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     SequenceGroup currentSequenceGroup = null;\r
  37     SequenceGroup[] allGroups = null;\r
  38     Graphics graphics;\r
  39 \r
  40     // The following vector holds the features which are\r
  41     // to be added, in the correct order or rendering\r
  42     Vector featuresDisplayed;\r
  43 \r
  44     // A higher level for grouping features of a\r
  45     // paritcular type\r
  46     Hashtable featureGroups = null;\r
  47 \r
  48     Color currentColour = null;\r
  49 \r
  50     boolean drawText = true;\r
  51     FontMetrics fm;\r
  52     int charOffset;\r
  53 \r
  54     /**\r
  55      * Creates a new FeatureRenderer object.\r
  56      *\r
  57      * @param av DOCUMENT ME!\r
  58      */\r
  59     public FeatureRenderer(AlignViewport av)\r
  60     {\r
  61         this.av = av;\r
  62         initColours();\r
  63     }\r
  64 \r
  65     //boolean highlightTransparent = true;\r
  66     /**\r
  67      * DOCUMENT ME!\r
  68      *\r
  69      * @param g DOCUMENT ME!\r
  70      * @param seq DOCUMENT ME!\r
  71      * @param sg DOCUMENT ME!\r
  72      * @param start DOCUMENT ME!\r
  73      * @param end DOCUMENT ME!\r
  74      * @param x1 DOCUMENT ME!\r
  75      * @param y1 DOCUMENT ME!\r
  76      * @param width DOCUMENT ME!\r
  77      * @param height DOCUMENT ME!\r
  78      */\r
  79     public void drawSequence(Graphics g, SequenceI seq,\r
  80         int start, int end, int x1, int y1, int width, int height)\r
  81     {\r
  82       fm = g.getFontMetrics();\r
  83 \r
  84         if(seq.getSequenceFeatures()==null)\r
  85           return;\r
  86 \r
  87         Enumeration e = null, e2;\r
  88         String type;\r
  89         if(featuresDisplayed!=null)\r
  90           e = featuresDisplayed.elements();\r
  91         else\r
  92          e = seq.getSequenceFeatures().elements();\r
  93 \r
  94 \r
  95         while (e.hasMoreElements())\r
  96         {\r
  97             SequenceFeature sf=null;\r
  98             if(featuresDisplayed!=null)\r
  99             {\r
 100               e2 = seq.getSequenceFeatures().elements();\r
 101               type = e.nextElement().toString();\r
 102               while(e2.hasMoreElements())\r
 103               {\r
 104                 sf = (SequenceFeature) e2.nextElement();\r
 105                 if(sf.getType().equals(type))\r
 106                   break;\r
 107                 else\r
 108                   sf = null;\r
 109               }\r
 110             }\r
 111             else\r
 112             {\r
 113               sf = (SequenceFeature) e.nextElement();\r
 114               type = sf.getType();\r
 115             }\r
 116 \r
 117             if(sf==null)\r
 118               continue;\r
 119 \r
 120             if(featureGroups!=null\r
 121                && sf.getFeatureGroup()!=null\r
 122                && featureGroups.containsKey(sf.getFeatureGroup())\r
 123                && !((Boolean)featureGroups.get(sf.getFeatureGroup())).booleanValue())\r
 124             {\r
 125               continue;\r
 126             }\r
 127 \r
 128 \r
 129             if (sf.getBegin() > seq.getEnd())\r
 130             {\r
 131                 continue;\r
 132             }\r
 133 \r
 134             if (type.equals("disulfide bond"))\r
 135             {\r
 136 \r
 137               renderFeature(g, seq,\r
 138                             seq.findIndex(sf.getBegin()) - 1,\r
 139                             seq.findIndex(sf.getBegin()) - 1,\r
 140                             type, start, end, x1, y1, width, height);\r
 141               renderFeature(g, seq,\r
 142                             seq.findIndex(sf.getEnd()) - 1,\r
 143                             seq.findIndex(sf.getEnd()) - 1,\r
 144                             type, start, end, x1, y1, width, height);\r
 145 \r
 146             }\r
 147             else\r
 148               renderFeature(g, seq,\r
 149                             seq.findIndex(sf.getBegin()) - 1,\r
 150                             seq.findIndex(sf.getEnd()) - 1,\r
 151                           type, start, end, x1, y1, width, height);\r
 152 \r
 153       }\r
 154     }\r
 155 \r
 156     void renderFeature(Graphics g, SequenceI seq,\r
 157                        int fstart, int fend, String type, int start, int end,\r
 158                        int x1, int y1, int width, int height)\r
 159     {\r
 160       if ( ( (fstart <= end) && (fend >= start)))\r
 161       {\r
 162         if (fstart < start)\r
 163         { // fix for if the feature we have starts before the sequence start,\r
 164           fstart = start; // but the feature end is still valid!!\r
 165         }\r
 166 \r
 167         if (fend >= end)\r
 168         {\r
 169           fend = end;\r
 170         }\r
 171         for (int i = fstart; i <= fend; i++)\r
 172         {\r
 173           char s = seq.getSequence().charAt(i);\r
 174 \r
 175           if (jalview.util.Comparison.isGap(s))\r
 176           {\r
 177             continue;\r
 178           }\r
 179 \r
 180           currentColour = getColour(type);\r
 181 \r
 182           g.setColor(currentColour);\r
 183 \r
 184           g.fillRect( (i - start) * width, y1, width, height);\r
 185 \r
 186           if (drawText)\r
 187           {\r
 188             g.setColor(Color.white);\r
 189             charOffset = (width - fm.charWidth(s)) / 2;\r
 190             g.drawString(String.valueOf(s),\r
 191                          charOffset + x1 + (width * (i - start)),\r
 192                          (y1 + height) - height / 5);\r
 193           }\r
 194         }\r
 195       }\r
 196     }\r
 197 \r
 198     Image offscreen;\r
 199     Frame nullframe;\r
 200     public Color findFeatureColour(Color initialCol, SequenceI seq, int i)\r
 201     {\r
 202       currentColour = initialCol;\r
 203       if(offscreen == null)\r
 204       {\r
 205         nullframe = new Frame();\r
 206         nullframe.addNotify();\r
 207         offscreen = nullframe.createImage(1, 1);\r
 208       }\r
 209 \r
 210       drawSequence(offscreen.getGraphics(), seq, i, i, 0, 0, 1, 1);\r
 211       return currentColour;\r
 212     }\r
 213 \r
 214 \r
 215 \r
 216     public Color getColour(String featureType)\r
 217     {\r
 218       return (Color)featureColours.get(featureType);\r
 219     }\r
 220 \r
 221     public void setColour(String featureType, Color col)\r
 222     {\r
 223       featureColours.put(featureType, col);\r
 224     }\r
 225 \r
 226     public void addNewFeature(String name, Color col)\r
 227     {\r
 228       setColour(name, col);\r
 229       if (featuresDisplayed == null)\r
 230         featuresDisplayed = new Vector();\r
 231       featuresDisplayed.insertElementAt(name, 0);\r
 232     }\r
 233 \r
 234 \r
 235  /*   public void setTransparency(float value)\r
 236     {\r
 237       transparency = value;\r
 238     }\r
 239 \r
 240     public float getTransparency()\r
 241     {\r
 242       return transparency;\r
 243     }*/\r
 244 \r
 245     public void setFeaturePriority(Object [][] data)\r
 246     {\r
 247       // The feature table will display high priority\r
 248       // features at the top, but theses are the ones\r
 249       // we need to render last, so invert the data\r
 250       if(featuresDisplayed!=null)\r
 251         featuresDisplayed.removeAllElements();\r
 252       else\r
 253         featuresDisplayed = new Vector();\r
 254 \r
 255       for(int i=data.length-1; i>-1; i--)\r
 256       {\r
 257        String type = data[i][0].toString();\r
 258        setColour(type, (Color)data[i][1]);\r
 259        if( ((Boolean)data[i][2]).booleanValue() )\r
 260          featuresDisplayed.addElement(type);\r
 261       }\r
 262     }\r
 263 \r
 264     Hashtable featureColours = new Hashtable();\r
 265     void initColours()\r
 266     {\r
 267       featureColours.put("active site", new Color(255, 75, 0));\r
 268       featureColours.put("binding site", new Color(245, 85, 0));\r
 269       featureColours.put("calcium-binding region", new Color(235, 95, 0));\r
 270       featureColours.put("chain", new Color(225, 105, 0));\r
 271       featureColours.put("coiled-coil region", new Color(215, 115, 0));\r
 272       featureColours.put("compositionally biased region", new Color(205, 125, 0));\r
 273       featureColours.put("cross-link", new Color(195, 135, 0));\r
 274       featureColours.put("disulfide bond", new Color(185, 145, 0));\r
 275       featureColours.put("DNA-binding region", new Color(175, 155, 0));\r
 276       featureColours.put("domain", new Color(165, 165, 0));\r
 277       featureColours.put("glycosylation site", new Color(155, 175, 0));\r
 278       featureColours.put("helix", new Color(145, 185, 0));\r
 279       featureColours.put("initiator methionine", new Color(135, 195, 5));\r
 280       featureColours.put("lipid moiety-binding region", new Color(125, 205, 15));\r
 281       featureColours.put("metal ion-binding site", new Color(115, 215, 25));\r
 282       featureColours.put("modified residue", new Color(105, 225, 35));\r
 283       featureColours.put("mutagenesis site", new Color(95, 235, 45));\r
 284       featureColours.put("non-consecutive residues", new Color(85, 245, 55));\r
 285       featureColours.put("non-terminal residue", new Color(75, 255, 65));\r
 286       featureColours.put("nucleotide phosphate-binding region",\r
 287                          new Color(65, 245, 75));\r
 288       featureColours.put("peptide", new Color(55, 235, 85));\r
 289       featureColours.put("propeptide", new Color(45, 225, 95));\r
 290       featureColours.put("region of interest", new Color(35, 215, 105));\r
 291       featureColours.put("repeat", new Color(25, 205, 115));\r
 292       featureColours.put("selenocysteine", new Color(15, 195, 125));\r
 293       featureColours.put("sequence conflict", new Color(5, 185, 135));\r
 294       featureColours.put("sequence variant", new Color(0, 175, 145));\r
 295       featureColours.put("short sequence motif", new Color(0, 165, 155));\r
 296       featureColours.put("signal peptide", new Color(0, 155, 165));\r
 297       featureColours.put("site", new Color(0, 145, 175));\r
 298       featureColours.put("splice variant", new Color(0, 135, 185));\r
 299       featureColours.put("strand", new Color(0, 125, 195));\r
 300       featureColours.put("topological domain", new Color(0, 115, 205));\r
 301       featureColours.put("transit peptide", new Color(0, 105, 215));\r
 302       featureColours.put("transmembrane region", new Color(0, 95, 225));\r
 303       featureColours.put("turn", new Color(0, 85, 235));\r
 304       featureColours.put("unsure residue", new Color(0, 75, 245));\r
 305       featureColours.put("zinc finger region", new Color(0, 65, 255));\r
 306     }\r
 307 \r
 308 }\r
 309 \r
 310 \r
 311 \r