src/jalview/gui/AlignmentPanel.java

   1 package jalview.gui;\r
   2 \r
   3 import jalview.jbgui.GAlignmentPanel;\r
   4 import jalview.schemes.*;\r
   5 import jalview.analysis.*;\r
   6 import jalview.datamodel.*;\r
   7 import java.awt.*;\r
   8 import java.awt.event.*;\r
   9 import java.awt.print.*;\r
  10 \r
  11 public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable\r
  12 {\r
  13 \r
  14   AlignViewport     av;\r
  15   OverviewPanel overviewPanel;\r
  16   SeqPanel   seqPanel;\r
  17   IdPanel    idPanel;\r
  18   public AlignFrame alignFrame;\r
  19   ScalePanel scalePanel;\r
  20   ScorePanel scorePanel;\r
  21 \r
  22   public AlignmentPanel(AlignFrame af, AlignViewport av)\r
  23   {\r
  24     alignFrame = af;\r
  25     this.av         = av;\r
  26     seqPanel        = new SeqPanel  (av, this);\r
  27     idPanel         = new IdPanel   (av, this);\r
  28     scalePanel = new ScalePanel(av, this);\r
  29     scorePanel = new ScorePanel(av);\r
  30 \r
  31     idPanelHolder.add(idPanel, BorderLayout.CENTER);\r
  32     idPanel.addNotify();\r
  33     scalePanelHolder.add(scalePanel, BorderLayout.CENTER);\r
  34     scorePanelHolder.add(scorePanel, BorderLayout.CENTER);\r
  35     seqPanelHolder.add(seqPanel, BorderLayout.CENTER);\r
  36     setScrollValues(0,0);\r
  37 \r
  38     hscroll.addAdjustmentListener(this);\r
  39     vscroll.addAdjustmentListener(this);\r
  40 \r
  41     addComponentListener(new ComponentAdapter()\r
  42    {\r
  43        public void componentResized(ComponentEvent evt)\r
  44      {\r
  45           RefreshPanels();\r
  46      }\r
  47    });\r
  48   }\r
  49 \r
  50  public void highlightSearchResults(int [] results)\r
  51  {\r
  52    seqPanel.seqCanvas.highlightSearchResults( results );\r
  53 \r
  54    // do we need to scroll the panel?\r
  55    if(results!=null && (av.getStartSeq()>results[0]\r
  56                         || av.getEndSeq()<results[0]\r
  57                         || av.getStartRes()>results[1]\r
  58                         || av.getEndRes()<results[2]))\r
  59        setScrollValues(results[1], results[0]);\r
  60 \r
  61 \r
  62  }\r
  63 \r
  64 \r
  65  public OverviewPanel getOverviewPanel()\r
  66  {\r
  67    return overviewPanel;\r
  68  }\r
  69 \r
  70  public void setOverviewPanel(OverviewPanel op)\r
  71  {\r
  72    overviewPanel = op;\r
  73  }\r
  74 \r
  75 \r
  76   public void setGraphPanelVisible(boolean b)\r
  77   {\r
  78     scorePanelHolder.setVisible(b);\r
  79     idSpaceFillerPanel.setVisible(b);\r
  80     RefreshPanels();\r
  81   }\r
  82 \r
  83   public void setWrapAlignment(boolean wrap)\r
  84   {\r
  85       scalePanelHolder.setVisible(!wrap);\r
  86       scorePanelHolder.setVisible(!wrap);\r
  87 \r
  88       hscroll.setVisible(!wrap);\r
  89       idSpaceFillerPanel.setVisible(!wrap);\r
  90       idSpaceFillerPanel1.setVisible(!wrap);\r
  91   }\r
  92 \r
  93 \r
  94   public void setColourScheme()\r
  95   {\r
  96     ColourSchemeI cs = av.getGlobalColourScheme();\r
  97 \r
  98     if(av.getConservationSelected())\r
  99     {\r
 100 \r
 101       Alignment al = (Alignment)av.getAlignment();\r
 102       Conservation c = new Conservation("All",\r
 103                             ResidueProperties.propHash, 3, al.getSequences(), 0,\r
 104                             al.getWidth() );\r
 105 \r
 106        c.calculate();\r
 107        c.verdict(false, 100);\r
 108        ConservationColourScheme ccs = new ConservationColourScheme(c, cs);\r
 109 \r
 110        av.setGlobalColourScheme( ccs );\r
 111 \r
 112     }\r
 113     seqPanel.seqCanvas.paintFlag = true;\r
 114     repaint();\r
 115   }\r
 116   /*\r
 117     seqCanvas.paintFlag = true;\r
 118     if (av.getSelection().size() == 0)\r
 119     {\r
 120       seqCanvas.globalColorScheme = cs;\r
 121       for (int i = 0; i < av.alignment.getGroups().size();i++)\r
 122       {\r
 123         SequenceGroup sg = (SequenceGroup)av.alignment.getGroups().elementAt(i);\r
 124         sg.cs = cs;\r
 125         if(!showConservation\r
 126             && !(sg.cs instanceof Blosum62ColourScheme)\r
 127             && sg.cs instanceof ConservationColourScheme)\r
 128          {\r
 129            // remove ConservationColouring from existing Conservation group\r
 130            ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
 131            sg.cs = ccs.cs;\r
 132          }\r
 133          else if(showConservation && !(sg.cs instanceof ConservationColourScheme))\r
 134          {\r
 135            // add ConservationColouring to new group\r
 136            Conservation c = sg.getConservation();\r
 137            Alignment al = (Alignment) av.getAlignment();\r
 138            c = new Conservation("All", al.cons,\r
 139                                 ResidueProperties.propHash, 3, sg.sequences, 0,\r
 140                                 al.getWidth() );\r
 141            c.calculate();\r
 142            c.verdict(false, 100);\r
 143            sg.setConservation(c);\r
 144            sg.cs = new ConservationColourScheme(sg);\r
 145          }\r
 146       }\r
 147     }\r
 148     else\r
 149     {\r
 150       SequenceGroup sg = av.alignment.findGroup((Sequence)av.sel.sequenceAt(0));\r
 151 \r
 152       if( isNewSelection(sg) )\r
 153       {\r
 154         sg = av.getAlignment().addGroup();\r
 155         for (int i=0; i < av.getSelection().size(); i++)\r
 156         {\r
 157           av.alignment.removeFromGroup(av.alignment.findGroup( (Sequence) av.\r
 158               sel.sequenceAt(i)),\r
 159                                        (Sequence) av.sel.sequenceAt(i));\r
 160           av.alignment.addToGroup(sg, (Sequence) av.sel.sequenceAt(i));\r
 161         }\r
 162       }\r
 163 \r
 164 \r
 165       sg.cs = cs;\r
 166 \r
 167       // Selection is made, we only want to change the conservationColour for selected group\r
 168       if(  showConservation\r
 169            && !(sg.cs instanceof ConservationColourScheme)\r
 170            && !(sg.cs instanceof Blosum62ColourScheme))\r
 171       {\r
 172         Conservation c = sg.getConservation();\r
 173         Alignment al = (Alignment) av.getAlignment();\r
 174 \r
 175         c = new Conservation("All", al.cons,\r
 176                              ResidueProperties.propHash, 3, sg.sequences, 0,\r
 177                              al.getWidth() );\r
 178         c.calculate();\r
 179         c.verdict(false, 100);\r
 180         sg.setConservation(c);\r
 181         sg.cs = new ConservationColourScheme(sg);\r
 182     }\r
 183     else  if( !showConservation && sg.cs instanceof ConservationColourScheme)\r
 184     {\r
 185       ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
 186       sg.cs = ccs.cs;\r
 187     }\r
 188    }\r
 189    repaint();\r
 190   }\r
 191 \r
 192   boolean isNewSelection(SequenceGroup sg)\r
 193   {\r
 194     if(sg==null)\r
 195       return true;\r
 196 \r
 197     if(sg.getSize()!=av.getSelection().size())\r
 198       return true;\r
 199 \r
 200     for(int i=0; i<sg.getSize(); i++)\r
 201      if( !av.getSelection().contains( sg.getSequenceAt(i) ))\r
 202        return true;\r
 203 \r
 204     return false;\r
 205   }\r
 206 \r
 207 \r
 208   public ColourSchemeI getColourScheme()\r
 209   {\r
 210     if(av.getSelection().size()>0)\r
 211        return av.alignment.findGroup((Sequence)av.sel.sequenceAt(0)).cs;\r
 212     else\r
 213       return seqCanvas.globalColorScheme;\r
 214   }\r
 215 */\r
 216 \r
 217 /*  public void setColourScheme(jalview.schemes.ColourSchemeI cs, boolean conservation)\r
 218   {\r
 219     seqPanel.setColourScheme(cs, conservation);\r
 220 \r
 221     av.setGlobalColourScheme(cs);\r
 222 \r
 223     if(overviewPanel!=null)\r
 224       overviewPanel.updateOverviewImage();\r
 225   }\r
 226 \r
 227    void updateResidueView()\r
 228    {\r
 229      if (viewport.getSelection().size() == 0)\r
 230       {\r
 231         for (int i = 0; i < viewport.alignment.getGroups().size(); i++)\r
 232         {\r
 233           SequenceGroup sg = (SequenceGroup) viewport.alignment.getGroups().elementAt(i);\r
 234           sg.setDisplayBoxes( viewBoxesMenuItem.isSelected() );\r
 235           sg.setDisplayText( viewTextMenuItem.isSelected() );\r
 236           sg.setColourText( colourTextMenuItem.isSelected() );\r
 237         }\r
 238       }\r
 239       else\r
 240       {\r
 241         SequenceGroup sg = viewport.alignment.findGroup( (Sequence) viewport.sel.sequenceAt(0));\r
 242         if (alignPanel.seqPanel.isNewSelection(sg))\r
 243         {\r
 244           sg = viewport.getAlignment().addGroup();\r
 245           for (int i = 0; i < viewport.getSelection().size(); i++)\r
 246           {\r
 247             viewport.alignment.removeFromGroup(viewport.alignment.findGroup( (\r
 248                 Sequence) viewport.sel.sequenceAt(i)),\r
 249                                                (Sequence) viewport.sel.sequenceAt(\r
 250                 i));\r
 251             viewport.alignment.addToGroup(sg,\r
 252                                           (Sequence) viewport.sel.sequenceAt(i));\r
 253           }\r
 254         }\r
 255 \r
 256         sg.setDisplayBoxes(viewBoxesMenuItem.isSelected());\r
 257         sg.setDisplayText(viewTextMenuItem.isSelected());\r
 258         sg.setColourText(colourTextMenuItem.isSelected());\r
 259       }\r
 260      alignPanel.RefreshPanels();\r
 261    }*/\r
 262 \r
 263 \r
 264 \r
 265   public void RefreshPanels()\r
 266   {\r
 267     invalidate();\r
 268     seqPanel.seqCanvas.paintFlag = true;\r
 269     idPanel.idCanvas.paintFlag = true;\r
 270     idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );\r
 271     setScrollValues(av.getStartRes(), av.getStartSeq());\r
 272     av.getConsensus(true);\r
 273     validate();\r
 274     repaint();\r
 275     if(overviewPanel!=null)\r
 276       overviewPanel.updateOverviewImage();\r
 277 \r
 278   }\r
 279 \r
 280   int hextent = 0;\r
 281   int vextent = 0;\r
 282 \r
 283   public void setScrollValues(int x, int y)\r
 284   {\r
 285     hextent = seqPanel.seqCanvas.getWidth()/av.getCharWidth();\r
 286     vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight();\r
 287 \r
 288     if(hextent+x  >  av.getAlignment().getWidth())\r
 289       x =  av.getAlignment().getWidth()- hextent;\r
 290 \r
 291     if(vextent+y > av.getAlignment().getHeight())\r
 292       y = av.getAlignment().getHeight() - vextent;\r
 293 \r
 294     if(y<0)\r
 295       y = 0;\r
 296 \r
 297     if(x<0)\r
 298       x=0;\r
 299 \r
 300     hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());\r
 301     vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );\r
 302     repaint();\r
 303 \r
 304   }\r
 305 \r
 306 \r
 307   public void adjustmentValueChanged(AdjustmentEvent evt)\r
 308   {\r
 309 \r
 310     if (evt.getSource() == hscroll)\r
 311     {\r
 312       int x = hscroll.getValue();\r
 313       av.setStartRes(x);\r
 314       av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);\r
 315     }\r
 316 \r
 317     if (evt.getSource() == vscroll)\r
 318     {\r
 319         int offy = vscroll.getValue();\r
 320         av.setStartSeq(offy);\r
 321         av.setEndSeq(offy + seqPanel.seqCanvas.getHeight()/av.getCharHeight());\r
 322     }\r
 323 \r
 324 \r
 325     if(overviewPanel!=null)\r
 326       overviewPanel.setBoxPosition();\r
 327 \r
 328     seqPanel.seqCanvas.paintFlag=true;\r
 329     repaint();\r
 330   }\r
 331 \r
 332 \r
 333   public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException\r
 334   {\r
 335 \r
 336     pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());\r
 337 \r
 338     int pwidth = (int)pf.getImageableWidth();\r
 339     int pheight = (int)pf.getImageableHeight();\r
 340     int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();\r
 341 \r
 342     pg.setColor(Color.white);\r
 343     pg.fillRect(0,0,pwidth, pheight);\r
 344     pg.setFont( av.getFont() );\r
 345 \r
 346     ////////////////////////////////////\r
 347     /// How many sequences and residues can we fit on a printable page?\r
 348     int totalRes = (pwidth - idWidth)/av.getCharWidth();\r
 349     int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1;\r
 350     int pagesWide = av.getAlignment().getWidth() / totalRes +1;\r
 351     int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;\r
 352 \r
 353     if (pi >= pagesWide*pagesHigh)\r
 354      return Printable.NO_SUCH_PAGE;\r
 355 \r
 356     /////////////////////////////\r
 357     /// Only print these sequences and residues on this page\r
 358     int startRes, endRes, startSeq, endSeq;\r
 359     startRes = (pi % pagesWide) * totalRes;\r
 360     endRes = startRes + totalRes-1;\r
 361     if(endRes>av.getAlignment().getWidth())\r
 362       endRes = av.getAlignment().getWidth();\r
 363 \r
 364      startSeq = (pi / pagesWide) * totalSeq;\r
 365      endSeq = startSeq + totalSeq;\r
 366      if(endSeq > av.getAlignment().getHeight())\r
 367        endSeq = av.getAlignment().getHeight();\r
 368 \r
 369 \r
 370     ////////////////\r
 371     //draw Scale\r
 372     pg.translate(idWidth,0);\r
 373     scalePanel.scaleCanvas.drawScale(pg, startRes, endRes, pwidth-idWidth);\r
 374 \r
 375     pg.translate(-idWidth, 30);\r
 376     ////////////////\r
 377     // Draw the ids\r
 378     Color currentColor=null;\r
 379     Color currentTextColor=null;\r
 380     for(int i=startSeq; i<endSeq; i++)\r
 381     {\r
 382       if (av.getSelection().contains(av.getAlignment().getSequenceAt(i)))\r
 383       {\r
 384         currentColor = Color.gray;\r
 385         currentTextColor = Color.black;\r
 386       }\r
 387       else\r
 388       {\r
 389         currentColor = av.getAlignment().getSequenceAt(i).getColor();\r
 390         currentTextColor = Color.black;\r
 391       }\r
 392 \r
 393       pg.setColor(currentColor);\r
 394       pg.fillRect(0,  jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),\r
 395                               idWidth,\r
 396                               av.getCharHeight());\r
 397 \r
 398       pg.setColor(currentTextColor);\r
 399 \r
 400       String string = av.getAlignment().getSequenceAt(i).getDisplayId();\r
 401       pg.drawString(string, 0,  jalview.analysis.AlignmentUtil.getPixelHeight\r
 402                     (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));\r
 403     }\r
 404 \r
 405     // draw main sequence panel\r
 406     pg.translate(idWidth,0);\r
 407     pg.setClip(0,0,pwidth-idWidth, pheight);\r
 408     seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);\r
 409 \r
 410     return Printable.PAGE_EXISTS;\r
 411   }\r
 412 \r
 413 }\r
 414 \r
 415 \r
 416 \r