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