src/jalview/gui/FeatureRenderer.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package jalview.gui;\r
  20 \r
  21 import jalview.datamodel.*;\r
  22 \r
  23 import java.awt.*;\r
  24 \r
  25 import java.util.*;\r
  26 \r
  27 import java.awt.image.*;\r
  28 \r
  29 \r
  30 /**\r
  31  * DOCUMENT ME!\r
  32  *\r
  33  * @author $author$\r
  34  * @version $Revision$\r
  35  */\r
  36 public class FeatureRenderer\r
  37 {\r
  38     AlignViewport av;\r
  39     Color resBoxColour;\r
  40     float transparency = 1.0f;\r
  41     FontMetrics fm;\r
  42     int charOffset;\r
  43 \r
  44     Hashtable featureColours = new Hashtable();\r
  45 \r
  46 \r
  47     // A higher level for grouping features of a\r
  48    // particular type\r
  49     Hashtable featureGroups = null;\r
  50 \r
  51     // This is actually an Integer held in the hashtable,\r
  52     // Retrieved using the key feature type\r
  53     Object currentColour;\r
  54 \r
  55     String [] renderOrder;\r
  56 \r
  57     /**\r
  58      * Creates a new FeatureRenderer object.\r
  59      *\r
  60      * @param av DOCUMENT ME!\r
  61      */\r
  62     public FeatureRenderer(AlignViewport av)\r
  63     {\r
  64         this.av = av;\r
  65     }\r
  66 \r
  67     public void transferSettings(FeatureRenderer fr)\r
  68     {\r
  69       renderOrder = fr.renderOrder;\r
  70       featureGroups = fr.featureGroups;\r
  71       featureColours = fr.featureColours;\r
  72       transparency =  fr.transparency;\r
  73     }\r
  74 \r
  75     BufferedImage offscreenImage;\r
  76     boolean offscreenRender = false;\r
  77     public Color findFeatureColour(Color initialCol, SequenceI seq, int res)\r
  78     {\r
  79       return new Color( findFeatureColour (initialCol.getRGB(),\r
  80                         seq, res ));\r
  81     }\r
  82 \r
  83     /**\r
  84      * This is used by the Molecule Viewer and Overview to\r
  85      * get the accurate colourof the rendered sequence\r
  86      */\r
  87     public int findFeatureColour(int initialCol, SequenceI seq, int column)\r
  88     {\r
  89       if(!av.showSequenceFeatures)\r
  90         return initialCol;\r
  91 \r
  92       if(seq!=lastSeq)\r
  93       {\r
  94         lastSeq = seq;\r
  95         sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();\r
  96         if(sequenceFeatures==null)\r
  97           return initialCol;\r
  98 \r
  99         sfSize = sequenceFeatures.length;\r
 100       }\r
 101 \r
 102       if(jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))\r
 103         return Color.white.getRGB();\r
 104 \r
 105 \r
 106       //Only bother making an offscreen image if transparency is applied\r
 107       if(transparency!=1.0f && offscreenImage==null)\r
 108       {\r
 109         offscreenImage = new BufferedImage(1,1,BufferedImage.TYPE_INT_ARGB);\r
 110       }\r
 111 \r
 112       currentColour = null;\r
 113 \r
 114       offscreenRender = true;\r
 115 \r
 116       if(offscreenImage!=null)\r
 117       {\r
 118         offscreenImage.setRGB(0,0,initialCol);\r
 119         drawSequence(offscreenImage.getGraphics(),\r
 120                      lastSeq,\r
 121                      column,column,0);\r
 122 \r
 123         return offscreenImage.getRGB(0,0);\r
 124       }\r
 125       else\r
 126       {\r
 127         drawSequence(null,\r
 128                     lastSeq,\r
 129                     lastSeq.findPosition(column),\r
 130                     -1, -1);\r
 131 \r
 132         if (currentColour == null)\r
 133           return initialCol;\r
 134         else\r
 135           return  ((Integer)currentColour).intValue();\r
 136       }\r
 137 \r
 138 \r
 139     }\r
 140 \r
 141 \r
 142     /**\r
 143      * DOCUMENT ME!\r
 144      *\r
 145      * @param g DOCUMENT ME!\r
 146      * @param seq DOCUMENT ME!\r
 147      * @param sg DOCUMENT ME!\r
 148      * @param start DOCUMENT ME!\r
 149      * @param end DOCUMENT ME!\r
 150      * @param x1 DOCUMENT ME!\r
 151      * @param y1 DOCUMENT ME!\r
 152      * @param width DOCUMENT ME!\r
 153      * @param height DOCUMENT ME!\r
 154      */\r
 155    // String type;\r
 156    // SequenceFeature sf;\r
 157     SequenceI lastSeq;\r
 158     SequenceFeature [] sequenceFeatures;\r
 159     int sfSize, sfindex, spos, epos;\r
 160 \r
 161     public void drawSequence(Graphics g, SequenceI seq,\r
 162                              int start, int end, int y1)\r
 163     {\r
 164       if ( seq.getDatasetSequence().getSequenceFeatures() == null\r
 165           || seq.getDatasetSequence().getSequenceFeatures().length==0)\r
 166         return;\r
 167 \r
 168       if(g!=null)\r
 169         fm = g.getFontMetrics();\r
 170 \r
 171 \r
 172       if (av.featuresDisplayed == null\r
 173           || renderOrder==null\r
 174           || newFeatureAdded)\r
 175        {\r
 176          findAllFeatures();\r
 177          if(av.featuresDisplayed.size()<1)\r
 178            return;\r
 179 \r
 180          sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
 181          sfSize = sequenceFeatures.length;\r
 182        }\r
 183 \r
 184        if(lastSeq==null || seq!=lastSeq)\r
 185       {\r
 186         lastSeq = seq;\r
 187         sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
 188         sfSize = sequenceFeatures.length;\r
 189       }\r
 190 \r
 191 \r
 192       if (transparency != 1 && g!=null)\r
 193       {\r
 194         Graphics2D g2 = (Graphics2D) g;\r
 195         g2.setComposite(\r
 196             AlphaComposite.getInstance(\r
 197                 AlphaComposite.SRC_OVER, transparency));\r
 198       }\r
 199 \r
 200       if(!offscreenRender)\r
 201       {\r
 202         spos = lastSeq.findPosition(start);\r
 203         epos = lastSeq.findPosition(end);\r
 204       }\r
 205 \r
 206 \r
 207       String type;\r
 208       for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)\r
 209        {\r
 210         type =  renderOrder[renderIndex];\r
 211 \r
 212         if(!av.featuresDisplayed.containsKey(type))\r
 213           continue;\r
 214 \r
 215         // loop through all features in sequence to find\r
 216         // current feature to render\r
 217         for (sfindex = 0; sfindex < sfSize; sfindex++)\r
 218         {\r
 219           if(sequenceFeatures.length<=sfindex)\r
 220           {\r
 221             continue;\r
 222           }\r
 223           if (!sequenceFeatures[sfindex].type.equals(type))\r
 224             continue;\r
 225 \r
 226           if (featureGroups != null\r
 227               && sequenceFeatures[sfindex].featureGroup != null\r
 228               &&\r
 229               featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)\r
 230               &&\r
 231               ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).\r
 232               booleanValue())\r
 233           {\r
 234             continue;\r
 235           }\r
 236 \r
 237           if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos\r
 238                             || sequenceFeatures[sfindex].getEnd() < spos))\r
 239             continue;\r
 240 \r
 241           if (offscreenRender && offscreenImage==null)\r
 242           {\r
 243             if (sequenceFeatures[sfindex].begin <= start &&\r
 244                 sequenceFeatures[sfindex].end  >= start)\r
 245             {\r
 246               currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].\r
 247                  type);\r
 248             }\r
 249           }\r
 250           else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))\r
 251           {\r
 252 \r
 253             renderFeature(g, seq,\r
 254                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 255                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 256                           new Color( ( (Integer) av.featuresDisplayed.get(\r
 257                 sequenceFeatures[sfindex].type)).intValue()),\r
 258                           start, end, y1);\r
 259             renderFeature(g, seq,\r
 260                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 261                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 262                           new Color( ( (Integer) av.featuresDisplayed.get(\r
 263                 sequenceFeatures[sfindex].type)).intValue()),\r
 264                           start, end, y1);\r
 265 \r
 266           }\r
 267           else\r
 268             renderFeature(g, seq,\r
 269                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 270                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 271                           getColour(sequenceFeatures[sfindex].type),\r
 272                           start, end, y1);\r
 273 \r
 274 \r
 275         }\r
 276 \r
 277       }\r
 278 \r
 279         if(transparency!=1.0f && g!=null)\r
 280         {\r
 281           Graphics2D g2 = (Graphics2D) g;\r
 282           g2.setComposite(\r
 283               AlphaComposite.getInstance(\r
 284                   AlphaComposite.SRC_OVER, 1.0f));\r
 285         }\r
 286     }\r
 287 \r
 288 \r
 289     char s;\r
 290     int i;\r
 291     void renderFeature(Graphics g, SequenceI seq,\r
 292                        int fstart, int fend, Color featureColour, int start, int end,  int y1)\r
 293     {\r
 294 \r
 295       if (((fstart <= end) && (fend >= start)))\r
 296       {\r
 297         if (fstart < start)\r
 298         { // fix for if the feature we have starts before the sequence start,\r
 299           fstart = start; // but the feature end is still valid!!\r
 300         }\r
 301 \r
 302         if (fend >= end)\r
 303         {\r
 304           fend = end;\r
 305         }\r
 306           int pady = (y1 + av.charHeight) - av.charHeight / 5;\r
 307           for (i = fstart; i <= fend; i++)\r
 308           {\r
 309             s = seq.getSequence().charAt(i);\r
 310 \r
 311             if (jalview.util.Comparison.isGap(s))\r
 312             {\r
 313               continue;\r
 314             }\r
 315 \r
 316             g.setColor(featureColour);\r
 317 \r
 318             g.fillRect( (i - start) * av.charWidth, y1, av.charWidth,av.charHeight);\r
 319 \r
 320             if(offscreenRender || !av.validCharWidth)\r
 321               continue;\r
 322 \r
 323             g.setColor(Color.white);\r
 324             charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
 325             g.drawString(String.valueOf(s),\r
 326                          charOffset + (av.charWidth * (i - start)),\r
 327                          pady);\r
 328 \r
 329           }\r
 330       }\r
 331     }\r
 332 \r
 333 \r
 334     boolean newFeatureAdded = false;\r
 335 \r
 336     public void featuresAdded()\r
 337     {\r
 338       findAllFeatures();\r
 339     }\r
 340 \r
 341    boolean findingFeatures = false;\r
 342    synchronized void findAllFeatures()\r
 343    {\r
 344       newFeatureAdded = false;\r
 345 \r
 346       if(findingFeatures)\r
 347       {\r
 348         newFeatureAdded = true;\r
 349         return;\r
 350       }\r
 351 \r
 352       findingFeatures = true;\r
 353       jalview.schemes.UserColourScheme ucs = new\r
 354           jalview.schemes.UserColourScheme();\r
 355 \r
 356       if(av.featuresDisplayed==null)\r
 357         av.featuresDisplayed = new Hashtable();\r
 358 \r
 359       av.featuresDisplayed.clear();\r
 360 \r
 361       Vector allfeatures = new Vector();\r
 362       for (int i = 0; i < av.alignment.getHeight(); i++)\r
 363       {\r
 364         SequenceFeature [] features\r
 365             = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
 366 \r
 367         if (features == null)\r
 368           continue;\r
 369 \r
 370         int index = 0;\r
 371         while (index < features.length)\r
 372         {\r
 373           if (!av.featuresDisplayed.containsKey(features[index].getType()))\r
 374           {\r
 375             if(!(features[index].begin == 0 && features[index].end ==0))\r
 376             {\r
 377               // If beginning and end are 0, the feature is for the whole sequence\r
 378               // and we don't want to render the feature in the normal way\r
 379 \r
 380               if (getColour(features[index].getType()) == null)\r
 381               {\r
 382                  featureColours.put(features[index].getType(),\r
 383                                    ucs.createColourFromName(features[index].\r
 384                     getType()));\r
 385               }\r
 386 \r
 387               av.featuresDisplayed.put(features[index].getType(),\r
 388                                        new Integer(getColour(features[index].\r
 389                   getType()).getRGB()));\r
 390               allfeatures.addElement(features[index].getType());\r
 391             }\r
 392           }\r
 393           index++;\r
 394         }\r
 395       }\r
 396 \r
 397       renderOrder = new String[allfeatures.size()];\r
 398       Enumeration en = allfeatures.elements();\r
 399       int i = allfeatures.size()-1;\r
 400       while(en.hasMoreElements())\r
 401       {\r
 402         renderOrder[i] = en.nextElement().toString();\r
 403         i--;\r
 404       }\r
 405 \r
 406       findingFeatures = false;\r
 407     }\r
 408 \r
 409     public Color getColour(String featureType)\r
 410     {\r
 411       Color colour = (Color)featureColours.get(featureType);\r
 412       return colour;\r
 413     }\r
 414 \r
 415 \r
 416     public void addNewFeature(String name, Color col, String group)\r
 417     {\r
 418 \r
 419       setColour(name, col);\r
 420       if(av.featuresDisplayed==null)\r
 421         av.featuresDisplayed = new Hashtable();\r
 422 \r
 423       if(group == null)\r
 424         group = "NOGROUP";\r
 425 \r
 426       av.featuresDisplayed.put(name, new Integer(col.getRGB()));\r
 427     }\r
 428 \r
 429     public void setColour(String featureType, Color col)\r
 430     {\r
 431       featureColours.put(featureType, col);\r
 432     }\r
 433 \r
 434     public void setTransparency(float value)\r
 435     {\r
 436       transparency = value;\r
 437     }\r
 438 \r
 439     public float getTransparency()\r
 440     {\r
 441       return transparency;\r
 442     }\r
 443 \r
 444     public void setFeaturePriority(Object [][] data)\r
 445     {\r
 446       // The feature table will display high priority\r
 447       // features at the top, but theses are the ones\r
 448       // we need to render last, so invert the data\r
 449       if(av.featuresDisplayed!=null)\r
 450         av.featuresDisplayed.clear();\r
 451       else\r
 452         av.featuresDisplayed = new Hashtable();\r
 453 \r
 454       renderOrder = new String[data.length];\r
 455 \r
 456       if (data.length > 0)\r
 457         for (int i = 0; i < data.length; i++)\r
 458         {\r
 459           String type = data[i][0].toString();\r
 460           setColour(type, (Color) data[i][1]);\r
 461           if ( ( (Boolean) data[i][2]).booleanValue())\r
 462           {\r
 463             av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));\r
 464           }\r
 465 \r
 466           renderOrder[data.length - i - 1] = type;\r
 467         }\r
 468 \r
 469     }\r
 470 \r
 471 \r
 472 \r
 473 \r
 474 }\r