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 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     SequenceGroup currentSequenceGroup = null;\r
  40     SequenceGroup[] allGroups = null;\r
  41     Color resBoxColour;\r
  42     Graphics graphics;\r
  43     float transparency = .4f;\r
  44 \r
  45     // The following vector holds the features which are\r
  46     // to be added, in the correct order or rendering\r
  47     Vector featuresDisplayed;\r
  48 \r
  49     /**\r
  50      * Creates a new FeatureRenderer object.\r
  51      *\r
  52      * @param av DOCUMENT ME!\r
  53      */\r
  54     public FeatureRenderer(AlignViewport av)\r
  55     {\r
  56         this.av = av;\r
  57         initColours();\r
  58         String version = System.getProperty("java.version");\r
  59         if (version.indexOf("1.1") == 0)\r
  60           highlightTransparent = false;\r
  61 \r
  62     }\r
  63 \r
  64 boolean highlightTransparent = true;\r
  65     /**\r
  66      * DOCUMENT ME!\r
  67      *\r
  68      * @param g DOCUMENT ME!\r
  69      * @param seq DOCUMENT ME!\r
  70      * @param sg DOCUMENT ME!\r
  71      * @param start DOCUMENT ME!\r
  72      * @param end DOCUMENT ME!\r
  73      * @param x1 DOCUMENT ME!\r
  74      * @param y1 DOCUMENT ME!\r
  75      * @param width DOCUMENT ME!\r
  76      * @param height DOCUMENT ME!\r
  77      */\r
  78     public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,\r
  79         int start, int end, int x1, int y1, int width, int height)\r
  80     {\r
  81 \r
  82         if(seq.getSequenceFeatures()==null)\r
  83           return;\r
  84 \r
  85         Enumeration e = null, e2;\r
  86         String type;\r
  87         if(featuresDisplayed!=null)\r
  88           e = featuresDisplayed.elements();\r
  89         else\r
  90          e = seq.getSequenceFeatures().elements();\r
  91 \r
  92        if(highlightTransparent)\r
  93         {\r
  94         //  MyGraphics.SetTransparency(g, transparency);\r
  95         }\r
  96 \r
  97 \r
  98         while (e.hasMoreElements())\r
  99         {\r
 100             SequenceFeature sf=null;\r
 101             if(featuresDisplayed!=null)\r
 102             {\r
 103               e2 = seq.getSequenceFeatures().elements();\r
 104               type = e.nextElement().toString();\r
 105               while(e2.hasMoreElements())\r
 106               {\r
 107                 sf = (SequenceFeature) e2.nextElement();\r
 108                 if(sf.getType().equals(type))\r
 109                   break;\r
 110                 else\r
 111                   sf = null;\r
 112               }\r
 113             }\r
 114             else\r
 115             {\r
 116               sf = (SequenceFeature) e.nextElement();\r
 117               type = sf.getType();\r
 118             }\r
 119 \r
 120             if(sf==null)\r
 121               continue;\r
 122 \r
 123 \r
 124             if (sf.getBegin() > seq.getEnd())\r
 125             {\r
 126                 continue;\r
 127             }\r
 128 \r
 129             int fstart = seq.findIndex(sf.getBegin()) - 1;\r
 130             int fend = seq.findIndex(sf.getEnd()) - 1;\r
 131 \r
 132             if (((fstart <= end) && (fend >= start)))\r
 133             {\r
 134                 if (fstart < start)\r
 135                 { // fix for if the feature we have starts before the sequence start,\r
 136                     fstart = start; // but the feature end is still valid!!\r
 137                 }\r
 138 \r
 139                 if (fend >= end)\r
 140                 {\r
 141                     fend = end;\r
 142                 }\r
 143 \r
 144                 if (fstart == fend)\r
 145                 {\r
 146                     g.setColor(getColour(type));\r
 147                     g.fillRoundRect((fstart - start) * width, y1, width,\r
 148                         height, 4, 4);\r
 149                     g.setColor(Color.white);\r
 150 \r
 151                     char s = seq.getSequence().charAt(fstart);\r
 152                     FontMetrics fm = g.getFontMetrics();\r
 153                     int charOffset = (width - fm.charWidth(s)) / 2;\r
 154                     int pady = height / 5;\r
 155                     g.drawString(String.valueOf(s),\r
 156                         charOffset + x1 + (width * (fstart - start)),\r
 157                         (y1 + height) - pady);\r
 158                 }\r
 159                 else\r
 160                 {\r
 161                     for (int i = fstart; i <= fend; i++)\r
 162                     {\r
 163                         char s = seq.getSequence().charAt(i);\r
 164 \r
 165                         if (jalview.util.Comparison.isGap(s))\r
 166                         {\r
 167                             continue;\r
 168                         }\r
 169 \r
 170                         g.setColor(getColour(type));\r
 171                         g.fillRect((i - start) * width, y1, width, height);\r
 172 \r
 173                         g.setColor(Color.white);\r
 174 \r
 175                         FontMetrics fm = g.getFontMetrics();\r
 176                         int charOffset = (width - fm.charWidth(s)) / 2;\r
 177                         int pady = height / 5;\r
 178                         g.drawString(String.valueOf(s),\r
 179                             charOffset + x1 + (width * (i - start)),\r
 180                             (y1 + height) - pady);\r
 181                     }\r
 182                 }\r
 183             }\r
 184           }\r
 185 \r
 186           if (highlightTransparent)\r
 187           {\r
 188         //    MyGraphics.SetTransparency(g, 1.0f);\r
 189           }\r
 190     }\r
 191 \r
 192     public Color getColour(String featureType)\r
 193     {\r
 194       return (Color)featureColours.get(featureType);\r
 195     }\r
 196 \r
 197     public void setColour(String featureType, Color col)\r
 198     {\r
 199       featureColours.put(featureType, col);\r
 200     }\r
 201 \r
 202     public void setTransparency(float value)\r
 203     {\r
 204       transparency = value;\r
 205     }\r
 206 \r
 207     public float getTransparency()\r
 208     {\r
 209       return transparency;\r
 210     }\r
 211 \r
 212     public void setFeaturePriority(Object [][] data)\r
 213     {\r
 214       // The feature table will display high priority\r
 215       // features at the top, but theses are the ones\r
 216       // we need to render last, so invert the data\r
 217       featuresDisplayed = new Vector();\r
 218       for(int i=data.length-1; i>-1; i--)\r
 219       {\r
 220        String type = data[i][0].toString();\r
 221        setColour(type, (Color)data[i][1]);\r
 222        if( ((Boolean)data[i][2]).booleanValue() )\r
 223          featuresDisplayed.addElement(type);\r
 224       }\r
 225     }\r
 226 \r
 227     Hashtable featureColours = new Hashtable();\r
 228     void initColours()\r
 229     {\r
 230       featureColours.put("active site", new Color(255, 75, 0));\r
 231       featureColours.put("binding site", new Color(245, 85, 0));\r
 232       featureColours.put("calcium-binding region", new Color(235, 95, 0));\r
 233       featureColours.put("chain", new Color(225, 105, 0));\r
 234       featureColours.put("coiled-coil region", new Color(215, 115, 0));\r
 235       featureColours.put("compositionally biased region", new Color(205, 125, 0));\r
 236       featureColours.put("cross-link", new Color(195, 135, 0));\r
 237       featureColours.put("disulfide bond", new Color(185, 145, 0));\r
 238       featureColours.put("DNA-binding region", new Color(175, 155, 0));\r
 239       featureColours.put("domain", new Color(165, 165, 0));\r
 240       featureColours.put("glycosylation site", new Color(155, 175, 0));\r
 241       featureColours.put("helix", new Color(145, 185, 0));\r
 242       featureColours.put("initiator methionine", new Color(135, 195, 5));\r
 243       featureColours.put("lipid moiety-binding region", new Color(125, 205, 15));\r
 244       featureColours.put("metal ion-binding site", new Color(115, 215, 25));\r
 245       featureColours.put("modified residue", new Color(105, 225, 35));\r
 246       featureColours.put("mutagenesis site", new Color(95, 235, 45));\r
 247       featureColours.put("non-consecutive residues", new Color(85, 245, 55));\r
 248       featureColours.put("non-terminal residue", new Color(75, 255, 65));\r
 249       featureColours.put("nucleotide phosphate-binding region",\r
 250                          new Color(65, 245, 75));\r
 251       featureColours.put("peptide", new Color(55, 235, 85));\r
 252       featureColours.put("propeptide", new Color(45, 225, 95));\r
 253       featureColours.put("region of interest", new Color(35, 215, 105));\r
 254       featureColours.put("repeat", new Color(25, 205, 115));\r
 255       featureColours.put("selenocysteine", new Color(15, 195, 125));\r
 256       featureColours.put("sequence conflict", new Color(5, 185, 135));\r
 257       featureColours.put("sequence variant", new Color(0, 175, 145));\r
 258       featureColours.put("short sequence motif", new Color(0, 165, 155));\r
 259       featureColours.put("signal peptide", new Color(0, 155, 165));\r
 260       featureColours.put("site", new Color(0, 145, 175));\r
 261       featureColours.put("splice variant", new Color(0, 135, 185));\r
 262       featureColours.put("strand", new Color(0, 125, 195));\r
 263       featureColours.put("topological domain", new Color(0, 115, 205));\r
 264       featureColours.put("transit peptide", new Color(0, 105, 215));\r
 265       featureColours.put("transmembrane region", new Color(0, 95, 225));\r
 266       featureColours.put("turn", new Color(0, 85, 235));\r
 267       featureColours.put("unsure residue", new Color(0, 75, 245));\r
 268       featureColours.put("zinc finger region", new Color(0, 65, 255));\r
 269     }\r
 270 \r
 271 }\r
 272 \r
 273 \r
 274 \r