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