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