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     FontMetrics fm;\r
  43     int charOffset;\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     }\r
  59 \r
  60     /**\r
  61      * DOCUMENT ME!\r
  62      *\r
  63      * @param g DOCUMENT ME!\r
  64      * @param seq DOCUMENT ME!\r
  65      * @param sg DOCUMENT ME!\r
  66      * @param start DOCUMENT ME!\r
  67      * @param end DOCUMENT ME!\r
  68      * @param x1 DOCUMENT ME!\r
  69      * @param y1 DOCUMENT ME!\r
  70      * @param width DOCUMENT ME!\r
  71      * @param height DOCUMENT ME!\r
  72      */\r
  73     public void drawSequence(Graphics g, SequenceI seq,\r
  74                              int start, int end, int x1, int y1, int width, int height)\r
  75     {\r
  76 \r
  77       if (seq.getDatasetSequence().getSequenceFeatures() == null)\r
  78         return;\r
  79 \r
  80       fm = g.getFontMetrics();\r
  81 \r
  82       if (transparency != 1)\r
  83       {\r
  84         Graphics2D g2 = (Graphics2D) g;\r
  85         g2.setComposite(\r
  86             AlphaComposite.getInstance(\r
  87                 AlphaComposite.SRC_OVER, transparency));\r
  88       }\r
  89 \r
  90       String type;\r
  91       SequenceFeature sf;\r
  92       if (featuresDisplayed == null || featuresDisplayed.size()==0)\r
  93         findAllFeatures();\r
  94 \r
  95       Enumeration e = featuresDisplayed.elements(), e2;\r
  96 \r
  97       // Loop through each visible feature\r
  98       while (e.hasMoreElements())\r
  99       {\r
 100 \r
 101         type = e.nextElement().toString();\r
 102         e2 = seq.getDatasetSequence().getSequenceFeatures().elements();\r
 103         // loop through all features in sequence to find\r
 104         // current feature to render\r
 105           while (e2.hasMoreElements())\r
 106         {\r
 107 \r
 108           sf = (SequenceFeature) e2.nextElement();\r
 109           if (!type.equals(sf.getType()))\r
 110             continue;\r
 111 \r
 112           if (sf.getBegin() > seq.getEnd())\r
 113             continue;\r
 114 \r
 115           if (type.equals("disulfide bond"))\r
 116           {\r
 117 \r
 118             renderFeature(g, seq,\r
 119                           seq.findIndex(sf.getBegin()) - 1,\r
 120                           seq.findIndex(sf.getBegin()) - 1,\r
 121                           type, start, end, x1, y1, width, height);\r
 122             renderFeature(g, seq,\r
 123                           seq.findIndex(sf.getEnd()) - 1,\r
 124                           seq.findIndex(sf.getEnd()) - 1,\r
 125                           type, start, end, x1, y1, width, height);\r
 126 \r
 127           }\r
 128           else\r
 129             renderFeature(g, seq,\r
 130                           seq.findIndex(sf.getBegin()) - 1,\r
 131                           seq.findIndex(sf.getEnd()) - 1,\r
 132                           type, start, end, x1, y1, width, height);\r
 133         }\r
 134       }\r
 135 \r
 136         if(transparency!=1.0f)\r
 137         {\r
 138           Graphics2D g2 = (Graphics2D) g;\r
 139           g2.setComposite(\r
 140               AlphaComposite.getInstance(\r
 141                   AlphaComposite.SRC_OVER, 1.0f));\r
 142         }\r
 143     }\r
 144 \r
 145 \r
 146     void renderFeature(Graphics g, SequenceI seq,\r
 147                        int fstart, int fend, String type, int start, int end, int x1, int y1, int width, int height)\r
 148     {\r
 149 \r
 150       if (((fstart <= end) && (fend >= start)))\r
 151       {\r
 152           if (fstart < start)\r
 153           { // fix for if the feature we have starts before the sequence start,\r
 154               fstart = start; // but the feature end is still valid!!\r
 155           }\r
 156 \r
 157           if (fend >= end)\r
 158           {\r
 159             fend = end;\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 \r
 172             g.fillRect( (i - start) * width, y1, width, height);\r
 173 \r
 174             g.setColor(Color.white);\r
 175 \r
 176             charOffset = (width - fm.charWidth(s)) / 2;\r
 177             g.drawString(String.valueOf(s),\r
 178                          charOffset + x1 + (width * (i - start)),\r
 179                          (y1 + height) - height/5);//pady = height / 5;\r
 180           }\r
 181         }\r
 182     }\r
 183 \r
 184     void findAllFeatures()\r
 185     {\r
 186       Vector features = new Vector();\r
 187       SequenceFeature sf;\r
 188       featuresDisplayed = new Vector();\r
 189       Enumeration e;\r
 190       for (int i = 0; i < av.alignment.getHeight(); i++)\r
 191       {\r
 192         features = av.alignment.getSequenceAt(i).getDatasetSequence().\r
 193             getSequenceFeatures();\r
 194         if (features == null)\r
 195           continue;\r
 196 \r
 197         e = features.elements();\r
 198         while (e.hasMoreElements())\r
 199         {\r
 200           sf = (SequenceFeature) e.nextElement();\r
 201           if (!featuresDisplayed.contains(sf.getType()))\r
 202           {\r
 203             featuresDisplayed.addElement(sf.getType());\r
 204           }\r
 205         }\r
 206       }\r
 207     }\r
 208 \r
 209     public Color getColour(String featureType)\r
 210     {\r
 211       return (Color)featureColours.get(featureType);\r
 212     }\r
 213 \r
 214     public void setColour(String featureType, Color col)\r
 215     {\r
 216       featureColours.put(featureType, col);\r
 217     }\r
 218 \r
 219     public void setTransparency(float value)\r
 220     {\r
 221       transparency = value;\r
 222     }\r
 223 \r
 224     public float getTransparency()\r
 225     {\r
 226       return transparency;\r
 227     }\r
 228 \r
 229     public void setFeaturePriority(Object [][] data)\r
 230     {\r
 231       // The feature table will display high priority\r
 232       // features at the top, but theses are the ones\r
 233       // we need to render last, so invert the data\r
 234       featuresDisplayed = new Vector();\r
 235       for(int i=data.length-1; i>-1; i--)\r
 236       {\r
 237        String type = data[i][0].toString();\r
 238        setColour(type, (Color)data[i][1]);\r
 239        if( ((Boolean)data[i][2]).booleanValue() )\r
 240          featuresDisplayed.addElement(type);\r
 241       }\r
 242     }\r
 243 \r
 244     Hashtable featureColours = new Hashtable();\r
 245     void initColours()\r
 246     {\r
 247       featureColours.put("active site", new Color(255, 75, 0));\r
 248       featureColours.put("binding site", new Color(245, 85, 0));\r
 249       featureColours.put("calcium-binding region", new Color(235, 95, 0));\r
 250       featureColours.put("chain", new Color(225, 105, 0));\r
 251       featureColours.put("coiled-coil region", new Color(215, 115, 0));\r
 252       featureColours.put("compositionally biased region", new Color(205, 125, 0));\r
 253       featureColours.put("cross-link", new Color(195, 135, 0));\r
 254       featureColours.put("disulfide bond", new Color(230,230,0));\r
 255       featureColours.put("DNA-binding region", new Color(175, 155, 0));\r
 256       featureColours.put("domain", new Color(165, 165, 0));\r
 257       featureColours.put("glycosylation site", new Color(155, 175, 0));\r
 258       featureColours.put("helix", new Color(145, 185, 0));\r
 259       featureColours.put("initiator methionine", new Color(135, 195, 5));\r
 260       featureColours.put("lipid moiety-binding region", new Color(125, 205, 15));\r
 261       featureColours.put("metal ion-binding site", new Color(115, 215, 25));\r
 262       featureColours.put("modified residue", new Color(105, 225, 35));\r
 263       featureColours.put("mutagenesis site", new Color(95, 235, 45));\r
 264       featureColours.put("non-consecutive residues", new Color(85, 245, 55));\r
 265       featureColours.put("non-terminal residue", new Color(75, 255, 65));\r
 266       featureColours.put("nucleotide phosphate-binding region",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