.getWidth() + idWidth;
\r
472 pg.setColor(Color.white);
\r
473 pg.fillRect(0,0,pwidth, pheight);
\r
474 pg.setFont( av.getFont() );
\r
476 ////////////////////////////////////
\r
477 /// How many sequences and residues can we fit on a printable page?
\r
478 AlignmentI da = av.alignment;
\r
479 int endy = da.getHeight();
\r
480 int chunkHeight = (da.getHeight() + 2)*av.charHeight;
\r
481 int chunkWidth = (pwidth-idWidth)/av.charWidth;
\r
483 int noChunksOnPage = pheight / chunkHeight;
\r
484 int totalChunks = da.getWidth() / chunkWidth;
\r
486 if ( pi*noChunksOnPage > totalChunks )
\r
487 return Printable.NO_SUCH_PAGE;
\r
491 pg.setClip(0,0,pwidth, noChunksOnPage*chunkHeight);
\r
493 int row = pi*noChunksOnPage;
\r
494 pg.setColor(Color.black);
\r
495 for(int ypos=2*av.charHeight;
\r
496 ypos <= pheight && row*chunkWidth<da.getWidth();
\r
497 ypos += chunkHeight, row++ )
\r
499 for (int i = 0; i < endy; i++)
\r
501 SequenceI s = da.getSequenceAt(i);
\r
502 String string = s.getName();
\r
503 if (av.getShowFullId())
\r
504 string = s.getDisplayId();
\r
506 pg.drawString(string, 0,
\r
507 AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +
\r
508 av.charHeight - (av.charHeight / 5));
\r
512 // draw main sequence panel
\r
513 pg.translate(idWidth+4,0);
\r
514 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth-idWidth, pheight, pi*noChunksOnPage*chunkWidth);
\r
517 return Printable.PAGE_EXISTS;
\r
522 public void makeEPS()
\r
524 int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
\r
525 int width = seqPanel.getWidth() + idPanel.getWidth();
\r
527 if (!av.getWrapAlignment())
\r
529 height = (av.alignment.getHeight()+1) * av.charHeight + 30;
\r
530 width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
\r
535 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
\r
536 "LAST_DIRECTORY"), new String[]{"eps"}, "Encapsulated Postscript");
\r
537 chooser.setFileView(new jalview.io.JalviewFileView());
\r
538 chooser.setDialogTitle("Create EPS file from alignment");
\r
539 chooser.setToolTipText("Save");
\r
541 int value = chooser.showSaveDialog(this);
\r
542 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
\r
545 jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
\r
546 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
\r
547 EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width, height);
\r
549 if (av.getWrapAlignment())
\r
550 printWrappedAlignment(pg, width, height, 0);
\r
552 printUnwrapped(pg, width, height, 0);
\r
558 catch (Exception ex)
\r
560 ex.printStackTrace();
\r
564 public void makePNG()
\r
566 int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
\r
567 int width = seqPanel.getWidth() + idPanel.getWidth();
\r
569 if (!av.getWrapAlignment())
\r
571 height = (av.alignment.getHeight()+1) * av.charHeight + 30;
\r
572 width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
\r
579 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
\r
580 "LAST_DIRECTORY"), new String[]{"png"}, "Portable network graphics");
\r
581 chooser.setFileView(new jalview.io.JalviewFileView());
\r
582 chooser.setDialogTitle("Create EPS file from alignment");
\r
583 chooser.setToolTipText("Save");
\r
585 int value = chooser.showSaveDialog(this);
\r
586 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
\r
589 jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
\r
590 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
\r
592 BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
\r
593 Graphics png = bi.getGraphics();
\r
596 if (av.getWrapAlignment())
\r
597 printWrappedAlignment(png, width, height, 0);
\r
599 printUnwrapped(png, width, height, 0);
\r
601 ImageIO.write(bi, "png", out);
\r
604 catch (Exception ex)
\r
606 ex.printStackTrace();
\r