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 (featureGroups != null\r
 191               && sequenceFeatures[sfindex].featureGroup != null\r
 192               &&\r
 193               featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)\r
 194               &&\r
 195               ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).\r
 196               booleanValue())\r
 197           {\r
 198             continue;\r
 199           }\r
 200 \r
 201           if (!overview && (sequenceFeatures[sfindex].getBegin() > epos\r
 202                             || sequenceFeatures[sfindex].getEnd() < spos))\r
 203             continue;\r
 204 \r
 205           if (overview)\r
 206           {\r
 207             if (sequenceFeatures[sfindex].begin <= start &&\r
 208                 sequenceFeatures[sfindex].end >= start)\r
 209             {\r
 210               currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].\r
 211                   type);\r
 212             }\r
 213 \r
 214           }\r
 215           else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))\r
 216           {\r
 217 \r
 218             renderFeature(g, seq,\r
 219                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 220                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 221                           new Color( ( (Integer) av.featuresDisplayed.get(\r
 222                 sequenceFeatures[sfindex].type)).intValue()),\r
 223                           start, end, y1, width, height);\r
 224             renderFeature(g, seq,\r
 225                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 226                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 227                           new Color( ( (Integer) av.featuresDisplayed.get(\r
 228                 sequenceFeatures[sfindex].type)).intValue()),\r
 229                           start, end, y1, width, height);\r
 230 \r
 231           }\r
 232           else\r
 233             renderFeature(g, seq,\r
 234                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 235                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 236                           getColour(sequenceFeatures[sfindex].type),\r
 237                           start, end, y1, width, height);\r
 238 \r
 239         }\r
 240       }\r
 241     }\r
 242 \r
 243 \r
 244     char s;\r
 245     int i;\r
 246     void renderFeature(Graphics g, SequenceI seq,\r
 247                        int fstart, int fend, Color featureColour, int start, int end,  int y1, int width, int height)\r
 248     {\r
 249 \r
 250       if (((fstart <= end) && (fend >= start)))\r
 251       {\r
 252         if (fstart < start)\r
 253         { // fix for if the feature we have starts before the sequence start,\r
 254           fstart = start; // but the feature end is still valid!!\r
 255         }\r
 256 \r
 257         if (fend >= end)\r
 258         {\r
 259           fend = end;\r
 260         }\r
 261 \r
 262           for (i = fstart; i <= fend; i++)\r
 263           {\r
 264             s = seq.getSequence().charAt(i);\r
 265 \r
 266             if (jalview.util.Comparison.isGap(s))\r
 267             {\r
 268               continue;\r
 269             }\r
 270 \r
 271             g.setColor(featureColour);\r
 272 \r
 273             g.fillRect( (i - start) * width, y1, width, height);\r
 274 \r
 275             g.setColor(Color.white);\r
 276             charOffset = (width - fm.charWidth(s)) / 2;\r
 277             g.drawString(String.valueOf(s),\r
 278                          charOffset + (width * (i - start)),\r
 279                          (y1 + height) - height / 5); //pady = height / 5;\r
 280 \r
 281           }\r
 282       }\r
 283     }\r
 284 \r
 285     void findAllFeatures()\r
 286     {\r
 287       av.featuresDisplayed = new Hashtable();\r
 288       Vector allfeatures = new Vector();\r
 289       for (int i = 0; i < av.alignment.getHeight(); i++)\r
 290       {\r
 291         SequenceFeature [] features = av.alignment.getSequenceAt(i).getSequenceFeatures();\r
 292 \r
 293         if (features == null)\r
 294           continue;\r
 295 \r
 296         int index = 0;\r
 297         while (index < features.length)\r
 298         {\r
 299           if (!av.featuresDisplayed.containsKey(features[index].getType()))\r
 300           {\r
 301             av.featuresDisplayed.put(features[index].getType(),\r
 302                                   new Integer( getColour(features[index].getType()).getRGB()) );\r
 303             allfeatures.addElement(features[index].getType());\r
 304           }\r
 305           index++;\r
 306         }\r
 307       }\r
 308 \r
 309       renderOrder = new String[allfeatures.size()];\r
 310       Enumeration en = allfeatures.elements();\r
 311       int i = allfeatures.size()-1;\r
 312       while(en.hasMoreElements())\r
 313       {\r
 314         renderOrder[i] = en.nextElement().toString();\r
 315         i--;\r
 316       }\r
 317     }\r
 318 \r
 319     public Color getColour(String featureType)\r
 320     {\r
 321       return (Color)featureColours.get(featureType);\r
 322     }\r
 323 \r
 324     public void addNewFeature(String name, Color col)\r
 325     {\r
 326 \r
 327       setColour(name, col);\r
 328       if(av.featuresDisplayed==null)\r
 329         av.featuresDisplayed = new Hashtable();\r
 330 \r
 331 \r
 332       av.featuresDisplayed.put(name, "NOGROUP");\r
 333     }\r
 334 \r
 335     public void setColour(String featureType, Color col)\r
 336     {\r
 337       featureColours.put(featureType, col);\r
 338     }\r
 339 \r
 340     public void setFeaturePriority(Object [][] data)\r
 341     {\r
 342         // The feature table will display high priority\r
 343         // features at the top, but theses are the ones\r
 344         // we need to render last, so invert the data\r
 345         if(av.featuresDisplayed!=null)\r
 346           av.featuresDisplayed.clear();\r
 347 \r
 348         renderOrder = new String[data.length];\r
 349 \r
 350         if (data.length > 0)\r
 351           for (int i = 0; i < data.length; i++)\r
 352           {\r
 353             String type = data[i][0].toString();\r
 354             setColour(type, (Color) data[i][1]);\r
 355             if ( ( (Boolean) data[i][2]).booleanValue())\r
 356             {\r
 357               av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));\r
 358             }\r
 359 \r
 360             renderOrder[data.length - i - 1] = type;\r
 361           }\r
 362     }\r
 363 \r
 364     Hashtable featureColours = new Hashtable();\r
 365     void initColours()\r
 366     {\r
 367       featureColours.put("active site", new Color(255, 75, 0));\r
 368       featureColours.put("binding site", new Color(245, 85, 0));\r
 369       featureColours.put("calcium-binding region", new Color(235, 95, 0));\r
 370       featureColours.put("chain", new Color(225, 105, 0));\r
 371       featureColours.put("coiled-coil region", new Color(215, 115, 0));\r
 372       featureColours.put("compositionally biased region", new Color(205, 125, 0));\r
 373       featureColours.put("cross-link", new Color(195, 135, 0));\r
 374       featureColours.put("disulfide bond", new Color(185, 145, 0));\r
 375       featureColours.put("DNA-binding region", new Color(175, 155, 0));\r
 376       featureColours.put("domain", new Color(165, 165, 0));\r
 377       featureColours.put("glycosylation site", new Color(155, 175, 0));\r
 378       featureColours.put("helix", new Color(145, 185, 0));\r
 379       featureColours.put("initiator methionine", new Color(135, 195, 5));\r
 380       featureColours.put("lipid moiety-binding region", new Color(125, 205, 15));\r
 381       featureColours.put("metal ion-binding site", new Color(115, 215, 25));\r
 382       featureColours.put("modified residue", new Color(105, 225, 35));\r
 383       featureColours.put("mutagenesis site", new Color(95, 235, 45));\r
 384       featureColours.put("non-consecutive residues", new Color(85, 245, 55));\r
 385       featureColours.put("non-terminal residue", new Color(75, 255, 65));\r
 386       featureColours.put("nucleotide phosphate-binding region",\r
 387                          new Color(65, 245, 75));\r
 388       featureColours.put("peptide", new Color(55, 235, 85));\r
 389       featureColours.put("propeptide", new Color(45, 225, 95));\r
 390       featureColours.put("region of interest", new Color(35, 215, 105));\r
 391       featureColours.put("repeat", new Color(25, 205, 115));\r
 392       featureColours.put("selenocysteine", new Color(15, 195, 125));\r
 393       featureColours.put("sequence conflict", new Color(5, 185, 135));\r
 394       featureColours.put("sequence variant", new Color(0, 175, 145));\r
 395       featureColours.put("short sequence motif", new Color(0, 165, 155));\r
 396       featureColours.put("signal peptide", new Color(0, 155, 165));\r
 397       featureColours.put("site", new Color(0, 145, 175));\r
 398       featureColours.put("splice variant", new Color(0, 135, 185));\r
 399       featureColours.put("strand", new Color(0, 125, 195));\r
 400       featureColours.put("topological domain", new Color(0, 115, 205));\r
 401       featureColours.put("transit peptide", new Color(0, 105, 215));\r
 402       featureColours.put("transmembrane region", new Color(0, 95, 225));\r
 403       featureColours.put("turn", new Color(0, 85, 235));\r
 404       featureColours.put("unsure residue", new Color(0, 75, 245));\r
 405       featureColours.put("zinc finger region", new Color(0, 65, 255));\r
 406     }\r
 407 \r
 408 }\r
 409 \r
 410 \r
 411 \r