src/jalview/appletgui/FeatureRenderer.java

   1 \r
   2 /*\r
   3  * Jalview - A Sequence Alignment Editor and Viewer\r
   4  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   5  *\r
   6  * This program is free software; you can redistribute it and/or\r
   7  * modify it under the terms of the GNU General Public License\r
   8  * as published by the Free Software Foundation; either version 2\r
   9  * of the License, or (at your option) any later version.\r
  10  *\r
  11  * This program is distributed in the hope that it will be useful,\r
  12  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  13  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  14  * GNU General Public License for more details.\r
  15  *\r
  16  * You should have received a copy of the GNU General Public License\r
  17  * along with this program; if not, write to the Free Software\r
  18  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  19  */\r
  20 package jalview.appletgui;\r
  21 \r
  22 import jalview.datamodel.*;\r
  23 \r
  24 import java.awt.*;\r
  25 \r
  26 import java.util.*;\r
  27 \r
  28 /**\r
  29  * DOCUMENT ME!\r
  30  *\r
  31  * @author $author$\r
  32  * @version $Revision$\r
  33  */\r
  34 public class FeatureRenderer\r
  35 {\r
  36     AlignViewport av;\r
  37 \r
  38 \r
  39     // A higher level for grouping features of a\r
  40     // particular type\r
  41     Hashtable featureGroups = null;\r
  42 \r
  43     // Holds web links for feature groups and feature types\r
  44     // in the form label|link\r
  45     Hashtable featureLinks = null;\r
  46 \r
  47 \r
  48     // This is actually an Integer held in the hashtable,\r
  49     // Retrieved using the key feature type\r
  50     Object currentColour;\r
  51 \r
  52     String [] renderOrder;\r
  53 \r
  54     FontMetrics fm;\r
  55     int charOffset;\r
  56 \r
  57     float transparency = 1f;\r
  58 \r
  59     TransparencySetter transparencySetter = null;\r
  60 \r
  61     /**\r
  62      * Creates a new FeatureRenderer object.\r
  63      *\r
  64      * @param av DOCUMENT ME!\r
  65      */\r
  66     public FeatureRenderer(AlignViewport av)\r
  67     {\r
  68         this.av = av;\r
  69         initColours();\r
  70 \r
  71         if(!System.getProperty("java.version").startsWith("1.1"))\r
  72              transparencySetter = new TransparencySetter();\r
  73     }\r
  74 \r
  75     public void addFeatureLink(String feature, String link)\r
  76     {\r
  77       if(featureLinks == null)\r
  78         featureLinks = new Hashtable();\r
  79 \r
  80        featureLinks.put(feature, link);\r
  81     }\r
  82 \r
  83 \r
  84     public void transferSettings(FeatureRenderer fr)\r
  85     {\r
  86       renderOrder = fr.renderOrder;\r
  87       featureGroups = fr.featureGroups;\r
  88       featureColours = fr.featureColours;\r
  89     }\r
  90 \r
  91 \r
  92     public Color findFeatureColour(Color initialCol, SequenceI seq, int i)\r
  93     {\r
  94       overview = true;\r
  95       if(!av.showSequenceFeatures)\r
  96         return initialCol;\r
  97 \r
  98         lastSequence = seq;\r
  99         sequenceFeatures = lastSequence.getSequenceFeatures();\r
 100         if(sequenceFeatures==null)\r
 101           return initialCol;\r
 102 \r
 103         sfSize = sequenceFeatures.length;\r
 104 \r
 105       if(jalview.util.Comparison.isGap(lastSequence.getCharAt(i)))\r
 106         return Color.white;\r
 107 \r
 108       currentColour = null;\r
 109 \r
 110       drawSequence(null, lastSequence, lastSequence.findPosition(i), -1,-1, -1, -1);\r
 111 \r
 112       if(currentColour==null)\r
 113         return initialCol;\r
 114 \r
 115       return new Color( ((Integer)currentColour).intValue() );\r
 116     }\r
 117 \r
 118     /**\r
 119      * This is used by the Molecule Viewer to get the accurate colour\r
 120      * of the rendered sequence\r
 121      */\r
 122     boolean overview = false;\r
 123 \r
 124     int white = Color.white.getRGB();\r
 125     public int findFeatureColour(int initialCol, int seqIndex, int column)\r
 126     {\r
 127       if(!av.showSequenceFeatures)\r
 128         return initialCol;\r
 129 \r
 130       if(seqIndex!=lastSequenceIndex)\r
 131       {\r
 132         lastSequence = av.alignment.getSequenceAt(seqIndex);\r
 133         lastSequenceIndex = seqIndex;\r
 134         sequenceFeatures = lastSequence.getSequenceFeatures();\r
 135         if(sequenceFeatures==null)\r
 136           return initialCol;\r
 137 \r
 138         sfSize = sequenceFeatures.length;\r
 139       }\r
 140 \r
 141 \r
 142       if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))\r
 143         return Color.white.getRGB();\r
 144 \r
 145       currentColour = null;\r
 146 \r
 147       drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1, -1, -1);\r
 148 \r
 149       if(currentColour==null)\r
 150         return initialCol;\r
 151 \r
 152       return  ((Integer)currentColour).intValue();\r
 153     }\r
 154 \r
 155 \r
 156     /**\r
 157      * DOCUMENT ME!\r
 158      *\r
 159      * @param g DOCUMENT ME!\r
 160      * @param seq DOCUMENT ME!\r
 161      * @param sg DOCUMENT ME!\r
 162      * @param start DOCUMENT ME!\r
 163      * @param end DOCUMENT ME!\r
 164      * @param x1 DOCUMENT ME!\r
 165      * @param y1 DOCUMENT ME!\r
 166      * @param width DOCUMENT ME!\r
 167      * @param height DOCUMENT ME!\r
 168      */\r
 169    // String type;\r
 170    // SequenceFeature sf;\r
 171     int lastSequenceIndex=-1;\r
 172     SequenceI lastSequence;\r
 173     SequenceFeature [] sequenceFeatures;\r
 174     int sfSize, sfindex, spos, epos;\r
 175 \r
 176     public void drawSequence(Graphics g, SequenceI seq,\r
 177                              int start, int end, int y1, int width, int height)\r
 178     {\r
 179       if (   seq.getSequenceFeatures() == null\r
 180           || seq.getSequenceFeatures().length==0)\r
 181         return;\r
 182 \r
 183       if(transparencySetter!=null && g!=null)\r
 184       {\r
 185         transparencySetter.setTransparency(g, transparency);\r
 186       }\r
 187 \r
 188       if (av.featuresDisplayed == null || renderOrder==null)\r
 189        {\r
 190          findAllFeatures();\r
 191          if(av.featuresDisplayed.size()<1)\r
 192            return;\r
 193 \r
 194          sequenceFeatures = seq.getSequenceFeatures();\r
 195          sfSize = sequenceFeatures.length;\r
 196        }\r
 197        if(lastSequence==null || seq!=lastSequence)\r
 198       {\r
 199         lastSequence = seq;\r
 200         sequenceFeatures = seq.getSequenceFeatures();\r
 201         sfSize = sequenceFeatures.length;\r
 202       }\r
 203       if(!overview)\r
 204       {\r
 205         spos = lastSequence.findPosition(start);\r
 206         epos = lastSequence.findPosition(end);\r
 207         if(g!=null)\r
 208           fm = g.getFontMetrics();\r
 209       }\r
 210       String type;\r
 211       for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)\r
 212        {\r
 213         type =  renderOrder[renderIndex];\r
 214         if(!av.featuresDisplayed.containsKey(type))\r
 215           continue;\r
 216 \r
 217         // loop through all features in sequence to find\r
 218         // current feature to render\r
 219         for (sfindex = 0; sfindex < sfSize; sfindex++)\r
 220         {\r
 221           if (!sequenceFeatures[sfindex].type.equals(type))\r
 222             continue;\r
 223 \r
 224           if (featureGroups != null\r
 225               && sequenceFeatures[sfindex].featureGroup != null\r
 226               &&\r
 227               featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)\r
 228               &&\r
 229               ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).\r
 230               booleanValue())\r
 231           {\r
 232             continue;\r
 233           }\r
 234 \r
 235           if (!overview && (sequenceFeatures[sfindex].getBegin() > epos\r
 236                             || sequenceFeatures[sfindex].getEnd() < spos))\r
 237             continue;\r
 238 \r
 239           if (overview)\r
 240           {\r
 241             if (sequenceFeatures[sfindex].begin <= start &&\r
 242                 sequenceFeatures[sfindex].end >= start)\r
 243             {\r
 244               currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].\r
 245                   type);\r
 246             }\r
 247 \r
 248           }\r
 249           else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))\r
 250           {\r
 251 \r
 252             renderFeature(g, seq,\r
 253                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 254                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 255                           new Color( ( (Integer) av.featuresDisplayed.get(\r
 256                 sequenceFeatures[sfindex].type)).intValue()),\r
 257                           start, end, y1, width, height);\r
 258             renderFeature(g, seq,\r
 259                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 260                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 261                           new Color( ( (Integer) av.featuresDisplayed.get(\r
 262                 sequenceFeatures[sfindex].type)).intValue()),\r
 263                           start, end, y1, width, height);\r
 264 \r
 265           }\r
 266           else\r
 267             renderFeature(g, seq,\r
 268                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 269                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 270                           getColour(sequenceFeatures[sfindex].type),\r
 271                           start, end, y1, width, height);\r
 272 \r
 273         }\r
 274       }\r
 275 \r
 276       if(transparencySetter!=null && g!=null)\r
 277       {\r
 278         transparencySetter.setTransparency(g, 1.0f);\r
 279       }\r
 280     }\r
 281 \r
 282 \r
 283     char s;\r
 284     int i;\r
 285     void renderFeature(Graphics g, SequenceI seq,\r
 286                        int fstart, int fend, Color featureColour, int start, int end,  int y1, int width, int height)\r
 287     {\r
 288 \r
 289       if (((fstart <= end) && (fend >= start)))\r
 290       {\r
 291         if (fstart < start)\r
 292         { // fix for if the feature we have starts before the sequence start,\r
 293           fstart = start; // but the feature end is still valid!!\r
 294         }\r
 295 \r
 296         if (fend >= end)\r
 297         {\r
 298           fend = end;\r
 299         }\r
 300 \r
 301           for (i = fstart; i <= fend; i++)\r
 302           {\r
 303             s = seq.getSequence().charAt(i);\r
 304 \r
 305             if (jalview.util.Comparison.isGap(s))\r
 306             {\r
 307               continue;\r
 308             }\r
 309 \r
 310             g.setColor(featureColour);\r
 311 \r
 312             g.fillRect( (i - start) * width, y1, width, height);\r
 313 \r
 314             if(!av.validCharWidth)\r
 315               continue;\r
 316 \r
 317             g.setColor(Color.white);\r
 318             charOffset = (width - fm.charWidth(s)) / 2;\r
 319             g.drawString(String.valueOf(s),\r
 320                          charOffset + (width * (i - start)),\r
 321                          (y1 + height) - height / 5); //pady = height / 5;\r
 322 \r
 323           }\r
 324       }\r
 325     }\r
 326 \r
 327     void findAllFeatures()\r
 328     {\r
 329       av.featuresDisplayed = new Hashtable();\r
 330       Vector allfeatures = new Vector();\r
 331       for (int i = 0; i < av.alignment.getHeight(); i++)\r
 332       {\r
 333         SequenceFeature [] features = av.alignment.getSequenceAt(i).getSequenceFeatures();\r
 334 \r
 335         if (features == null)\r
 336           continue;\r
 337 \r
 338         int index = 0;\r
 339         while (index < features.length)\r
 340         {\r
 341           if (!av.featuresDisplayed.containsKey(features[index].getType()))\r
 342           {\r
 343             av.featuresDisplayed.put(features[index].getType(),\r
 344                                   new Integer( getColour(features[index].getType()).getRGB()) );\r
 345             allfeatures.addElement(features[index].getType());\r
 346           }\r
 347           index++;\r
 348         }\r
 349       }\r
 350 \r
 351       renderOrder = new String[allfeatures.size()];\r
 352       Enumeration en = allfeatures.elements();\r
 353       int i = allfeatures.size()-1;\r
 354       while(en.hasMoreElements())\r
 355       {\r
 356         renderOrder[i] = en.nextElement().toString();\r
 357         i--;\r
 358       }\r
 359     }\r
 360 \r
 361     public Color getColour(String featureType)\r
 362     {\r
 363       return (Color)featureColours.get(featureType);\r
 364     }\r
 365 \r
 366     public void addNewFeature(String name, Color col)\r
 367     {\r
 368 \r
 369       setColour(name, col);\r
 370       if(av.featuresDisplayed==null)\r
 371         av.featuresDisplayed = new Hashtable();\r
 372 \r
 373 \r
 374       av.featuresDisplayed.put(name, "NOGROUP");\r
 375     }\r
 376 \r
 377     public void setColour(String featureType, Color col)\r
 378     {\r
 379       featureColours.put(featureType, col);\r
 380     }\r
 381 \r
 382     public void setFeaturePriority(Object [][] data)\r
 383     {\r
 384         // The feature table will display high priority\r
 385         // features at the top, but theses are the ones\r
 386         // we need to render last, so invert the data\r
 387         if(av.featuresDisplayed!=null)\r
 388           av.featuresDisplayed.clear();\r
 389 \r
 390         renderOrder = new String[data.length];\r
 391 \r
 392         if (data.length > 0)\r
 393           for (int i = 0; i < data.length; i++)\r
 394           {\r
 395             String type = data[i][0].toString();\r
 396             setColour(type, (Color) data[i][1]);\r
 397             if ( ( (Boolean) data[i][2]).booleanValue())\r
 398             {\r
 399               av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));\r
 400             }\r
 401 \r
 402             renderOrder[data.length - i - 1] = type;\r
 403           }\r
 404     }\r
 405 \r
 406     Hashtable featureColours = new Hashtable();\r
 407     void initColours()\r
 408     {\r
 409       featureColours.put("active site", new Color(255, 75, 0));\r
 410       featureColours.put("binding site", new Color(245, 85, 0));\r
 411       featureColours.put("calcium-binding region", new Color(235, 95, 0));\r
 412       featureColours.put("chain", new Color(225, 105, 0));\r
 413       featureColours.put("coiled-coil region", new Color(215, 115, 0));\r
 414       featureColours.put("compositionally biased region", new Color(205, 125, 0));\r
 415       featureColours.put("cross-link", new Color(195, 135, 0));\r
 416       featureColours.put("disulfide bond", new Color(185, 145, 0));\r
 417       featureColours.put("DNA-binding region", new Color(175, 155, 0));\r
 418       featureColours.put("domain", new Color(165, 165, 0));\r
 419       featureColours.put("glycosylation site", new Color(155, 175, 0));\r
 420       featureColours.put("helix", new Color(145, 185, 0));\r
 421       featureColours.put("initiator methionine", new Color(135, 195, 5));\r
 422       featureColours.put("lipid moiety-binding region", new Color(125, 205, 15));\r
 423       featureColours.put("metal ion-binding site", new Color(115, 215, 25));\r
 424       featureColours.put("modified residue", new Color(105, 225, 35));\r
 425       featureColours.put("mutagenesis site", new Color(95, 235, 45));\r
 426       featureColours.put("non-consecutive residues", new Color(85, 245, 55));\r
 427       featureColours.put("non-terminal residue", new Color(75, 255, 65));\r
 428       featureColours.put("nucleotide phosphate-binding region",\r
 429                          new Color(65, 245, 75));\r
 430       featureColours.put("peptide", new Color(55, 235, 85));\r
 431       featureColours.put("propeptide", new Color(45, 225, 95));\r
 432       featureColours.put("region of interest", new Color(35, 215, 105));\r
 433       featureColours.put("repeat", new Color(25, 205, 115));\r
 434       featureColours.put("selenocysteine", new Color(15, 195, 125));\r
 435       featureColours.put("sequence conflict", new Color(5, 185, 135));\r
 436       featureColours.put("sequence variant", new Color(0, 175, 145));\r
 437       featureColours.put("short sequence motif", new Color(0, 165, 155));\r
 438       featureColours.put("signal peptide", new Color(0, 155, 165));\r
 439       featureColours.put("site", new Color(0, 145, 175));\r
 440       featureColours.put("splice variant", new Color(0, 135, 185));\r
 441       featureColours.put("strand", new Color(0, 125, 195));\r
 442       featureColours.put("topological domain", new Color(0, 115, 205));\r
 443       featureColours.put("transit peptide", new Color(0, 105, 215));\r
 444       featureColours.put("transmembrane region", new Color(0, 95, 225));\r
 445       featureColours.put("turn", new Color(0, 85, 235));\r
 446       featureColours.put("unsure residue", new Color(0, 75, 245));\r
 447       featureColours.put("zinc finger region", new Color(0, 65, 255));\r
 448     }\r
 449 }\r
 450 \r
 451   class TransparencySetter\r
 452   {\r
 453     void setTransparency(Graphics g, float value)\r
 454     {\r
 455       Graphics2D g2 = (Graphics2D) g;\r
 456       g2.setComposite(\r
 457           AlphaComposite.getInstance(\r
 458               AlphaComposite.SRC_OVER, value));\r
 459     }\r
 460   }\r
 461 \r
 462 \r
 463 \r
 464 \r