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 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     Color resBoxColour;\r
  40     float transparency = 1.0f;\r
  41     FontMetrics fm;\r
  42     int charOffset;\r
  43     boolean drawText = true;\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 = null;\r
  48 \r
  49     // A higher level for grouping features of a\r
  50    // particular type\r
  51     Hashtable featureGroups = null;\r
  52 \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     /**\r
  66      * This is used by the Molecule Viewer to get the accurate colour\r
  67      * of the rendered sequence\r
  68      */\r
  69     BufferedImage bi;\r
  70     public Color findFeatureColour(Color initialCol, SequenceI seq, int i)\r
  71     {\r
  72       if(!av.showSequenceFeatures)\r
  73         return initialCol;\r
  74 \r
  75       if (bi == null)\r
  76         bi = new BufferedImage(1, 1, BufferedImage.TYPE_INT_RGB);\r
  77 \r
  78       bi.setRGB(0,0, initialCol.getRGB());\r
  79 \r
  80       drawText = false;\r
  81 \r
  82       drawSequence(bi.getGraphics(), seq, i, i, 0, 0, 1, 1);\r
  83       drawText = true;\r
  84 \r
  85       return new Color(bi.getRGB(0, 0));\r
  86     }\r
  87 \r
  88 \r
  89     /**\r
  90      * DOCUMENT ME!\r
  91      *\r
  92      * @param g DOCUMENT ME!\r
  93      * @param seq DOCUMENT ME!\r
  94      * @param sg DOCUMENT ME!\r
  95      * @param start DOCUMENT ME!\r
  96      * @param end DOCUMENT ME!\r
  97      * @param x1 DOCUMENT ME!\r
  98      * @param y1 DOCUMENT ME!\r
  99      * @param width DOCUMENT ME!\r
 100      * @param height DOCUMENT ME!\r
 101      */\r
 102     public void drawSequence(Graphics g, SequenceI seq,\r
 103                              int start, int end, int x1, int y1, int width, int height)\r
 104     {\r
 105 \r
 106         //System.out.println(start+" "+end+" "+x1+" "+y1);\r
 107       if (seq.getDatasetSequence().getSequenceFeatures() == null\r
 108           || seq.getDatasetSequence().getSequenceFeatures().size()==0)\r
 109         return;\r
 110 \r
 111       fm = g.getFontMetrics();\r
 112 \r
 113       if (transparency != 1)\r
 114       {\r
 115         Graphics2D g2 = (Graphics2D) g;\r
 116         g2.setComposite(\r
 117             AlphaComposite.getInstance(\r
 118                 AlphaComposite.SRC_OVER, transparency));\r
 119       }\r
 120 \r
 121       String type;\r
 122       SequenceFeature sf;\r
 123       if (featuresDisplayed == null)\r
 124         findAllFeatures();\r
 125 \r
 126       Enumeration e = featuresDisplayed.elements(), e2;\r
 127 \r
 128       // Loop through each visible feature\r
 129       while (e.hasMoreElements())\r
 130       {\r
 131 \r
 132         type = e.nextElement().toString();\r
 133         e2 = seq.getDatasetSequence().getSequenceFeatures().elements();\r
 134         // loop through all features in sequence to find\r
 135         // current feature to render\r
 136           while (e2.hasMoreElements())\r
 137         {\r
 138 \r
 139           sf = (SequenceFeature) e2.nextElement();\r
 140           if (!type.equals(sf.getType()))\r
 141             continue;\r
 142 \r
 143           if(featureGroups!=null\r
 144              && sf.getFeatureGroup()!=null\r
 145              && featureGroups.containsKey(sf.getFeatureGroup())\r
 146              && !((Boolean)featureGroups.get(sf.getFeatureGroup())).booleanValue())\r
 147           {\r
 148             continue;\r
 149           }\r
 150 \r
 151           if (sf.getBegin() > seq.getEnd())\r
 152             continue;\r
 153 \r
 154           if (type.equals("disulfide bond"))\r
 155           {\r
 156 \r
 157             renderFeature(g, seq,\r
 158                           seq.findIndex(sf.getBegin()) - 1,\r
 159                           seq.findIndex(sf.getBegin()) - 1,\r
 160                           type, start, end, x1, y1, width, height);\r
 161             renderFeature(g, seq,\r
 162                           seq.findIndex(sf.getEnd()) - 1,\r
 163                           seq.findIndex(sf.getEnd()) - 1,\r
 164                           type, start, end, x1, y1, width, height);\r
 165 \r
 166           }\r
 167           else\r
 168             renderFeature(g, seq,\r
 169                           seq.findIndex(sf.getBegin()) - 1,\r
 170                           seq.findIndex(sf.getEnd()) - 1,\r
 171                           type, start, end, x1, y1, width, height);\r
 172         }\r
 173       }\r
 174 \r
 175         if(transparency!=1.0f)\r
 176         {\r
 177           Graphics2D g2 = (Graphics2D) g;\r
 178           g2.setComposite(\r
 179               AlphaComposite.getInstance(\r
 180                   AlphaComposite.SRC_OVER, 1.0f));\r
 181         }\r
 182     }\r
 183 \r
 184 \r
 185     void renderFeature(Graphics g, SequenceI seq,\r
 186                        int fstart, int fend, String type, int start, int end, int x1, int y1, int width, int height)\r
 187     {\r
 188 \r
 189       if (((fstart <= end) && (fend >= start)))\r
 190       {\r
 191           if (fstart < start)\r
 192           { // fix for if the feature we have starts before the sequence start,\r
 193               fstart = start; // but the feature end is still valid!!\r
 194           }\r
 195 \r
 196           if (fend >= end)\r
 197           {\r
 198             fend = end;\r
 199           }\r
 200           for (int i = fstart; i <= fend; i++)\r
 201           {\r
 202             char s = seq.getSequence().charAt(i);\r
 203 \r
 204             if (jalview.util.Comparison.isGap(s))\r
 205             {\r
 206               continue;\r
 207             }\r
 208 \r
 209             g.setColor(getColour(type));\r
 210 \r
 211             g.fillRect( (i - start) * width, y1, width, height);\r
 212 \r
 213             if(drawText)\r
 214            {\r
 215              g.setColor(Color.white);\r
 216              charOffset = (width - fm.charWidth(s)) / 2;\r
 217              g.drawString(String.valueOf(s),\r
 218                           charOffset + x1 + (width * (i - start)),\r
 219                           (y1 + height) - height / 5); //pady = height / 5;\r
 220            }\r
 221           }\r
 222         }\r
 223     }\r
 224 \r
 225     void findAllFeatures()\r
 226     {\r
 227       Vector features = new Vector();\r
 228       SequenceFeature sf;\r
 229       featuresDisplayed = new Vector();\r
 230       Enumeration e;\r
 231       for (int i = 0; i < av.alignment.getHeight(); i++)\r
 232       {\r
 233         features = av.alignment.getSequenceAt(i).getDatasetSequence().\r
 234             getSequenceFeatures();\r
 235         if (features == null)\r
 236           continue;\r
 237 \r
 238         e = features.elements();\r
 239         while (e.hasMoreElements())\r
 240         {\r
 241           sf = (SequenceFeature) e.nextElement();\r
 242           if (!featuresDisplayed.contains(sf.getType()))\r
 243           {\r
 244             featuresDisplayed.addElement(sf.getType());\r
 245           }\r
 246         }\r
 247       }\r
 248     }\r
 249 \r
 250     public Color getColour(String featureType)\r
 251     {\r
 252       return (Color)featureColours.get(featureType);\r
 253     }\r
 254 \r
 255     public void addNewFeature(String name, Color col)\r
 256     {\r
 257       setColour(name, col);\r
 258       if(featuresDisplayed==null)\r
 259         featuresDisplayed = new Vector();\r
 260       featuresDisplayed.insertElementAt(name, 0);\r
 261     }\r
 262 \r
 263     public void setColour(String featureType, Color col)\r
 264     {\r
 265       featureColours.put(featureType, col);\r
 266     }\r
 267 \r
 268     public void setTransparency(float value)\r
 269     {\r
 270       transparency = value;\r
 271     }\r
 272 \r
 273     public float getTransparency()\r
 274     {\r
 275       return transparency;\r
 276     }\r
 277 \r
 278     public void setFeaturePriority(Object [][] data)\r
 279     {\r
 280       // The feature table will display high priority\r
 281       // features at the top, but theses are the ones\r
 282       // we need to render last, so invert the data\r
 283       featuresDisplayed.clear();\r
 284       for(int i=data.length-1; i>-1; i--)\r
 285       {\r
 286        String type = data[i][0].toString();\r
 287        setColour(type, (Color)data[i][1]);\r
 288        if( ((Boolean)data[i][2]).booleanValue() )\r
 289          featuresDisplayed.addElement(type);\r
 290       }\r
 291     }\r
 292 \r
 293     Hashtable featureColours = new Hashtable();\r
 294     void initColours()\r
 295     {\r
 296       featureColours.put("active site", new Color(255, 75, 0));\r
 297       featureColours.put("binding site", new Color(245, 85, 0));\r
 298       featureColours.put("calcium-binding region", new Color(235, 95, 0));\r
 299       featureColours.put("chain", new Color(225, 105, 0));\r
 300       featureColours.put("coiled-coil region", new Color(215, 115, 0));\r
 301       featureColours.put("compositionally biased region", new Color(205, 125, 0));\r
 302       featureColours.put("cross-link", new Color(195, 135, 0));\r
 303       featureColours.put("disulfide bond", new Color(230,230,0));\r
 304       featureColours.put("DNA-binding region", new Color(175, 155, 0));\r
 305       featureColours.put("domain", new Color(165, 165, 0));\r
 306       featureColours.put("glycosylation site", new Color(155, 175, 0));\r
 307       featureColours.put("helix", new Color(145, 185, 0));\r
 308       featureColours.put("initiator methionine", new Color(135, 195, 5));\r
 309       featureColours.put("lipid moiety-binding region", new Color(125, 205, 15));\r
 310       featureColours.put("metal ion-binding site", new Color(115, 215, 25));\r
 311       featureColours.put("modified residue", new Color(105, 225, 35));\r
 312       featureColours.put("mutagenesis site", new Color(95, 235, 45));\r
 313       featureColours.put("non-consecutive residues", new Color(85, 245, 55));\r
 314       featureColours.put("non-terminal residue", new Color(75, 255, 65));\r
 315       featureColours.put("nucleotide phosphate-binding region",new Color(65, 245, 75));\r
 316       featureColours.put("peptide", new Color(55, 235, 85));\r
 317       featureColours.put("propeptide", new Color(45, 225, 95));\r
 318       featureColours.put("region of interest", new Color(35, 215, 105));\r
 319       featureColours.put("repeat", new Color(25, 205, 115));\r
 320       featureColours.put("selenocysteine", new Color(15, 195, 125));\r
 321       featureColours.put("sequence conflict", new Color(5, 185, 135));\r
 322       featureColours.put("sequence variant", new Color(0, 175, 145));\r
 323       featureColours.put("short sequence motif", new Color(0, 165, 155));\r
 324       featureColours.put("signal peptide", new Color(0, 155, 165));\r
 325       featureColours.put("site", new Color(0, 145, 175));\r
 326       featureColours.put("splice variant", new Color(0, 135, 185));\r
 327       featureColours.put("strand", new Color(0, 125, 195));\r
 328       featureColours.put("topological domain", new Color(0, 115, 205));\r
 329       featureColours.put("transit peptide", new Color(0, 105, 215));\r
 330       featureColours.put("transmembrane region", new Color(0, 95, 225));\r
 331       featureColours.put("turn", new Color(0, 85, 235));\r
 332       featureColours.put("unsure residue", new Color(0, 75, 245));\r
 333       featureColours.put("zinc finger region", new Color(0, 65, 255));\r
 334     }\r
 335 \r
 336 }\r