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 \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     SequenceGroup currentSequenceGroup = null;\r
  38     SequenceGroup[] allGroups = null;\r
  39     Color resBoxColour;\r
  40     Graphics graphics;\r
  41     float transparency = 1.0f;\r
  42 \r
  43     // The following vector holds the features which are\r
  44     // to be added, in the correct order or rendering\r
  45     Vector featuresDisplayed;\r
  46 \r
  47     /**\r
  48      * Creates a new FeatureRenderer object.\r
  49      *\r
  50      * @param av DOCUMENT ME!\r
  51      */\r
  52     public FeatureRenderer(AlignViewport av)\r
  53     {\r
  54         this.av = av;\r
  55         initColours();\r
  56     }\r
  57 \r
  58     /**\r
  59      * DOCUMENT ME!\r
  60      *\r
  61      * @param g DOCUMENT ME!\r
  62      * @param seq DOCUMENT ME!\r
  63      * @param sg DOCUMENT ME!\r
  64      * @param start DOCUMENT ME!\r
  65      * @param end DOCUMENT ME!\r
  66      * @param x1 DOCUMENT ME!\r
  67      * @param y1 DOCUMENT ME!\r
  68      * @param width DOCUMENT ME!\r
  69      * @param height DOCUMENT ME!\r
  70      */\r
  71     public void drawSequence(Graphics g1, SequenceI seq, SequenceGroup[] sg,\r
  72         int start, int end, int x1, int y1, int width, int height)\r
  73     {\r
  74 \r
  75         if(seq.getSequenceFeatures()==null)\r
  76           return;\r
  77 \r
  78         Enumeration e = null, e2;\r
  79         String type;\r
  80         if(featuresDisplayed!=null)\r
  81           e = featuresDisplayed.elements();\r
  82         else\r
  83          e = seq.getSequenceFeatures().elements();\r
  84 \r
  85         Graphics2D g = (Graphics2D)g1;\r
  86         g.setComposite(\r
  87         AlphaComposite.getInstance(\r
  88                AlphaComposite.SRC_OVER,transparency));\r
  89 \r
  90         while (e.hasMoreElements())\r
  91         {\r
  92             SequenceFeature sf=null;\r
  93             if(featuresDisplayed!=null)\r
  94             {\r
  95               e2 = seq.getSequenceFeatures().elements();\r
  96               type = e.nextElement().toString();\r
  97               while(e2.hasMoreElements())\r
  98               {\r
  99                 sf = (SequenceFeature) e2.nextElement();\r
 100                 if(sf.getType().equals(type))\r
 101                   break;\r
 102                 else\r
 103                   sf = null;\r
 104               }\r
 105             }\r
 106             else\r
 107             {\r
 108               sf = (SequenceFeature) e.nextElement();\r
 109               type = sf.getType();\r
 110             }\r
 111 \r
 112             if(sf==null)\r
 113               continue;\r
 114 \r
 115 \r
 116             if (sf.getBegin() > seq.getEnd())\r
 117             {\r
 118                 continue;\r
 119             }\r
 120 \r
 121             int fstart = seq.findIndex(sf.getBegin()) - 1;\r
 122             int fend = seq.findIndex(sf.getEnd()) - 1;\r
 123 \r
 124             if (((fstart <= end) && (fend >= start)))\r
 125             {\r
 126                 if (fstart < start)\r
 127                 { // fix for if the feature we have starts before the sequence start,\r
 128                     fstart = start; // but the feature end is still valid!!\r
 129                 }\r
 130 \r
 131                 if (fend >= end)\r
 132                 {\r
 133                     fend = end;\r
 134                 }\r
 135 \r
 136                 if (fstart == fend)\r
 137                 {\r
 138                     g.setColor(getColour(type));\r
 139                     g.fillRoundRect((fstart - start) * width, y1, width,\r
 140                         height, 4, 4);\r
 141                     g.setColor(Color.white);\r
 142 \r
 143                     char s = seq.getSequence().charAt(fstart);\r
 144                     FontMetrics fm = g.getFontMetrics();\r
 145                     int charOffset = (width - fm.charWidth(s)) / 2;\r
 146                     int pady = height / 5;\r
 147                     g.drawString(String.valueOf(s),\r
 148                         charOffset + x1 + (width * (fstart - start)),\r
 149                         (y1 + height) - pady);\r
 150                 }\r
 151                 else\r
 152                 {\r
 153                     for (int i = fstart; i <= fend; i++)\r
 154                     {\r
 155                         char s = seq.getSequence().charAt(i);\r
 156 \r
 157                         if (jalview.util.Comparison.isGap(s))\r
 158                         {\r
 159                             continue;\r
 160                         }\r
 161 \r
 162                         g.setColor(getColour(type));\r
 163                         g.fillRect((i - start) * width, y1, width, height);\r
 164 \r
 165                         g.setColor(Color.white);\r
 166 \r
 167                         FontMetrics fm = g.getFontMetrics();\r
 168                         int charOffset = (width - fm.charWidth(s)) / 2;\r
 169                         int pady = height / 5;\r
 170                         g.drawString(String.valueOf(s),\r
 171                             charOffset + x1 + (width * (i - start)),\r
 172                             (y1 + height) - pady);\r
 173                     }\r
 174                 }\r
 175             }\r
 176         }\r
 177         g.setComposite(\r
 178         AlphaComposite.getInstance(\r
 179                AlphaComposite.SRC_OVER,1.0f));\r
 180 \r
 181     }\r
 182 \r
 183     public Color getColour(String featureType)\r
 184     {\r
 185       return (Color)featureColours.get(featureType);\r
 186     }\r
 187 \r
 188     public void setColour(String featureType, Color col)\r
 189     {\r
 190       featureColours.put(featureType, col);\r
 191     }\r
 192 \r
 193     public void setTransparency(float value)\r
 194     {\r
 195       transparency = value;\r
 196     }\r
 197 \r
 198     public float getTransparency()\r
 199     {\r
 200       return transparency;\r
 201     }\r
 202 \r
 203     public void setFeaturePriority(Object [][] data)\r
 204     {\r
 205       // The feature table will display high priority\r
 206       // features at the top, but theses are the ones\r
 207       // we need to render last, so invert the data\r
 208       featuresDisplayed = new Vector();\r
 209       for(int i=data.length-1; i>-1; i--)\r
 210       {\r
 211        String type = data[i][0].toString();\r
 212        setColour(type, (Color)data[i][1]);\r
 213        if( ((Boolean)data[i][2]).booleanValue() )\r
 214          featuresDisplayed.addElement(type);\r
 215       }\r
 216     }\r
 217 \r
 218     Hashtable featureColours = new Hashtable();\r
 219     void initColours()\r
 220     {\r
 221       featureColours.put("active site", new Color(255, 75, 0));\r
 222       featureColours.put("binding site", new Color(245, 85, 0));\r
 223       featureColours.put("calcium-binding region", new Color(235, 95, 0));\r
 224       featureColours.put("chain", new Color(225, 105, 0));\r
 225       featureColours.put("coiled-coil region", new Color(215, 115, 0));\r
 226       featureColours.put("compositionally biased region", new Color(205, 125, 0));\r
 227       featureColours.put("cross-link", new Color(195, 135, 0));\r
 228       featureColours.put("disulfide bond", new Color(185, 145, 0));\r
 229       featureColours.put("DNA-binding region", new Color(175, 155, 0));\r
 230       featureColours.put("domain", new Color(165, 165, 0));\r
 231       featureColours.put("glycosylation site", new Color(155, 175, 0));\r
 232       featureColours.put("helix", new Color(145, 185, 0));\r
 233       featureColours.put("initiator methionine", new Color(135, 195, 5));\r
 234       featureColours.put("lipid moiety-binding region", new Color(125, 205, 15));\r
 235       featureColours.put("metal ion-binding site", new Color(115, 215, 25));\r
 236       featureColours.put("modified residue", new Color(105, 225, 35));\r
 237       featureColours.put("mutagenesis site", new Color(95, 235, 45));\r
 238       featureColours.put("non-consecutive residues", new Color(85, 245, 55));\r
 239       featureColours.put("non-terminal residue", new Color(75, 255, 65));\r
 240       featureColours.put("nucleotide phosphate-binding region",\r
 241                          new Color(65, 245, 75));\r
 242       featureColours.put("peptide", new Color(55, 235, 85));\r
 243       featureColours.put("propeptide", new Color(45, 225, 95));\r
 244       featureColours.put("region of interest", new Color(35, 215, 105));\r
 245       featureColours.put("repeat", new Color(25, 205, 115));\r
 246       featureColours.put("selenocysteine", new Color(15, 195, 125));\r
 247       featureColours.put("sequence conflict", new Color(5, 185, 135));\r
 248       featureColours.put("sequence variant", new Color(0, 175, 145));\r
 249       featureColours.put("short sequence motif", new Color(0, 165, 155));\r
 250       featureColours.put("signal peptide", new Color(0, 155, 165));\r
 251       featureColours.put("site", new Color(0, 145, 175));\r
 252       featureColours.put("splice variant", new Color(0, 135, 185));\r
 253       featureColours.put("strand", new Color(0, 125, 195));\r
 254       featureColours.put("topological domain", new Color(0, 115, 205));\r
 255       featureColours.put("transit peptide", new Color(0, 105, 215));\r
 256       featureColours.put("transmembrane region", new Color(0, 95, 225));\r
 257       featureColours.put("turn", new Color(0, 85, 235));\r
 258       featureColours.put("unsure residue", new Color(0, 75, 245));\r
 259       featureColours.put("zinc finger region", new Color(0, 65, 255));\r
 260     }\r
 261 \r
 262 }\r