src/jalview/gui/FeatureRenderer.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2006 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 import javax.swing.JComboBox;\r
  29 import javax.swing.JPanel;\r
  30 import javax.swing.JLabel;\r
  31 import javax.swing.JOptionPane;\r
  32 \r
  33 \r
  34 /**\r
  35  * DOCUMENT ME!\r
  36  *\r
  37  * @author $author$\r
  38  * @version $Revision$\r
  39  */\r
  40 public class FeatureRenderer\r
  41 {\r
  42     AlignViewport av;\r
  43     Color resBoxColour;\r
  44     float transparency = 1.0f;\r
  45     FontMetrics fm;\r
  46     int charOffset;\r
  47 \r
  48     Hashtable featureColours = new Hashtable();\r
  49 \r
  50 \r
  51     // A higher level for grouping features of a\r
  52    // particular type\r
  53     Hashtable featureGroups = null;\r
  54 \r
  55     // This is actually an Integer held in the hashtable,\r
  56     // Retrieved using the key feature type\r
  57     Object currentColour;\r
  58 \r
  59     String [] renderOrder;\r
  60 \r
  61     /**\r
  62      * Creates a new FeatureRenderer object.\r
  63      *\r
  64      * @param av DOCUMENT ME!\r
  65      */\r
  66     public FeatureRenderer(AlignViewport av)\r
  67     {\r
  68         this.av = av;\r
  69     }\r
  70 \r
  71     public void transferSettings(FeatureRenderer fr)\r
  72     {\r
  73       renderOrder = fr.renderOrder;\r
  74       featureGroups = fr.featureGroups;\r
  75       featureColours = fr.featureColours;\r
  76       transparency =  fr.transparency;\r
  77     }\r
  78 \r
  79     BufferedImage offscreenImage;\r
  80     boolean offscreenRender = false;\r
  81     public Color findFeatureColour(Color initialCol, SequenceI seq, int res)\r
  82     {\r
  83       return new Color( findFeatureColour (initialCol.getRGB(),\r
  84                         seq, res ));\r
  85     }\r
  86 \r
  87     /**\r
  88      * This is used by the Molecule Viewer and Overview to\r
  89      * get the accurate colourof the rendered sequence\r
  90      */\r
  91     public int findFeatureColour(int initialCol, SequenceI seq, int column)\r
  92     {\r
  93       if(!av.showSequenceFeatures)\r
  94         return initialCol;\r
  95 \r
  96       if(seq!=lastSeq)\r
  97       {\r
  98         lastSeq = seq;\r
  99         sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();\r
 100         if(sequenceFeatures==null)\r
 101           return initialCol;\r
 102 \r
 103         sfSize = sequenceFeatures.length;\r
 104       }\r
 105 \r
 106       if(jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))\r
 107         return Color.white.getRGB();\r
 108 \r
 109 \r
 110       //Only bother making an offscreen image if transparency is applied\r
 111       if(transparency!=1.0f && offscreenImage==null)\r
 112       {\r
 113         offscreenImage = new BufferedImage(1,1,BufferedImage.TYPE_INT_ARGB);\r
 114       }\r
 115 \r
 116       currentColour = null;\r
 117 \r
 118       offscreenRender = true;\r
 119 \r
 120       if(offscreenImage!=null)\r
 121       {\r
 122         offscreenImage.setRGB(0,0,initialCol);\r
 123         drawSequence(offscreenImage.getGraphics(),\r
 124                      lastSeq,\r
 125                      column,column,0);\r
 126 \r
 127         return offscreenImage.getRGB(0,0);\r
 128       }\r
 129       else\r
 130       {\r
 131         drawSequence(null,\r
 132                     lastSeq,\r
 133                     lastSeq.findPosition(column),\r
 134                     -1, -1);\r
 135 \r
 136         if (currentColour == null)\r
 137           return initialCol;\r
 138         else\r
 139           return  ((Integer)currentColour).intValue();\r
 140       }\r
 141 \r
 142 \r
 143     }\r
 144 \r
 145 \r
 146     /**\r
 147      * DOCUMENT ME!\r
 148      *\r
 149      * @param g DOCUMENT ME!\r
 150      * @param seq DOCUMENT ME!\r
 151      * @param sg DOCUMENT ME!\r
 152      * @param start DOCUMENT ME!\r
 153      * @param end DOCUMENT ME!\r
 154      * @param x1 DOCUMENT ME!\r
 155      * @param y1 DOCUMENT ME!\r
 156      * @param width DOCUMENT ME!\r
 157      * @param height DOCUMENT ME!\r
 158      */\r
 159    // String type;\r
 160    // SequenceFeature sf;\r
 161     SequenceI lastSeq;\r
 162     SequenceFeature [] sequenceFeatures;\r
 163     int sfSize, sfindex, spos, epos;\r
 164 \r
 165     public void drawSequence(Graphics g, SequenceI seq,\r
 166                              int start, int end, int y1)\r
 167     {\r
 168       if ( seq.getDatasetSequence().getSequenceFeatures() == null\r
 169           || seq.getDatasetSequence().getSequenceFeatures().length==0)\r
 170         return;\r
 171 \r
 172       if(g!=null)\r
 173         fm = g.getFontMetrics();\r
 174 \r
 175 \r
 176       if (av.featuresDisplayed == null\r
 177           || renderOrder==null\r
 178           || newFeatureAdded)\r
 179        {\r
 180          findAllFeatures();\r
 181          if(av.featuresDisplayed.size()<1)\r
 182            return;\r
 183 \r
 184          sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
 185          sfSize = sequenceFeatures.length;\r
 186        }\r
 187 \r
 188        if(lastSeq==null || seq!=lastSeq)\r
 189       {\r
 190         lastSeq = seq;\r
 191         sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
 192         sfSize = sequenceFeatures.length;\r
 193       }\r
 194 \r
 195 \r
 196       if (transparency != 1 && g!=null)\r
 197       {\r
 198         Graphics2D g2 = (Graphics2D) g;\r
 199         g2.setComposite(\r
 200             AlphaComposite.getInstance(\r
 201                 AlphaComposite.SRC_OVER, transparency));\r
 202       }\r
 203 \r
 204       if(!offscreenRender)\r
 205       {\r
 206         spos = lastSeq.findPosition(start);\r
 207         epos = lastSeq.findPosition(end);\r
 208       }\r
 209 \r
 210 \r
 211       String type;\r
 212       for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)\r
 213        {\r
 214         type =  renderOrder[renderIndex];\r
 215 \r
 216         if(!av.featuresDisplayed.containsKey(type))\r
 217           continue;\r
 218 \r
 219         // loop through all features in sequence to find\r
 220         // current feature to render\r
 221         for (sfindex = 0; sfindex < sfSize; sfindex++)\r
 222         {\r
 223           if(sequenceFeatures.length<=sfindex)\r
 224           {\r
 225             continue;\r
 226           }\r
 227           if (!sequenceFeatures[sfindex].type.equals(type))\r
 228             continue;\r
 229 \r
 230           if (featureGroups != null\r
 231               && sequenceFeatures[sfindex].featureGroup != null\r
 232               &&\r
 233               featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)\r
 234               &&\r
 235               ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).\r
 236               booleanValue())\r
 237           {\r
 238             continue;\r
 239           }\r
 240 \r
 241           if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos\r
 242                             || sequenceFeatures[sfindex].getEnd() < spos))\r
 243             continue;\r
 244 \r
 245           if (offscreenRender && offscreenImage==null)\r
 246           {\r
 247             if (sequenceFeatures[sfindex].begin <= start &&\r
 248                 sequenceFeatures[sfindex].end  >= start)\r
 249             {\r
 250               currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].\r
 251                  type);\r
 252             }\r
 253           }\r
 254           else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))\r
 255           {\r
 256 \r
 257             renderFeature(g, seq,\r
 258                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 259                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 260                           new Color( ( (Integer) av.featuresDisplayed.get(\r
 261                 sequenceFeatures[sfindex].type)).intValue()),\r
 262                           start, end, y1);\r
 263             renderFeature(g, seq,\r
 264                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 265                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 266                           new Color( ( (Integer) av.featuresDisplayed.get(\r
 267                 sequenceFeatures[sfindex].type)).intValue()),\r
 268                           start, end, y1);\r
 269 \r
 270           }\r
 271           else\r
 272             renderFeature(g, seq,\r
 273                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 274                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 275                           getColour(sequenceFeatures[sfindex].type),\r
 276                           start, end, y1);\r
 277 \r
 278 \r
 279         }\r
 280 \r
 281       }\r
 282 \r
 283         if(transparency!=1.0f && g!=null)\r
 284         {\r
 285           Graphics2D g2 = (Graphics2D) g;\r
 286           g2.setComposite(\r
 287               AlphaComposite.getInstance(\r
 288                   AlphaComposite.SRC_OVER, 1.0f));\r
 289         }\r
 290     }\r
 291 \r
 292 \r
 293     char s;\r
 294     int i;\r
 295     void renderFeature(Graphics g, SequenceI seq,\r
 296                        int fstart, int fend, Color featureColour, int start, int end,  int y1)\r
 297     {\r
 298 \r
 299       if (((fstart <= end) && (fend >= start)))\r
 300       {\r
 301         if (fstart < start)\r
 302         { // fix for if the feature we have starts before the sequence start,\r
 303           fstart = start; // but the feature end is still valid!!\r
 304         }\r
 305 \r
 306         if (fend >= end)\r
 307         {\r
 308           fend = end;\r
 309         }\r
 310           int pady = (y1 + av.charHeight) - av.charHeight / 5;\r
 311           for (i = fstart; i <= fend; i++)\r
 312           {\r
 313             s = seq.getSequence().charAt(i);\r
 314 \r
 315             if (jalview.util.Comparison.isGap(s))\r
 316             {\r
 317               continue;\r
 318             }\r
 319 \r
 320             g.setColor(featureColour);\r
 321 \r
 322             g.fillRect( (i - start) * av.charWidth, y1, av.charWidth,av.charHeight);\r
 323 \r
 324             if(offscreenRender || !av.validCharWidth)\r
 325               continue;\r
 326 \r
 327             g.setColor(Color.white);\r
 328             charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
 329             g.drawString(String.valueOf(s),\r
 330                          charOffset + (av.charWidth * (i - start)),\r
 331                          pady);\r
 332 \r
 333           }\r
 334       }\r
 335     }\r
 336 \r
 337 \r
 338     boolean newFeatureAdded = false;\r
 339 \r
 340     public void featuresAdded()\r
 341     {\r
 342       findAllFeatures();\r
 343     }\r
 344 \r
 345    boolean findingFeatures = false;\r
 346    synchronized void findAllFeatures()\r
 347    {\r
 348       newFeatureAdded = false;\r
 349 \r
 350       if(findingFeatures)\r
 351       {\r
 352         newFeatureAdded = true;\r
 353         return;\r
 354       }\r
 355 \r
 356       findingFeatures = true;\r
 357       jalview.schemes.UserColourScheme ucs = new\r
 358           jalview.schemes.UserColourScheme();\r
 359 \r
 360       if(av.featuresDisplayed==null)\r
 361         av.featuresDisplayed = new Hashtable();\r
 362 \r
 363       av.featuresDisplayed.clear();\r
 364 \r
 365       Vector allfeatures = new Vector();\r
 366       for (int i = 0; i < av.alignment.getHeight(); i++)\r
 367       {\r
 368         SequenceFeature [] features\r
 369             = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
 370 \r
 371         if (features == null)\r
 372           continue;\r
 373 \r
 374         int index = 0;\r
 375         while (index < features.length)\r
 376         {\r
 377           if (!av.featuresDisplayed.containsKey(features[index].getType()))\r
 378           {\r
 379             if(!(features[index].begin == 0 && features[index].end ==0))\r
 380             {\r
 381               // If beginning and end are 0, the feature is for the whole sequence\r
 382               // and we don't want to render the feature in the normal way\r
 383 \r
 384               if (getColour(features[index].getType()) == null)\r
 385               {\r
 386                  featureColours.put(features[index].getType(),\r
 387                                    ucs.createColourFromName(features[index].\r
 388                     getType()));\r
 389               }\r
 390 \r
 391               av.featuresDisplayed.put(features[index].getType(),\r
 392                                        new Integer(getColour(features[index].\r
 393                   getType()).getRGB()));\r
 394               allfeatures.addElement(features[index].getType());\r
 395             }\r
 396           }\r
 397           index++;\r
 398         }\r
 399       }\r
 400 \r
 401       renderOrder = new String[allfeatures.size()];\r
 402       Enumeration en = allfeatures.elements();\r
 403       int i = allfeatures.size()-1;\r
 404       while(en.hasMoreElements())\r
 405       {\r
 406         renderOrder[i] = en.nextElement().toString();\r
 407         i--;\r
 408       }\r
 409 \r
 410       findingFeatures = false;\r
 411     }\r
 412 \r
 413     public Color getColour(String featureType)\r
 414     {\r
 415       Color colour = (Color)featureColours.get(featureType);\r
 416       return colour;\r
 417     }\r
 418 \r
 419 \r
 420     static String lastFeatureAdded = "feature_1";\r
 421     static String lastSourceAdded = "Jalview";\r
 422 \r
 423     public boolean createNewFeatures(SequenceI[] sequences,\r
 424                                   SequenceFeature [] features)\r
 425     {\r
 426 \r
 427       JComboBox name = new JComboBox();\r
 428       JComboBox source = new JComboBox();\r
 429 \r
 430       JPanel panel = new JPanel(new GridLayout(2, 2));\r
 431       panel.add(new JLabel("New Sequence Feature Name"));\r
 432       panel.add(name);\r
 433       panel.add(new JLabel("Source:"));\r
 434       panel.add(source);\r
 435      // name.setPreferredSize(new Dimension(300, 20));\r
 436       name.setEditable(true);\r
 437       source.setEditable(true);\r
 438 \r
 439       Enumeration en;\r
 440       if (av.featuresDisplayed != null)\r
 441       {\r
 442         en = av.featuresDisplayed.keys();\r
 443         while (en.hasMoreElements())\r
 444         {\r
 445           name.addItem(en.nextElement().toString());\r
 446         }\r
 447       }\r
 448 \r
 449       if (featureGroups != null)\r
 450       {\r
 451         en = featureGroups.keys();\r
 452         while (en.hasMoreElements())\r
 453         {\r
 454           source.addItem(en.nextElement().toString());\r
 455         }\r
 456       }\r
 457 \r
 458       name.setSelectedItem(lastFeatureAdded);\r
 459       source.setSelectedItem(lastSourceAdded);\r
 460 \r
 461       int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
 462           panel, "Create New Sequence Feature(s)",\r
 463           JOptionPane.OK_CANCEL_OPTION);\r
 464 \r
 465 \r
 466       if(reply==JOptionPane.OK_OPTION\r
 467          && name.getSelectedItem()!=null\r
 468          && source.getSelectedItem()!=null)\r
 469       {\r
 470         lastFeatureAdded = name.getSelectedItem().toString();\r
 471         lastSourceAdded = source.getSelectedItem().toString();\r
 472         for(int i=0; i<sequences.length; i++)\r
 473         {\r
 474           features[i].type = lastFeatureAdded;\r
 475           features[i].featureGroup = lastSourceAdded;\r
 476           sequences[i].addSequenceFeature(features[i]);\r
 477         }\r
 478 \r
 479         if (av.featuresDisplayed == null)\r
 480           av.featuresDisplayed = new Hashtable();\r
 481 \r
 482         if(featureGroups==null)\r
 483           featureGroups = new Hashtable();\r
 484 \r
 485         featureGroups.put(lastSourceAdded, new Boolean(true));\r
 486 \r
 487         Color col = getColour(lastFeatureAdded);\r
 488         if(col==null)\r
 489         {\r
 490           col = new Color(60, 160, 115);\r
 491           setColour(lastFeatureAdded, col);\r
 492         }\r
 493 \r
 494         av.featuresDisplayed.put(lastSourceAdded, new Integer(col.getRGB()));\r
 495         findAllFeatures();\r
 496         return true;\r
 497       }\r
 498       else\r
 499         return false;\r
 500 \r
 501     }\r
 502 \r
 503     public void setColour(String featureType, Color col)\r
 504     {\r
 505       featureColours.put(featureType, col);\r
 506     }\r
 507 \r
 508     public void setTransparency(float value)\r
 509     {\r
 510       transparency = value;\r
 511     }\r
 512 \r
 513     public float getTransparency()\r
 514     {\r
 515       return transparency;\r
 516     }\r
 517 \r
 518     public void setFeaturePriority(Object [][] data)\r
 519     {\r
 520       // The feature table will display high priority\r
 521       // features at the top, but theses are the ones\r
 522       // we need to render last, so invert the data\r
 523       if(av.featuresDisplayed!=null)\r
 524         av.featuresDisplayed.clear();\r
 525       else\r
 526         av.featuresDisplayed = new Hashtable();\r
 527 \r
 528       renderOrder = new String[data.length];\r
 529 \r
 530       if (data.length > 0)\r
 531         for (int i = 0; i < data.length; i++)\r
 532         {\r
 533           String type = data[i][0].toString();\r
 534           setColour(type, (Color) data[i][1]);\r
 535           if ( ( (Boolean) data[i][2]).booleanValue())\r
 536           {\r
 537             av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));\r
 538           }\r
 539 \r
 540           renderOrder[data.length - i - 1] = type;\r
 541         }\r
 542 \r
 543     }\r
 544 \r
 545 \r
 546 \r
 547 \r
 548 }\r