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 \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     Color resBoxColour;\r
  38     float transparency = 1.0f;\r
  39     FontMetrics fm;\r
  40     int charOffset;\r
  41 \r
  42     // A higher level for grouping features of a\r
  43    // particular type\r
  44     Hashtable featureGroups = null;\r
  45 \r
  46 \r
  47     // This is actually an Integer held in the hashtable,\r
  48     // Retrieved using the key feature type\r
  49     Object currentColour;\r
  50 \r
  51     String [] renderOrder;\r
  52 \r
  53 \r
  54     /**\r
  55      * Creates a new FeatureRenderer object.\r
  56      *\r
  57      * @param av DOCUMENT ME!\r
  58      */\r
  59     public FeatureRenderer(AlignViewport av)\r
  60     {\r
  61         this.av = av;\r
  62         initColours();\r
  63     }\r
  64 \r
  65 \r
  66     public Color findFeatureColour(Color initialCol, SequenceI seq, int i)\r
  67     {\r
  68       if(!av.showSequenceFeatures)\r
  69         return initialCol;\r
  70 \r
  71         lastSequence = seq;\r
  72         sequenceFeatures = lastSequence.getDatasetSequence().getSequenceFeatures();\r
  73         if(sequenceFeatures==null)\r
  74           return initialCol;\r
  75 \r
  76         sfSize = sequenceFeatures.length;\r
  77 \r
  78       if(jalview.util.Comparison.isGap(lastSequence.getCharAt(i)))\r
  79         return Color.white;\r
  80 \r
  81       currentColour = null;\r
  82 \r
  83       drawSequence(null, lastSequence, lastSequence.findPosition(i), -1,-1, -1, -1);\r
  84 \r
  85       if(currentColour==null)\r
  86         return initialCol;\r
  87 \r
  88       return new Color( ((Integer)currentColour).intValue() );\r
  89     }\r
  90     /**\r
  91      * This is used by the Molecule Viewer to get the accurate colour\r
  92      * of the rendered sequence\r
  93      */\r
  94 \r
  95     boolean overview = false;\r
  96 \r
  97     int white = Color.white.getRGB();\r
  98     public int findFeatureColour(int initialCol, int seqIndex, int column)\r
  99     {\r
 100       if(!av.showSequenceFeatures)\r
 101         return initialCol;\r
 102 \r
 103       if(seqIndex!=lastSequenceIndex)\r
 104       {\r
 105         lastSequence = av.alignment.getSequenceAt(seqIndex);\r
 106         lastSequenceIndex = seqIndex;\r
 107         sequenceFeatures = lastSequence.getDatasetSequence().getSequenceFeatures();\r
 108         if(sequenceFeatures==null)\r
 109           return initialCol;\r
 110 \r
 111         sfSize = sequenceFeatures.length;\r
 112       }\r
 113 \r
 114 \r
 115       if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))\r
 116         return Color.white.getRGB();\r
 117 \r
 118       currentColour = null;\r
 119 \r
 120       drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1, -1, -1);\r
 121 \r
 122       if(currentColour==null)\r
 123         return initialCol;\r
 124 \r
 125       return  ((Integer)currentColour).intValue();\r
 126     }\r
 127 \r
 128 \r
 129     /**\r
 130      * DOCUMENT ME!\r
 131      *\r
 132      * @param g DOCUMENT ME!\r
 133      * @param seq DOCUMENT ME!\r
 134      * @param sg DOCUMENT ME!\r
 135      * @param start DOCUMENT ME!\r
 136      * @param end DOCUMENT ME!\r
 137      * @param x1 DOCUMENT ME!\r
 138      * @param y1 DOCUMENT ME!\r
 139      * @param width DOCUMENT ME!\r
 140      * @param height DOCUMENT ME!\r
 141      */\r
 142    // String type;\r
 143    // SequenceFeature sf;\r
 144     int lastSequenceIndex=-1;\r
 145     SequenceI lastSequence;\r
 146     SequenceFeature [] sequenceFeatures;\r
 147     int sfSize, sfindex, spos, epos;\r
 148 \r
 149     public void drawSequence(Graphics g, SequenceI seq,\r
 150                              int start, int end, int y1, int width, int height)\r
 151     {\r
 152       if (   seq.getDatasetSequence().getSequenceFeatures() == null\r
 153           || seq.getDatasetSequence().getSequenceFeatures().length==0)\r
 154         return;\r
 155 \r
 156 \r
 157       if(g!=null)\r
 158         fm = g.getFontMetrics();\r
 159 \r
 160 \r
 161       if (av.featuresDisplayed == null || renderOrder==null)\r
 162        {\r
 163          findAllFeatures();\r
 164          sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
 165          sfSize = sequenceFeatures.length;\r
 166        }\r
 167 \r
 168        if(lastSequence==null || seq!=lastSequence)\r
 169       {\r
 170         lastSequence = seq;\r
 171         sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
 172         sfSize = sequenceFeatures.length;\r
 173       }\r
 174 \r
 175 \r
 176       if (transparency != 1 && g!=null)\r
 177       {\r
 178         Graphics2D g2 = (Graphics2D) g;\r
 179         g2.setComposite(\r
 180             AlphaComposite.getInstance(\r
 181                 AlphaComposite.SRC_OVER, transparency));\r
 182       }\r
 183 \r
 184       if(!overview)\r
 185       {\r
 186         spos = lastSequence.findPosition(start);\r
 187         epos = lastSequence.findPosition(end);\r
 188       }\r
 189 \r
 190       String type;\r
 191       for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)\r
 192        {\r
 193         type =  renderOrder[renderIndex];\r
 194 \r
 195         // loop through all features in sequence to find\r
 196         // current feature to render\r
 197         for (sfindex = 0; sfindex < sfSize; sfindex++)\r
 198         {\r
 199           if (!sequenceFeatures[sfindex].type.equals(type))\r
 200             continue;\r
 201 \r
 202           if (featureGroups != null\r
 203               && sequenceFeatures[sfindex].featureGroup != null\r
 204               &&\r
 205               featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)\r
 206               &&\r
 207               ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).\r
 208               booleanValue())\r
 209           {\r
 210             continue;\r
 211           }\r
 212 \r
 213           if (!overview && (sequenceFeatures[sfindex].getBegin() > epos\r
 214                             || sequenceFeatures[sfindex].getEnd() < spos))\r
 215             continue;\r
 216 \r
 217           if (overview)\r
 218           {\r
 219 \r
 220             if (sequenceFeatures[sfindex].begin - 1 <= start &&\r
 221                 sequenceFeatures[sfindex].end + 1 >= start)\r
 222             {\r
 223               currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].\r
 224                   type);\r
 225             }\r
 226 \r
 227           }\r
 228           else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))\r
 229           {\r
 230 \r
 231             renderFeature(g, seq,\r
 232                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 233                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 234                           new Color( ( (Integer) av.featuresDisplayed.get(\r
 235                 sequenceFeatures[sfindex].type)).intValue()),\r
 236                           start, end, y1, width, height);\r
 237             renderFeature(g, seq,\r
 238                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 239                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 240                           new Color( ( (Integer) av.featuresDisplayed.get(\r
 241                 sequenceFeatures[sfindex].type)).intValue()),\r
 242                           start, end, y1, width, height);\r
 243 \r
 244           }\r
 245           else\r
 246             renderFeature(g, seq,\r
 247                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 248                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 249                           getColour(sequenceFeatures[sfindex].type),\r
 250                           start, end, y1, width, height);\r
 251 \r
 252 \r
 253         }\r
 254 \r
 255       }\r
 256 \r
 257         if(transparency!=1.0f && g!=null)\r
 258         {\r
 259           Graphics2D g2 = (Graphics2D) g;\r
 260           g2.setComposite(\r
 261               AlphaComposite.getInstance(\r
 262                   AlphaComposite.SRC_OVER, 1.0f));\r
 263         }\r
 264     }\r
 265 \r
 266 \r
 267     char s;\r
 268     int i;\r
 269     void renderFeature(Graphics g, SequenceI seq,\r
 270                        int fstart, int fend, Color featureColour, int start, int end,  int y1, int width, int height)\r
 271     {\r
 272 \r
 273       if (((fstart <= end) && (fend >= start)))\r
 274       {\r
 275         if (fstart < start)\r
 276         { // fix for if the feature we have starts before the sequence start,\r
 277           fstart = start; // but the feature end is still valid!!\r
 278         }\r
 279 \r
 280         if (fend >= end)\r
 281         {\r
 282           fend = end;\r
 283         }\r
 284 \r
 285           for (i = fstart; i <= fend; i++)\r
 286           {\r
 287             s = seq.getSequence().charAt(i);\r
 288 \r
 289             if (jalview.util.Comparison.isGap(s))\r
 290             {\r
 291               continue;\r
 292             }\r
 293 \r
 294             g.setColor(featureColour);\r
 295 \r
 296             g.fillRect( (i - start) * width, y1, width, height);\r
 297 \r
 298             g.setColor(Color.white);\r
 299             charOffset = (width - fm.charWidth(s)) / 2;\r
 300             g.drawString(String.valueOf(s),\r
 301                          charOffset + (width * (i - start)),\r
 302                          (y1 + height) - height / 5); //pady = height / 5;\r
 303 \r
 304           }\r
 305       }\r
 306     }\r
 307 \r
 308     void findAllFeatures()\r
 309     {\r
 310       av.featuresDisplayed = new Hashtable();\r
 311       for (int i = 0; i < av.alignment.getHeight(); i++)\r
 312       {\r
 313         SequenceFeature [] features = av.alignment.getSequenceAt(i).getDatasetSequence().\r
 314             getSequenceFeatures();\r
 315 \r
 316         if (features == null)\r
 317           continue;\r
 318 \r
 319         int index = 0;\r
 320         while (index < features.length)\r
 321         {\r
 322           if (!av.featuresDisplayed.containsKey(features[index].getType()))\r
 323           {\r
 324             av.featuresDisplayed.put(features[index].getType(),\r
 325                                   new Integer( getColour(features[index].getType()).getRGB()) );\r
 326           }\r
 327           index++;\r
 328         }\r
 329       }\r
 330 \r
 331       renderOrder = new String[av.featuresDisplayed.size()];\r
 332       Enumeration en = av.featuresDisplayed.keys();\r
 333       int i = 0;\r
 334       while(en.hasMoreElements())\r
 335       {\r
 336         renderOrder[i] = en.nextElement().toString();\r
 337         i++;\r
 338       }\r
 339     }\r
 340 \r
 341     public Color getColour(String featureType)\r
 342     {\r
 343       return (Color)featureColours.get(featureType);\r
 344     }\r
 345 \r
 346     public void addNewFeature(String name, Color col)\r
 347     {\r
 348 \r
 349       setColour(name, col);\r
 350       if(av.featuresDisplayed==null)\r
 351         av.featuresDisplayed = new Hashtable();\r
 352 \r
 353 \r
 354       av.featuresDisplayed.put(name, "NOGROUP");\r
 355     }\r
 356 \r
 357     public void setColour(String featureType, Color col)\r
 358     {\r
 359       featureColours.put(featureType, col);\r
 360     }\r
 361 \r
 362     public void setTransparency(float value)\r
 363     {\r
 364       transparency = value;\r
 365     }\r
 366 \r
 367     public float getTransparency()\r
 368     {\r
 369       return transparency;\r
 370     }\r
 371 \r
 372     public void setFeaturePriority(Object [][] data)\r
 373     {\r
 374       // The feature table will display high priority\r
 375       // features at the top, but theses are the ones\r
 376       // we need to render last, so invert the data\r
 377       av.featuresDisplayed.clear();\r
 378 \r
 379       renderOrder = new String[data.length];\r
 380 \r
 381       if(data.length>0)\r
 382       for(int i=data.length-1; i>-1; i--)\r
 383       {\r
 384        String type = data[i][0].toString();\r
 385        setColour(type, (Color)data[i][1]);\r
 386        if( ((Boolean)data[i][2]).booleanValue() )\r
 387        {\r
 388          av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));\r
 389        }\r
 390        renderOrder[i] = type;\r
 391       }\r
 392 \r
 393     }\r
 394 \r
 395     Hashtable featureColours = new Hashtable();\r
 396     void initColours()\r
 397     {\r
 398       featureColours.put("active site", new Color(255, 75, 0));\r
 399       featureColours.put("binding site", new Color(245, 85, 0));\r
 400       featureColours.put("calcium-binding region", new Color(235, 95, 0));\r
 401       featureColours.put("chain", new Color(225, 105, 0));\r
 402       featureColours.put("coiled-coil region", new Color(215, 115, 0));\r
 403       featureColours.put("compositionally biased region", new Color(205, 125, 0));\r
 404       featureColours.put("cross-link", new Color(195, 135, 0));\r
 405       featureColours.put("disulfide bond", new Color(230,230,0));\r
 406       featureColours.put("DNA-binding region", new Color(175, 155, 0));\r
 407       featureColours.put("domain", new Color(165, 165, 0));\r
 408       featureColours.put("glycosylation site", new Color(155, 175, 0));\r
 409       featureColours.put("helix", new Color(145, 185, 0));\r
 410       featureColours.put("initiator methionine", new Color(135, 195, 5));\r
 411       featureColours.put("lipid moiety-binding region", new Color(125, 205, 15));\r
 412       featureColours.put("metal ion-binding site", new Color(115, 215, 25));\r
 413       featureColours.put("modified residue", new Color(105, 225, 35));\r
 414       featureColours.put("mutagenesis site", new Color(95, 235, 45));\r
 415       featureColours.put("non-consecutive residues", new Color(85, 245, 55));\r
 416       featureColours.put("non-terminal residue", new Color(75, 255, 65));\r
 417       featureColours.put("nucleotide phosphate-binding region",new Color(65, 245, 75));\r
 418       featureColours.put("peptide", new Color(55, 235, 85));\r
 419       featureColours.put("propeptide", new Color(45, 225, 95));\r
 420       featureColours.put("region of interest", new Color(35, 215, 105));\r
 421       featureColours.put("repeat", new Color(25, 205, 115));\r
 422       featureColours.put("selenocysteine", new Color(15, 195, 125));\r
 423       featureColours.put("sequence conflict", new Color(5, 185, 135));\r
 424       featureColours.put("sequence variant", new Color(0, 175, 145));\r
 425       featureColours.put("short sequence motif", new Color(0, 165, 155));\r
 426       featureColours.put("signal peptide", new Color(0, 155, 165));\r
 427       featureColours.put("site", new Color(0, 145, 175));\r
 428       featureColours.put("splice variant", new Color(0, 135, 185));\r
 429       featureColours.put("strand", new Color(0, 125, 195));\r
 430       featureColours.put("topological domain", new Color(0, 115, 205));\r
 431       featureColours.put("transit peptide", new Color(0, 105, 215));\r
 432       featureColours.put("transmembrane region", new Color(0, 95, 225));\r
 433       featureColours.put("turn", new Color(0, 85, 235));\r
 434       featureColours.put("unsure residue", new Color(0, 75, 245));\r
 435       featureColours.put("zinc finger region", new Color(0, 65, 255));\r
 436     }\r
 437 \r
 438 }\r