src/jalview/gui/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.gui;\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 import java.awt.image.*;\r
  28 \r
  29 \r
  30 /**\r
  31  * DOCUMENT ME!\r
  32  *\r
  33  * @author $author$\r
  34  * @version $Revision$\r
  35  */\r
  36 public class FeatureRenderer\r
  37 {\r
  38     AlignViewport av;\r
  39     Color resBoxColour;\r
  40     float transparency = 1.0f;\r
  41     FontMetrics fm;\r
  42     int charOffset;\r
  43 \r
  44     // A higher level for grouping features of a\r
  45    // particular type\r
  46     Hashtable featureGroups = 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 \r
  56     /**\r
  57      * Creates a new FeatureRenderer object.\r
  58      *\r
  59      * @param av DOCUMENT ME!\r
  60      */\r
  61     public FeatureRenderer(AlignViewport av)\r
  62     {\r
  63         this.av = av;\r
  64         initColours();\r
  65     }\r
  66 \r
  67     public void transferSettings(FeatureRenderer fr)\r
  68     {\r
  69       renderOrder = fr.renderOrder;\r
  70       featureGroups = fr.featureGroups;\r
  71       featureColours = fr.featureColours;\r
  72       transparency =  fr.transparency;\r
  73     }\r
  74 \r
  75     BufferedImage offscreenImage;\r
  76     boolean offscreenRender = false;\r
  77     public Color findFeatureColour(Color initialCol, SequenceI seq, int res)\r
  78     {\r
  79       int seqindex = av.alignment.findIndex(seq);\r
  80 \r
  81       return new Color( findFeatureColour (initialCol.getRGB(),\r
  82                         seqindex, res ));\r
  83     }\r
  84 \r
  85     /**\r
  86      * This is used by the Molecule Viewer to get the accurate colour\r
  87      * of the rendered sequence\r
  88      */\r
  89     public int findFeatureColour(int initialCol, int seqIndex, int column)\r
  90     {\r
  91       if(!av.showSequenceFeatures)\r
  92         return initialCol;\r
  93 \r
  94       if(seqIndex!=lastSequenceIndex)\r
  95       {\r
  96         lastSequence = av.alignment.getSequenceAt(seqIndex);\r
  97         lastSequenceIndex = seqIndex;\r
  98         sequenceFeatures = lastSequence.getDatasetSequence().getSequenceFeatures();\r
  99         if(sequenceFeatures==null)\r
 100           return initialCol;\r
 101 \r
 102         sfSize = sequenceFeatures.length;\r
 103       }\r
 104 \r
 105       if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))\r
 106         return Color.white.getRGB();\r
 107 \r
 108 \r
 109       //Only bother making an offscreen image if transparency is applied\r
 110       if(transparency!=1.0f && offscreenImage==null)\r
 111       {\r
 112         offscreenImage = new BufferedImage(1,1,BufferedImage.TYPE_INT_ARGB);\r
 113       }\r
 114 \r
 115       currentColour = null;\r
 116 \r
 117       offscreenRender = true;\r
 118 \r
 119       if(offscreenImage!=null)\r
 120       {\r
 121         offscreenImage.setRGB(0,0,initialCol);\r
 122         drawSequence(offscreenImage.getGraphics(),\r
 123                      lastSequence,\r
 124                      column,column,0);\r
 125 \r
 126         return offscreenImage.getRGB(0,0);\r
 127       }\r
 128       else\r
 129       {\r
 130         drawSequence(null,\r
 131                     lastSequence,\r
 132                     lastSequence.findPosition(column),\r
 133                     -1, -1);\r
 134 \r
 135         if (currentColour == null)\r
 136           return initialCol;\r
 137         else\r
 138           return  ((Integer)currentColour).intValue();\r
 139       }\r
 140 \r
 141 \r
 142     }\r
 143 \r
 144 \r
 145     /**\r
 146      * DOCUMENT ME!\r
 147      *\r
 148      * @param g DOCUMENT ME!\r
 149      * @param seq DOCUMENT ME!\r
 150      * @param sg DOCUMENT ME!\r
 151      * @param start DOCUMENT ME!\r
 152      * @param end DOCUMENT ME!\r
 153      * @param x1 DOCUMENT ME!\r
 154      * @param y1 DOCUMENT ME!\r
 155      * @param width DOCUMENT ME!\r
 156      * @param height DOCUMENT ME!\r
 157      */\r
 158    // String type;\r
 159    // SequenceFeature sf;\r
 160     int lastSequenceIndex=-1;\r
 161     SequenceI lastSequence;\r
 162     SequenceFeature [] sequenceFeatures;\r
 163     int sfSize, sfindex, spos, epos;\r
 164 \r
 165     public void drawSequence(Graphics g, SequenceI seq,\r
 166                              int start, int end, int y1)\r
 167     {\r
 168       if ( seq.getDatasetSequence().getSequenceFeatures() == null\r
 169           || seq.getDatasetSequence().getSequenceFeatures().length==0)\r
 170         return;\r
 171 \r
 172 \r
 173       if(g!=null)\r
 174         fm = g.getFontMetrics();\r
 175 \r
 176 \r
 177       if (av.featuresDisplayed == null || renderOrder==null)\r
 178        {\r
 179          findAllFeatures();\r
 180          if(av.featuresDisplayed.size()<1)\r
 181            return;\r
 182 \r
 183          sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
 184          sfSize = sequenceFeatures.length;\r
 185        }\r
 186 \r
 187        if(lastSequence==null || seq!=lastSequence)\r
 188       {\r
 189         lastSequence = seq;\r
 190         sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
 191         sfSize = sequenceFeatures.length;\r
 192       }\r
 193 \r
 194 \r
 195       if (transparency != 1 && g!=null)\r
 196       {\r
 197         Graphics2D g2 = (Graphics2D) g;\r
 198         g2.setComposite(\r
 199             AlphaComposite.getInstance(\r
 200                 AlphaComposite.SRC_OVER, transparency));\r
 201       }\r
 202 \r
 203       if(!offscreenRender)\r
 204       {\r
 205         spos = lastSequence.findPosition(start);\r
 206         epos = lastSequence.findPosition(end);\r
 207       }\r
 208 \r
 209 \r
 210       String type;\r
 211       for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)\r
 212        {\r
 213         type =  renderOrder[renderIndex];\r
 214         if(!av.featuresDisplayed.containsKey(type))\r
 215           continue;\r
 216 \r
 217         // loop through all features in sequence to find\r
 218         // current feature to render\r
 219         for (sfindex = 0; sfindex < sfSize; sfindex++)\r
 220         {\r
 221           if(sequenceFeatures.length<=sfindex)\r
 222           {\r
 223             continue;\r
 224           }\r
 225           if (!sequenceFeatures[sfindex].type.equals(type))\r
 226             continue;\r
 227 \r
 228           if (featureGroups != null\r
 229               && sequenceFeatures[sfindex].featureGroup != null\r
 230               &&\r
 231               featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)\r
 232               &&\r
 233               ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).\r
 234               booleanValue())\r
 235           {\r
 236             continue;\r
 237           }\r
 238 \r
 239           if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos\r
 240                             || sequenceFeatures[sfindex].getEnd() < spos))\r
 241             continue;\r
 242 \r
 243           if (offscreenRender && offscreenImage==null)\r
 244           {\r
 245             if (sequenceFeatures[sfindex].begin <= start &&\r
 246                 sequenceFeatures[sfindex].end  >= start)\r
 247             {\r
 248               currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].\r
 249                  type);\r
 250             }\r
 251           }\r
 252           else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))\r
 253           {\r
 254 \r
 255             renderFeature(g, seq,\r
 256                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 257                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 258                           new Color( ( (Integer) av.featuresDisplayed.get(\r
 259                 sequenceFeatures[sfindex].type)).intValue()),\r
 260                           start, end, y1);\r
 261             renderFeature(g, seq,\r
 262                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 263                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 264                           new Color( ( (Integer) av.featuresDisplayed.get(\r
 265                 sequenceFeatures[sfindex].type)).intValue()),\r
 266                           start, end, y1);\r
 267 \r
 268           }\r
 269           else\r
 270             renderFeature(g, seq,\r
 271                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 272                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 273                           getColour(sequenceFeatures[sfindex].type),\r
 274                           start, end, y1);\r
 275 \r
 276 \r
 277         }\r
 278 \r
 279       }\r
 280 \r
 281         if(transparency!=1.0f && g!=null)\r
 282         {\r
 283           Graphics2D g2 = (Graphics2D) g;\r
 284           g2.setComposite(\r
 285               AlphaComposite.getInstance(\r
 286                   AlphaComposite.SRC_OVER, 1.0f));\r
 287         }\r
 288     }\r
 289 \r
 290 \r
 291     char s;\r
 292     int i;\r
 293     void renderFeature(Graphics g, SequenceI seq,\r
 294                        int fstart, int fend, Color featureColour, int start, int end,  int y1)\r
 295     {\r
 296 \r
 297       if (((fstart <= end) && (fend >= start)))\r
 298       {\r
 299         if (fstart < start)\r
 300         { // fix for if the feature we have starts before the sequence start,\r
 301           fstart = start; // but the feature end is still valid!!\r
 302         }\r
 303 \r
 304         if (fend >= end)\r
 305         {\r
 306           fend = end;\r
 307         }\r
 308           int pady = (y1 + av.charHeight) - av.charHeight / 5;\r
 309           for (i = fstart; i <= fend; i++)\r
 310           {\r
 311             s = seq.getSequence().charAt(i);\r
 312 \r
 313             if (jalview.util.Comparison.isGap(s))\r
 314             {\r
 315               continue;\r
 316             }\r
 317 \r
 318             g.setColor(featureColour);\r
 319 \r
 320             g.fillRect( (i - start) * av.charWidth, y1, av.charWidth,av.charHeight);\r
 321 \r
 322             if(offscreenRender)\r
 323               continue;\r
 324 \r
 325             g.setColor(Color.white);\r
 326             charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
 327             g.drawString(String.valueOf(s),\r
 328                          charOffset + (av.charWidth * (i - start)),\r
 329                          pady);\r
 330 \r
 331           }\r
 332       }\r
 333     }\r
 334 \r
 335     void findAllFeatures()\r
 336     {\r
 337       av.featuresDisplayed = new Hashtable();\r
 338       Vector allfeatures = new Vector();\r
 339       for (int i = 0; i < av.alignment.getHeight(); i++)\r
 340       {\r
 341         SequenceFeature [] features\r
 342             = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
 343 \r
 344         if (features == null)\r
 345           continue;\r
 346 \r
 347         int index = 0;\r
 348         while (index < features.length)\r
 349         {\r
 350           if (!av.featuresDisplayed.containsKey(features[index].getType()))\r
 351           {\r
 352             av.featuresDisplayed.put(features[index].getType(),\r
 353                                   new Integer( getColour(features[index].getType()).getRGB()) );\r
 354             allfeatures.addElement(features[index].getType());\r
 355           }\r
 356           index++;\r
 357         }\r
 358       }\r
 359 \r
 360       renderOrder = new String[allfeatures.size()];\r
 361       Enumeration en = allfeatures.elements();\r
 362       int i = allfeatures.size()-1;\r
 363       while(en.hasMoreElements())\r
 364       {\r
 365         renderOrder[i] = en.nextElement().toString();\r
 366         i--;\r
 367       }\r
 368     }\r
 369 \r
 370     public Color getColour(String featureType)\r
 371     {\r
 372       return (Color)featureColours.get(featureType);\r
 373     }\r
 374 \r
 375     public void addNewFeature(String name, Color col, String group)\r
 376     {\r
 377 \r
 378       setColour(name, col);\r
 379       if(av.featuresDisplayed==null)\r
 380         av.featuresDisplayed = new Hashtable();\r
 381 \r
 382       if(group == null)\r
 383         group = "NOGROUP";\r
 384 \r
 385       av.featuresDisplayed.put(name, new Integer(col.getRGB()));\r
 386     }\r
 387 \r
 388     public void setColour(String featureType, Color col)\r
 389     {\r
 390       featureColours.put(featureType, col);\r
 391     }\r
 392 \r
 393     public void setTransparency(float value)\r
 394     {\r
 395       transparency = value;\r
 396     }\r
 397 \r
 398     public float getTransparency()\r
 399     {\r
 400       return transparency;\r
 401     }\r
 402 \r
 403     public void setFeaturePriority(Object [][] data)\r
 404     {\r
 405       // The feature table will display high priority\r
 406       // features at the top, but theses are the ones\r
 407       // we need to render last, so invert the data\r
 408       if(av.featuresDisplayed!=null)\r
 409         av.featuresDisplayed.clear();\r
 410       else\r
 411         av.featuresDisplayed = new Hashtable();\r
 412 \r
 413       renderOrder = new String[data.length];\r
 414 \r
 415       if (data.length > 0)\r
 416         for (int i = 0; i < data.length; i++)\r
 417         {\r
 418           String type = data[i][0].toString();\r
 419           setColour(type, (Color) data[i][1]);\r
 420           if ( ( (Boolean) data[i][2]).booleanValue())\r
 421           {\r
 422             av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));\r
 423           }\r
 424 \r
 425           renderOrder[data.length - i - 1] = type;\r
 426         }\r
 427 \r
 428     }\r
 429 \r
 430     Hashtable featureColours = new Hashtable();\r
 431     void initColours()\r
 432     {\r
 433       featureColours.put("active site", new Color(255, 75, 0));\r
 434       featureColours.put("binding site", new Color(245, 85, 0));\r
 435       featureColours.put("calcium-binding region", new Color(235, 95, 0));\r
 436       featureColours.put("chain", new Color(225, 105, 0));\r
 437       featureColours.put("coiled-coil region", new Color(215, 115, 0));\r
 438       featureColours.put("compositionally biased region", new Color(205, 125, 0));\r
 439       featureColours.put("cross-link", new Color(195, 135, 0));\r
 440       featureColours.put("disulfide bond", new Color(230,230,0));\r
 441       featureColours.put("DNA-binding region", new Color(175, 155, 0));\r
 442       featureColours.put("domain", new Color(165, 165, 0));\r
 443       featureColours.put("glycosylation site", new Color(155, 175, 0));\r
 444       featureColours.put("helix", new Color(145, 185, 0));\r
 445       featureColours.put("initiator methionine", new Color(135, 195, 5));\r
 446       featureColours.put("lipid moiety-binding region", new Color(125, 205, 15));\r
 447       featureColours.put("metal ion-binding site", new Color(115, 215, 25));\r
 448       featureColours.put("modified residue", new Color(105, 225, 35));\r
 449       featureColours.put("mutagenesis site", new Color(95, 235, 45));\r
 450       featureColours.put("non-consecutive residues", new Color(85, 245, 55));\r
 451       featureColours.put("non-terminal residue", new Color(75, 255, 65));\r
 452       featureColours.put("nucleotide phosphate-binding region",new Color(65, 245, 75));\r
 453       featureColours.put("peptide", new Color(55, 235, 85));\r
 454       featureColours.put("propeptide", new Color(45, 225, 95));\r
 455       featureColours.put("region of interest", new Color(35, 215, 105));\r
 456       featureColours.put("repeat", new Color(25, 205, 115));\r
 457       featureColours.put("selenocysteine", new Color(15, 195, 125));\r
 458       featureColours.put("sequence conflict", new Color(5, 185, 135));\r
 459       featureColours.put("sequence variant", new Color(0, 175, 145));\r
 460       featureColours.put("short sequence motif", new Color(0, 165, 155));\r
 461       featureColours.put("signal peptide", new Color(0, 155, 165));\r
 462       featureColours.put("site", new Color(0, 145, 175));\r
 463       featureColours.put("splice variant", new Color(0, 135, 185));\r
 464       featureColours.put("strand", new Color(0, 125, 195));\r
 465       featureColours.put("topological domain", new Color(0, 115, 205));\r
 466       featureColours.put("transit peptide", new Color(0, 105, 215));\r
 467       featureColours.put("transmembrane region", new Color(0, 95, 225));\r
 468       featureColours.put("turn", new Color(0, 85, 235));\r
 469       featureColours.put("unsure residue", new Color(0, 75, 245));\r
 470       featureColours.put("zinc finger region", new Color(0, 65, 255));\r
 471     }\r
 472 \r
 473 }\r