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 public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable
\r
15 OverviewPanel overviewPanel;
\r
18 SecondaryStructurePanel ssPanel;
\r
19 public AlignFrame alignFrame;
\r
20 ScalePanel scalePanel;
\r
21 ScorePanel scorePanel;
\r
23 public AlignmentPanel(AlignFrame af, final AlignViewport av)
\r
27 seqPanel = new SeqPanel (av, this);
\r
28 idPanel = new IdPanel (av, this);
\r
29 scalePanel = new ScalePanel(av, this);
\r
30 scorePanel = new ScorePanel(av);
\r
31 ssPanel = new SecondaryStructurePanel(av);
\r
33 secondaryPanelHolder.add(ssPanel, BorderLayout.CENTER);
\r
34 idPanelHolder.add(idPanel, BorderLayout.CENTER);
\r
35 idPanel.addNotify();
\r
36 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
\r
37 scorePanelHolder.add(scorePanel, BorderLayout.CENTER);
\r
38 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
\r
39 setScrollValues(0,0);
\r
41 hscroll.addAdjustmentListener(this);
\r
42 vscroll.addAdjustmentListener(this);
\r
44 addComponentListener(new ComponentAdapter()
\r
46 public void componentResized(ComponentEvent evt)
\r
52 hscroll.setFocusable(false);
\r
53 vscroll.setFocusable(false);
\r
56 addKeyListener(new KeyAdapter()
\r
58 public void keyPressed(KeyEvent evt)
\r
60 if(evt.getKeyCode()==27)
\r
62 av.setRubberbandGroup(null);
\r
71 public void highlightSearchResults(int [] results)
\r
73 seqPanel.seqCanvas.highlightSearchResults( results );
\r
75 // do we need to scroll the panel?
\r
76 if(results!=null && (av.getStartSeq()>results[0]
\r
77 || av.getEndSeq()<results[0]
\r
78 || av.getStartRes()>results[1]
\r
79 || av.getEndRes()<results[2]))
\r
80 setScrollValues(results[1], results[0]);
\r
86 public OverviewPanel getOverviewPanel()
\r
88 return overviewPanel;
\r
91 public void setOverviewPanel(OverviewPanel op)
\r
97 public void setGraphPanelVisible(boolean b)
\r
99 idSpaceFillerPanel.setVisible(b);
\r
100 scorePanelHolder.setVisible(b);
\r
103 // bit annoying to call this twice, can you do better?
\r
107 public void setSecondaryStructureVisible(boolean b)
\r
109 secondaryPanelHolder.setVisible(b);
\r
113 public void setWrapAlignment(boolean wrap)
\r
115 scalePanelHolder.setVisible(!wrap);
\r
116 scorePanelHolder.setVisible(!wrap);
\r
118 hscroll.setVisible(!wrap);
\r
119 idSpaceFillerPanel.setVisible(!wrap);
\r
120 idSpaceFillerPanel1.setVisible(!wrap);
\r
124 public void setColourScheme()
\r
126 ColourSchemeI cs = av.getGlobalColourScheme();
\r
128 if(av.getConservationSelected())
\r
131 Alignment al = (Alignment)av.getAlignment();
\r
132 Conservation c = new Conservation("All",
\r
133 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
137 c.verdict(false, 100);
\r
138 ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
\r
140 av.setGlobalColourScheme( ccs );
\r
147 public void RefreshPanels()
\r
151 seqPanel.seqCanvas.paintFlag = true;
\r
152 idPanel.idCanvas.paintFlag = true;
\r
153 idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );
\r
154 setScrollValues(av.getStartRes(), av.getStartSeq());
\r
155 av.getConsensus(true);
\r
156 if(overviewPanel!=null)
\r
157 overviewPanel.updateOverviewImage();
\r
167 public void setScrollValues(int x, int y)
\r
169 hextent = seqPanel.seqCanvas.getWidth()/av.getCharWidth();
\r
170 vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight();
\r
172 if(hextent+x > av.getAlignment().getWidth())
\r
173 x = av.getAlignment().getWidth()- hextent;
\r
175 if(vextent+y > av.getAlignment().getHeight())
\r
176 y = av.getAlignment().getHeight() - vextent;
\r
184 hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
\r
185 vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
\r
193 public void adjustmentValueChanged(AdjustmentEvent evt)
\r
196 if (evt.getSource() == hscroll)
\r
198 int x = hscroll.getValue();
\r
200 av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
\r
203 if (evt.getSource() == vscroll)
\r
205 int offy = vscroll.getValue();
\r
206 av.setStartSeq(offy);
\r
207 av.setEndSeq(offy + seqPanel.seqCanvas.getHeight()/av.getCharHeight());
\r
211 if(overviewPanel!=null)
\r
212 overviewPanel.setBoxPosition();
\r
214 seqPanel.seqCanvas.paintFlag=true;
\r
219 public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
\r
222 pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
\r
224 int pwidth = (int)pf.getImageableWidth();
\r
225 int pheight = (int)pf.getImageableHeight();
\r
226 int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();
\r
228 pg.setColor(Color.white);
\r
229 pg.fillRect(0,0,pwidth, pheight);
\r
230 pg.setFont( av.getFont() );
\r
232 ////////////////////////////////////
\r
233 /// How many sequences and residues can we fit on a printable page?
\r
234 int totalRes = (pwidth - idWidth)/av.getCharWidth();
\r
235 int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1;
\r
236 int pagesWide = av.getAlignment().getWidth() / totalRes +1;
\r
237 int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;
\r
239 if (pi >= pagesWide*pagesHigh)
\r
240 return Printable.NO_SUCH_PAGE;
\r
242 /////////////////////////////
\r
243 /// Only print these sequences and residues on this page
\r
244 int startRes, endRes, startSeq, endSeq;
\r
245 startRes = (pi % pagesWide) * totalRes;
\r
246 endRes = startRes + totalRes-1;
\r
247 if(endRes>av.getAlignment().getWidth())
\r
248 endRes = av.getAlignment().getWidth();
\r
250 startSeq = (pi / pagesWide) * totalSeq;
\r
251 endSeq = startSeq + totalSeq;
\r
252 if(endSeq > av.getAlignment().getHeight())
\r
253 endSeq = av.getAlignment().getHeight();
\r
258 pg.translate(idWidth,0);
\r
259 scalePanel.scaleCanvas.drawScale(pg, startRes, endRes, pwidth-idWidth);
\r
261 pg.translate(-idWidth, 30);
\r
264 Color currentColor=null;
\r
265 Color currentTextColor=null;
\r
266 for(int i=startSeq; i<endSeq; i++)
\r
268 if (av.getSelection().contains(av.getAlignment().getSequenceAt(i)))
\r
270 currentColor = Color.gray;
\r
271 currentTextColor = Color.black;
\r
275 currentColor = av.getAlignment().getSequenceAt(i).getColor();
\r
276 currentTextColor = Color.black;
\r
279 pg.setColor(currentColor);
\r
280 pg.fillRect(0, jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),
\r
282 av.getCharHeight());
\r
284 pg.setColor(currentTextColor);
\r
286 String string = av.getAlignment().getSequenceAt(i).getDisplayId();
\r
287 pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight
\r
288 (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));
\r
291 // draw main sequence panel
\r
292 pg.translate(idWidth,0);
\r
293 pg.setClip(0,0,pwidth-idWidth, pheight);
\r
294 seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);
\r
296 return Printable.PAGE_EXISTS;
\r