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