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     Hashtable featureColours = new Hashtable();\r
  39 \r
  40     // A higher level for grouping features of a\r
  41     // particular type\r
  42     Hashtable featureGroups = null;\r
  43 \r
  44     // Holds web links for feature groups and feature types\r
  45     // in the form label|link\r
  46     Hashtable featureLinks = null;\r
  47 \r
  48 \r
  49     // This is actually an Integer held in the hashtable,\r
  50     // Retrieved using the key feature type\r
  51     Object currentColour;\r
  52 \r
  53     String [] renderOrder;\r
  54 \r
  55     FontMetrics fm;\r
  56     int charOffset;\r
  57 \r
  58     float transparency = 1f;\r
  59 \r
  60     TransparencySetter transparencySetter = null;\r
  61 \r
  62     /**\r
  63      * Creates a new FeatureRenderer object.\r
  64      *\r
  65      * @param av DOCUMENT ME!\r
  66      */\r
  67     public FeatureRenderer(AlignViewport av)\r
  68     {\r
  69         this.av = av;\r
  70 \r
  71         if(!System.getProperty("java.version").startsWith("1.1"))\r
  72              transparencySetter = new TransparencySetter();\r
  73     }\r
  74 \r
  75 \r
  76     public void transferSettings(FeatureRenderer fr)\r
  77     {\r
  78       renderOrder = fr.renderOrder;\r
  79       featureGroups = fr.featureGroups;\r
  80       featureColours = fr.featureColours;\r
  81     }\r
  82 \r
  83 \r
  84     public Color findFeatureColour(Color initialCol, SequenceI seq, int i)\r
  85     {\r
  86       overview = true;\r
  87       if(!av.showSequenceFeatures)\r
  88         return initialCol;\r
  89 \r
  90         lastSequence = seq;\r
  91         sequenceFeatures = lastSequence.getSequenceFeatures();\r
  92         if(sequenceFeatures==null)\r
  93           return initialCol;\r
  94 \r
  95         sfSize = sequenceFeatures.length;\r
  96 \r
  97       if(jalview.util.Comparison.isGap(lastSequence.getCharAt(i)))\r
  98         return Color.white;\r
  99 \r
 100       currentColour = null;\r
 101 \r
 102       drawSequence(null, lastSequence, lastSequence.findPosition(i), -1,-1, -1, -1);\r
 103 \r
 104       if(currentColour==null)\r
 105         return initialCol;\r
 106 \r
 107       return new Color( ((Integer)currentColour).intValue() );\r
 108     }\r
 109 \r
 110     /**\r
 111      * This is used by the Molecule Viewer to get the accurate colour\r
 112      * of the rendered sequence\r
 113      */\r
 114     boolean overview = false;\r
 115 \r
 116     int white = Color.white.getRGB();\r
 117     public int findFeatureColour(int initialCol, int seqIndex, int column)\r
 118     {\r
 119       if(!av.showSequenceFeatures)\r
 120         return initialCol;\r
 121 \r
 122       if(seqIndex!=lastSequenceIndex)\r
 123       {\r
 124         lastSequence = av.alignment.getSequenceAt(seqIndex);\r
 125         lastSequenceIndex = seqIndex;\r
 126         sequenceFeatures = lastSequence.getSequenceFeatures();\r
 127         if(sequenceFeatures==null)\r
 128           return initialCol;\r
 129 \r
 130         sfSize = sequenceFeatures.length;\r
 131       }\r
 132 \r
 133 \r
 134       if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))\r
 135         return Color.white.getRGB();\r
 136 \r
 137       currentColour = null;\r
 138 \r
 139       drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1, -1, -1);\r
 140 \r
 141       if(currentColour==null)\r
 142         return initialCol;\r
 143 \r
 144       return  ((Integer)currentColour).intValue();\r
 145     }\r
 146 \r
 147 \r
 148     /**\r
 149      * DOCUMENT ME!\r
 150      *\r
 151      * @param g DOCUMENT ME!\r
 152      * @param seq DOCUMENT ME!\r
 153      * @param sg DOCUMENT ME!\r
 154      * @param start DOCUMENT ME!\r
 155      * @param end DOCUMENT ME!\r
 156      * @param x1 DOCUMENT ME!\r
 157      * @param y1 DOCUMENT ME!\r
 158      * @param width DOCUMENT ME!\r
 159      * @param height DOCUMENT ME!\r
 160      */\r
 161    // String type;\r
 162    // SequenceFeature sf;\r
 163     int lastSequenceIndex=-1;\r
 164     SequenceI lastSequence;\r
 165     SequenceFeature [] sequenceFeatures;\r
 166     int sfSize, sfindex, spos, epos;\r
 167 \r
 168     public void drawSequence(Graphics g, SequenceI seq,\r
 169                              int start, int end, int y1, int width, int height)\r
 170     {\r
 171       if (   seq.getSequenceFeatures() == null\r
 172           || seq.getSequenceFeatures().length==0)\r
 173         return;\r
 174 \r
 175       if(transparencySetter!=null && g!=null)\r
 176       {\r
 177         transparencySetter.setTransparency(g, transparency);\r
 178       }\r
 179 \r
 180       if (av.featuresDisplayed == null || renderOrder==null)\r
 181        {\r
 182          findAllFeatures();\r
 183          if(av.featuresDisplayed.size()<1)\r
 184            return;\r
 185 \r
 186          sequenceFeatures = seq.getSequenceFeatures();\r
 187          sfSize = sequenceFeatures.length;\r
 188        }\r
 189        if(lastSequence==null || seq!=lastSequence)\r
 190       {\r
 191         lastSequence = seq;\r
 192         sequenceFeatures = seq.getSequenceFeatures();\r
 193         sfSize = sequenceFeatures.length;\r
 194       }\r
 195       if(!overview)\r
 196       {\r
 197         spos = lastSequence.findPosition(start);\r
 198         epos = lastSequence.findPosition(end);\r
 199         if(g!=null)\r
 200           fm = g.getFontMetrics();\r
 201       }\r
 202       String type;\r
 203       for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)\r
 204        {\r
 205         type =  renderOrder[renderIndex];\r
 206         if(!av.featuresDisplayed.containsKey(type))\r
 207           continue;\r
 208 \r
 209         // loop through all features in sequence to find\r
 210         // current feature to render\r
 211         for (sfindex = 0; sfindex < sfSize; sfindex++)\r
 212         {\r
 213           if (!sequenceFeatures[sfindex].type.equals(type))\r
 214             continue;\r
 215 \r
 216           if (featureGroups != null\r
 217               && sequenceFeatures[sfindex].featureGroup != null\r
 218               &&\r
 219               featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)\r
 220               &&\r
 221               ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).\r
 222               booleanValue())\r
 223           {\r
 224             continue;\r
 225           }\r
 226 \r
 227           if (!overview && (sequenceFeatures[sfindex].getBegin() > epos\r
 228                             || sequenceFeatures[sfindex].getEnd() < spos))\r
 229             continue;\r
 230 \r
 231           if (overview)\r
 232           {\r
 233             if (sequenceFeatures[sfindex].begin <= start &&\r
 234                 sequenceFeatures[sfindex].end >= start)\r
 235             {\r
 236               currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].\r
 237                   type);\r
 238             }\r
 239 \r
 240           }\r
 241           else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))\r
 242           {\r
 243 \r
 244             renderFeature(g, seq,\r
 245                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 246                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 247                           new Color( ( (Integer) av.featuresDisplayed.get(\r
 248                 sequenceFeatures[sfindex].type)).intValue()),\r
 249                           start, end, y1, width, height);\r
 250             renderFeature(g, seq,\r
 251                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 252                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 253                           new Color( ( (Integer) av.featuresDisplayed.get(\r
 254                 sequenceFeatures[sfindex].type)).intValue()),\r
 255                           start, end, y1, width, height);\r
 256 \r
 257           }\r
 258           else\r
 259             renderFeature(g, seq,\r
 260                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 261                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 262                           getColour(sequenceFeatures[sfindex].type),\r
 263                           start, end, y1, width, height);\r
 264 \r
 265         }\r
 266       }\r
 267 \r
 268       if(transparencySetter!=null && g!=null)\r
 269       {\r
 270         transparencySetter.setTransparency(g, 1.0f);\r
 271       }\r
 272     }\r
 273 \r
 274 \r
 275     char s;\r
 276     int i;\r
 277     void renderFeature(Graphics g, SequenceI seq,\r
 278                        int fstart, int fend, Color featureColour, int start, int end,  int y1, int width, int height)\r
 279     {\r
 280 \r
 281       if (((fstart <= end) && (fend >= start)))\r
 282       {\r
 283         if (fstart < start)\r
 284         { // fix for if the feature we have starts before the sequence start,\r
 285           fstart = start; // but the feature end is still valid!!\r
 286         }\r
 287 \r
 288         if (fend >= end)\r
 289         {\r
 290           fend = end;\r
 291         }\r
 292 \r
 293           for (i = fstart; i <= fend; i++)\r
 294           {\r
 295             s = seq.getSequence().charAt(i);\r
 296 \r
 297             if (jalview.util.Comparison.isGap(s))\r
 298             {\r
 299               continue;\r
 300             }\r
 301 \r
 302             g.setColor(featureColour);\r
 303 \r
 304             g.fillRect( (i - start) * width, y1, width, height);\r
 305 \r
 306             if(!av.validCharWidth)\r
 307               continue;\r
 308 \r
 309             g.setColor(Color.white);\r
 310             charOffset = (width - fm.charWidth(s)) / 2;\r
 311             g.drawString(String.valueOf(s),\r
 312                          charOffset + (width * (i - start)),\r
 313                          (y1 + height) - height / 5); //pady = height / 5;\r
 314 \r
 315           }\r
 316       }\r
 317     }\r
 318 \r
 319     void findAllFeatures()\r
 320     {\r
 321       av.featuresDisplayed = new Hashtable();\r
 322       Vector allfeatures = new Vector();\r
 323       for (int i = 0; i < av.alignment.getHeight(); i++)\r
 324       {\r
 325         SequenceFeature [] features = av.alignment.getSequenceAt(i).getSequenceFeatures();\r
 326 \r
 327         if (features == null)\r
 328           continue;\r
 329 \r
 330         int index = 0;\r
 331         while (index < features.length)\r
 332         {\r
 333           if (!av.featuresDisplayed.containsKey(features[index].getType()))\r
 334           {\r
 335             av.featuresDisplayed.put(features[index].getType(),\r
 336                                   new Integer( getColour(features[index].getType()).getRGB()) );\r
 337             allfeatures.addElement(features[index].getType());\r
 338           }\r
 339           index++;\r
 340         }\r
 341       }\r
 342 \r
 343       renderOrder = new String[allfeatures.size()];\r
 344       Enumeration en = allfeatures.elements();\r
 345       int i = allfeatures.size()-1;\r
 346       while(en.hasMoreElements())\r
 347       {\r
 348         renderOrder[i] = en.nextElement().toString();\r
 349         i--;\r
 350       }\r
 351     }\r
 352 \r
 353     public Color getColour(String featureType)\r
 354     {\r
 355       return (Color)featureColours.get(featureType);\r
 356     }\r
 357 \r
 358     public void addNewFeature(String name, Color col)\r
 359     {\r
 360 \r
 361       setColour(name, col);\r
 362       if(av.featuresDisplayed==null)\r
 363         av.featuresDisplayed = new Hashtable();\r
 364 \r
 365 \r
 366       av.featuresDisplayed.put(name, "NOGROUP");\r
 367     }\r
 368 \r
 369     public void setColour(String featureType, Color col)\r
 370     {\r
 371       featureColours.put(featureType, col);\r
 372     }\r
 373 \r
 374     public void setFeaturePriority(Object [][] data)\r
 375     {\r
 376         // The feature table will display high priority\r
 377         // features at the top, but theses are the ones\r
 378         // we need to render last, so invert the data\r
 379         if(av.featuresDisplayed!=null)\r
 380           av.featuresDisplayed.clear();\r
 381 \r
 382         renderOrder = new String[data.length];\r
 383 \r
 384         if (data.length > 0)\r
 385           for (int i = 0; i < data.length; i++)\r
 386           {\r
 387             String type = data[i][0].toString();\r
 388             setColour(type, (Color) data[i][1]);\r
 389             if ( ( (Boolean) data[i][2]).booleanValue())\r
 390             {\r
 391               av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));\r
 392             }\r
 393 \r
 394             renderOrder[data.length - i - 1] = type;\r
 395           }\r
 396     }\r
 397 }\r
 398 \r
 399   class TransparencySetter\r
 400   {\r
 401     void setTransparency(Graphics g, float value)\r
 402     {\r
 403   //    Graphics2D g2 = (Graphics2D) g;\r
 404    //   g2.setComposite(\r
 405     //      AlphaComposite.getInstance(\r
 406     //          AlphaComposite.SRC_OVER, value));\r
 407     }\r
 408   }\r
 409 \r
 410 \r
 411 \r
 412 \r