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