src/jalview/gui/FeatureRenderer.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 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     boolean newFeatureAdded = false;\r
  58 \r
  59 \r
  60     /**\r
  61      * Creates a new FeatureRenderer object.\r
  62      *\r
  63      * @param av DOCUMENT ME!\r
  64      */\r
  65     public FeatureRenderer(AlignViewport av)\r
  66     {\r
  67         this.av = av;\r
  68     }\r
  69 \r
  70     public void transferSettings(FeatureRenderer fr)\r
  71     {\r
  72       renderOrder = fr.renderOrder;\r
  73       featureGroups = fr.featureGroups;\r
  74       featureColours = fr.featureColours;\r
  75       transparency =  fr.transparency;\r
  76     }\r
  77 \r
  78     BufferedImage offscreenImage;\r
  79     boolean offscreenRender = false;\r
  80     public Color findFeatureColour(Color initialCol, SequenceI seq, int res)\r
  81     {\r
  82       int seqindex = av.alignment.findIndex(seq);\r
  83 \r
  84       return new Color( findFeatureColour (initialCol.getRGB(),\r
  85                         seqindex, res ));\r
  86     }\r
  87 \r
  88     /**\r
  89      * This is used by the Molecule Viewer to get the accurate colour\r
  90      * of the rendered sequence\r
  91      */\r
  92     public int findFeatureColour(int initialCol, int seqIndex, int column)\r
  93     {\r
  94       if(!av.showSequenceFeatures)\r
  95         return initialCol;\r
  96 \r
  97       if(seqIndex!=lastSequenceIndex)\r
  98       {\r
  99         lastSequence = av.alignment.getSequenceAt(seqIndex);\r
 100         lastSequenceIndex = seqIndex;\r
 101         sequenceFeatures = lastSequence.getDatasetSequence().getSequenceFeatures();\r
 102         if(sequenceFeatures==null)\r
 103           return initialCol;\r
 104 \r
 105         sfSize = sequenceFeatures.length;\r
 106       }\r
 107 \r
 108       if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))\r
 109         return Color.white.getRGB();\r
 110 \r
 111 \r
 112       //Only bother making an offscreen image if transparency is applied\r
 113       if(transparency!=1.0f && offscreenImage==null)\r
 114       {\r
 115         offscreenImage = new BufferedImage(1,1,BufferedImage.TYPE_INT_ARGB);\r
 116       }\r
 117 \r
 118       currentColour = null;\r
 119 \r
 120       offscreenRender = true;\r
 121 \r
 122       if(offscreenImage!=null)\r
 123       {\r
 124         offscreenImage.setRGB(0,0,initialCol);\r
 125         drawSequence(offscreenImage.getGraphics(),\r
 126                      lastSequence,\r
 127                      column,column,0);\r
 128 \r
 129         return offscreenImage.getRGB(0,0);\r
 130       }\r
 131       else\r
 132       {\r
 133         drawSequence(null,\r
 134                     lastSequence,\r
 135                     lastSequence.findPosition(column),\r
 136                     -1, -1);\r
 137 \r
 138         if (currentColour == null)\r
 139           return initialCol;\r
 140         else\r
 141           return  ((Integer)currentColour).intValue();\r
 142       }\r
 143 \r
 144 \r
 145     }\r
 146 \r
 147 \r
 148     /**\r
 149      * DOCUMENT ME!\r
 150      *\r
 151      * @param g DOCUMENT ME!\r
 152      * @param seq DOCUMENT ME!\r
 153      * @param sg DOCUMENT ME!\r
 154      * @param start DOCUMENT ME!\r
 155      * @param end DOCUMENT ME!\r
 156      * @param x1 DOCUMENT ME!\r
 157      * @param y1 DOCUMENT ME!\r
 158      * @param width DOCUMENT ME!\r
 159      * @param height DOCUMENT ME!\r
 160      */\r
 161    // String type;\r
 162    // SequenceFeature sf;\r
 163     int lastSequenceIndex=-1;\r
 164     SequenceI lastSequence;\r
 165     SequenceFeature [] sequenceFeatures;\r
 166     int sfSize, sfindex, spos, epos;\r
 167 \r
 168     public void drawSequence(Graphics g, SequenceI seq,\r
 169                              int start, int end, int y1)\r
 170     {\r
 171       if ( seq.getDatasetSequence().getSequenceFeatures() == null\r
 172           || seq.getDatasetSequence().getSequenceFeatures().length==0)\r
 173         return;\r
 174 \r
 175 \r
 176       if(g!=null)\r
 177         fm = g.getFontMetrics();\r
 178 \r
 179 \r
 180       if (av.featuresDisplayed == null\r
 181           || renderOrder==null\r
 182           || newFeatureAdded)\r
 183        {\r
 184          findAllFeatures();\r
 185          if(av.featuresDisplayed.size()<1)\r
 186            return;\r
 187 \r
 188          sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
 189          sfSize = sequenceFeatures.length;\r
 190        }\r
 191 \r
 192        if(lastSequence==null || seq!=lastSequence)\r
 193       {\r
 194         lastSequence = seq;\r
 195         sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
 196         sfSize = sequenceFeatures.length;\r
 197       }\r
 198 \r
 199 \r
 200       if (transparency != 1 && g!=null)\r
 201       {\r
 202         Graphics2D g2 = (Graphics2D) g;\r
 203         g2.setComposite(\r
 204             AlphaComposite.getInstance(\r
 205                 AlphaComposite.SRC_OVER, transparency));\r
 206       }\r
 207 \r
 208       if(!offscreenRender)\r
 209       {\r
 210         spos = lastSequence.findPosition(start);\r
 211         epos = lastSequence.findPosition(end);\r
 212       }\r
 213 \r
 214 \r
 215       String type;\r
 216       for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)\r
 217        {\r
 218         type =  renderOrder[renderIndex];\r
 219 \r
 220         if(!av.featuresDisplayed.containsKey(type))\r
 221           continue;\r
 222 \r
 223         // loop through all features in sequence to find\r
 224         // current feature to render\r
 225         for (sfindex = 0; sfindex < sfSize; sfindex++)\r
 226         {\r
 227           if(sequenceFeatures.length<=sfindex)\r
 228           {\r
 229             continue;\r
 230           }\r
 231           if (!sequenceFeatures[sfindex].type.equals(type))\r
 232             continue;\r
 233 \r
 234           if (featureGroups != null\r
 235               && sequenceFeatures[sfindex].featureGroup != null\r
 236               &&\r
 237               featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)\r
 238               &&\r
 239               ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).\r
 240               booleanValue())\r
 241           {\r
 242             continue;\r
 243           }\r
 244 \r
 245           if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos\r
 246                             || sequenceFeatures[sfindex].getEnd() < spos))\r
 247             continue;\r
 248 \r
 249           if (offscreenRender && offscreenImage==null)\r
 250           {\r
 251             if (sequenceFeatures[sfindex].begin <= start &&\r
 252                 sequenceFeatures[sfindex].end  >= start)\r
 253             {\r
 254               currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].\r
 255                  type);\r
 256             }\r
 257           }\r
 258           else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))\r
 259           {\r
 260 \r
 261             renderFeature(g, seq,\r
 262                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 263                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 264                           new Color( ( (Integer) av.featuresDisplayed.get(\r
 265                 sequenceFeatures[sfindex].type)).intValue()),\r
 266                           start, end, y1);\r
 267             renderFeature(g, seq,\r
 268                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 269                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 270                           new Color( ( (Integer) av.featuresDisplayed.get(\r
 271                 sequenceFeatures[sfindex].type)).intValue()),\r
 272                           start, end, y1);\r
 273 \r
 274           }\r
 275           else\r
 276             renderFeature(g, seq,\r
 277                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 278                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 279                           getColour(sequenceFeatures[sfindex].type),\r
 280                           start, end, y1);\r
 281 \r
 282 \r
 283         }\r
 284 \r
 285       }\r
 286 \r
 287         if(transparency!=1.0f && g!=null)\r
 288         {\r
 289           Graphics2D g2 = (Graphics2D) g;\r
 290           g2.setComposite(\r
 291               AlphaComposite.getInstance(\r
 292                   AlphaComposite.SRC_OVER, 1.0f));\r
 293         }\r
 294     }\r
 295 \r
 296 \r
 297     char s;\r
 298     int i;\r
 299     void renderFeature(Graphics g, SequenceI seq,\r
 300                        int fstart, int fend, Color featureColour, int start, int end,  int y1)\r
 301     {\r
 302 \r
 303       if (((fstart <= end) && (fend >= start)))\r
 304       {\r
 305         if (fstart < start)\r
 306         { // fix for if the feature we have starts before the sequence start,\r
 307           fstart = start; // but the feature end is still valid!!\r
 308         }\r
 309 \r
 310         if (fend >= end)\r
 311         {\r
 312           fend = end;\r
 313         }\r
 314           int pady = (y1 + av.charHeight) - av.charHeight / 5;\r
 315           for (i = fstart; i <= fend; i++)\r
 316           {\r
 317             s = seq.getSequence().charAt(i);\r
 318 \r
 319             if (jalview.util.Comparison.isGap(s))\r
 320             {\r
 321               continue;\r
 322             }\r
 323 \r
 324             g.setColor(featureColour);\r
 325 \r
 326             g.fillRect( (i - start) * av.charWidth, y1, av.charWidth,av.charHeight);\r
 327 \r
 328             if(offscreenRender || !av.validCharWidth)\r
 329               continue;\r
 330 \r
 331             g.setColor(Color.white);\r
 332             charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
 333             g.drawString(String.valueOf(s),\r
 334                          charOffset + (av.charWidth * (i - start)),\r
 335                          pady);\r
 336 \r
 337           }\r
 338       }\r
 339     }\r
 340 \r
 341     int count = 0;\r
 342     synchronized public void featuresAdded()\r
 343     {\r
 344       newFeatureAdded = true;\r
 345       findAllFeatures();\r
 346       newFeatureAdded = false;\r
 347     }\r
 348 \r
 349    synchronized void findAllFeatures()\r
 350    {\r
 351       jalview.schemes.UserColourScheme ucs = new\r
 352           jalview.schemes.UserColourScheme();\r
 353 \r
 354       if(av.featuresDisplayed==null)\r
 355         av.featuresDisplayed = new Hashtable();\r
 356 \r
 357       av.featuresDisplayed.clear();\r
 358 \r
 359       Vector allfeatures = new Vector();\r
 360       for (int i = 0; i < av.alignment.getHeight(); i++)\r
 361       {\r
 362         SequenceFeature [] features\r
 363             = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
 364 \r
 365         if (features == null)\r
 366           continue;\r
 367 \r
 368         int index = 0;\r
 369         while (index < features.length)\r
 370         {\r
 371           if (!av.featuresDisplayed.containsKey(features[index].getType()))\r
 372           {\r
 373             if(!(features[index].begin == 0 && features[index].end ==0))\r
 374             {\r
 375               // If beginning and end are 0, the feature is for the whole sequence\r
 376               // and we don't want to render the feature in the normal way\r
 377 \r
 378               if (getColour(features[index].getType()) == null)\r
 379               {\r
 380                  featureColours.put(features[index].getType(),\r
 381                                    ucs.createColourFromName(features[index].\r
 382                     getType()));\r
 383               }\r
 384 \r
 385               av.featuresDisplayed.put(features[index].getType(),\r
 386                                        new Integer(getColour(features[index].\r
 387                   getType()).getRGB()));\r
 388               allfeatures.addElement(features[index].getType());\r
 389             }\r
 390           }\r
 391           index++;\r
 392         }\r
 393       }\r
 394 \r
 395       renderOrder = new String[allfeatures.size()];\r
 396       Enumeration en = allfeatures.elements();\r
 397       int i = allfeatures.size()-1;\r
 398       while(en.hasMoreElements())\r
 399       {\r
 400         renderOrder[i] = en.nextElement().toString();\r
 401         i--;\r
 402       }\r
 403     }\r
 404 \r
 405     public Color getColour(String featureType)\r
 406     {\r
 407       Color colour = (Color)featureColours.get(featureType);\r
 408       return colour;\r
 409     }\r
 410 \r
 411 \r
 412     public void addNewFeature(String name, Color col, String group)\r
 413     {\r
 414 \r
 415       setColour(name, col);\r
 416       if(av.featuresDisplayed==null)\r
 417         av.featuresDisplayed = new Hashtable();\r
 418 \r
 419       if(group == null)\r
 420         group = "NOGROUP";\r
 421 \r
 422       av.featuresDisplayed.put(name, new Integer(col.getRGB()));\r
 423     }\r
 424 \r
 425     public void setColour(String featureType, Color col)\r
 426     {\r
 427       featureColours.put(featureType, col);\r
 428     }\r
 429 \r
 430     public void setTransparency(float value)\r
 431     {\r
 432       transparency = value;\r
 433     }\r
 434 \r
 435     public float getTransparency()\r
 436     {\r
 437       return transparency;\r
 438     }\r
 439 \r
 440     public void setFeaturePriority(Object [][] data)\r
 441     {\r
 442       // The feature table will display high priority\r
 443       // features at the top, but theses are the ones\r
 444       // we need to render last, so invert the data\r
 445       if(av.featuresDisplayed!=null)\r
 446         av.featuresDisplayed.clear();\r
 447       else\r
 448         av.featuresDisplayed = new Hashtable();\r
 449 \r
 450       renderOrder = new String[data.length];\r
 451 \r
 452       if (data.length > 0)\r
 453         for (int i = 0; i < data.length; i++)\r
 454         {\r
 455           String type = data[i][0].toString();\r
 456           setColour(type, (Color) data[i][1]);\r
 457           if ( ( (Boolean) data[i][2]).booleanValue())\r
 458           {\r
 459             av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));\r
 460           }\r
 461 \r
 462           renderOrder[data.length - i - 1] = type;\r
 463         }\r
 464 \r
 465     }\r
 466 \r
 467 \r
 468 \r
 469 \r
 470 }\r