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.*;\r
  29 import javax.swing.JOptionPane;\r
  30 \r
  31 \r
  32 /**\r
  33  * DOCUMENT ME!\r
  34  *\r
  35  * @author $author$\r
  36  * @version $Revision$\r
  37  */\r
  38 public class FeatureRenderer\r
  39 {\r
  40     AlignViewport av;\r
  41     Color resBoxColour;\r
  42     float transparency = 1.0f;\r
  43     FontMetrics fm;\r
  44     int charOffset;\r
  45 \r
  46     Hashtable featureColours = new Hashtable();\r
  47 \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     // This is actually an Integer held in the hashtable,\r
  54     // Retrieved using the key feature type\r
  55     Object currentColour;\r
  56 \r
  57     String [] renderOrder;\r
  58 \r
  59     /**\r
  60      * Creates a new FeatureRenderer object.\r
  61      *\r
  62      * @param av DOCUMENT ME!\r
  63      */\r
  64     public FeatureRenderer(AlignViewport av)\r
  65     {\r
  66         this.av = av;\r
  67     }\r
  68 \r
  69     public void transferSettings(FeatureRenderer fr)\r
  70     {\r
  71       renderOrder = fr.renderOrder;\r
  72       featureGroups = fr.featureGroups;\r
  73       featureColours = fr.featureColours;\r
  74       transparency =  fr.transparency;\r
  75     }\r
  76 \r
  77     BufferedImage offscreenImage;\r
  78     boolean offscreenRender = false;\r
  79     public Color findFeatureColour(Color initialCol, SequenceI seq, int res)\r
  80     {\r
  81       return new Color( findFeatureColour (initialCol.getRGB(),\r
  82                         seq, res ));\r
  83     }\r
  84 \r
  85     /**\r
  86      * This is used by the Molecule Viewer and Overview to\r
  87      * get the accurate colourof the rendered sequence\r
  88      */\r
  89     public int findFeatureColour(int initialCol, SequenceI seq, int column)\r
  90     {\r
  91       if(!av.showSequenceFeatures)\r
  92         return initialCol;\r
  93 \r
  94       if(seq!=lastSeq)\r
  95       {\r
  96         lastSeq = seq;\r
  97         sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();\r
  98         if(sequenceFeatures==null)\r
  99           return initialCol;\r
 100 \r
 101         sfSize = sequenceFeatures.length;\r
 102       }\r
 103 \r
 104       if(jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))\r
 105         return Color.white.getRGB();\r
 106 \r
 107 \r
 108       //Only bother making an offscreen image if transparency is applied\r
 109       if(transparency!=1.0f && offscreenImage==null)\r
 110       {\r
 111         offscreenImage = new BufferedImage(1,1,BufferedImage.TYPE_INT_ARGB);\r
 112       }\r
 113 \r
 114       currentColour = null;\r
 115 \r
 116       offscreenRender = true;\r
 117 \r
 118       if(offscreenImage!=null)\r
 119       {\r
 120         offscreenImage.setRGB(0,0,initialCol);\r
 121         drawSequence(offscreenImage.getGraphics(),\r
 122                      lastSeq,\r
 123                      column,column,0);\r
 124 \r
 125         return offscreenImage.getRGB(0,0);\r
 126       }\r
 127       else\r
 128       {\r
 129         drawSequence(null,\r
 130                     lastSeq,\r
 131                     lastSeq.findPosition(column),\r
 132                     -1, -1);\r
 133 \r
 134         if (currentColour == null)\r
 135           return initialCol;\r
 136         else\r
 137           return  ((Integer)currentColour).intValue();\r
 138       }\r
 139 \r
 140 \r
 141     }\r
 142 \r
 143 \r
 144     /**\r
 145      * DOCUMENT ME!\r
 146      *\r
 147      * @param g DOCUMENT ME!\r
 148      * @param seq DOCUMENT ME!\r
 149      * @param sg DOCUMENT ME!\r
 150      * @param start DOCUMENT ME!\r
 151      * @param end DOCUMENT ME!\r
 152      * @param x1 DOCUMENT ME!\r
 153      * @param y1 DOCUMENT ME!\r
 154      * @param width DOCUMENT ME!\r
 155      * @param height DOCUMENT ME!\r
 156      */\r
 157    // String type;\r
 158    // SequenceFeature sf;\r
 159     SequenceI lastSeq;\r
 160     SequenceFeature [] sequenceFeatures;\r
 161     int sfSize, sfindex, spos, epos;\r
 162 \r
 163     public void drawSequence(Graphics g, SequenceI seq,\r
 164                              int start, int end, int y1)\r
 165     {\r
 166       if ( seq.getDatasetSequence().getSequenceFeatures() == null\r
 167           || seq.getDatasetSequence().getSequenceFeatures().length==0)\r
 168         return;\r
 169 \r
 170       if(g!=null)\r
 171         fm = g.getFontMetrics();\r
 172 \r
 173 \r
 174       if (av.featuresDisplayed == null\r
 175           || renderOrder==null\r
 176           || newFeatureAdded)\r
 177        {\r
 178          findAllFeatures();\r
 179          if(av.featuresDisplayed.size()<1)\r
 180            return;\r
 181 \r
 182          sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
 183          sfSize = sequenceFeatures.length;\r
 184        }\r
 185 \r
 186        if(lastSeq==null || seq!=lastSeq)\r
 187       {\r
 188         lastSeq = seq;\r
 189         sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
 190         sfSize = sequenceFeatures.length;\r
 191       }\r
 192 \r
 193 \r
 194       if (transparency != 1 && g!=null)\r
 195       {\r
 196         Graphics2D g2 = (Graphics2D) g;\r
 197         g2.setComposite(\r
 198             AlphaComposite.getInstance(\r
 199                 AlphaComposite.SRC_OVER, transparency));\r
 200       }\r
 201 \r
 202       if(!offscreenRender)\r
 203       {\r
 204         spos = lastSeq.findPosition(start);\r
 205         epos = lastSeq.findPosition(end);\r
 206       }\r
 207 \r
 208 \r
 209       String type;\r
 210       for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)\r
 211        {\r
 212         type =  renderOrder[renderIndex];\r
 213 \r
 214         if(!av.featuresDisplayed.containsKey(type))\r
 215           continue;\r
 216 \r
 217         // loop through all features in sequence to find\r
 218         // current feature to render\r
 219         for (sfindex = 0; sfindex < sfSize; sfindex++)\r
 220         {\r
 221           if(sequenceFeatures.length<=sfindex)\r
 222           {\r
 223             continue;\r
 224           }\r
 225           if (!sequenceFeatures[sfindex].type.equals(type))\r
 226             continue;\r
 227 \r
 228           if (featureGroups != null\r
 229               && sequenceFeatures[sfindex].featureGroup != null\r
 230               &&\r
 231               featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)\r
 232               &&\r
 233               ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).\r
 234               booleanValue())\r
 235           {\r
 236             continue;\r
 237           }\r
 238 \r
 239           if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos\r
 240                             || sequenceFeatures[sfindex].getEnd() < spos))\r
 241             continue;\r
 242 \r
 243           if (offscreenRender && offscreenImage==null)\r
 244           {\r
 245             if (sequenceFeatures[sfindex].begin <= start &&\r
 246                 sequenceFeatures[sfindex].end  >= start)\r
 247             {\r
 248               currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].\r
 249                  type);\r
 250             }\r
 251           }\r
 252           else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))\r
 253           {\r
 254 \r
 255             renderFeature(g, seq,\r
 256                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 257                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 258                           new Color( ( (Integer) av.featuresDisplayed.get(\r
 259                 sequenceFeatures[sfindex].type)).intValue()),\r
 260                           start, end, y1);\r
 261             renderFeature(g, seq,\r
 262                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 263                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 264                           new Color( ( (Integer) av.featuresDisplayed.get(\r
 265                 sequenceFeatures[sfindex].type)).intValue()),\r
 266                           start, end, y1);\r
 267 \r
 268           }\r
 269           else\r
 270             renderFeature(g, seq,\r
 271                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
 272                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
 273                           getColour(sequenceFeatures[sfindex].type),\r
 274                           start, end, y1);\r
 275 \r
 276 \r
 277         }\r
 278 \r
 279       }\r
 280 \r
 281         if(transparency!=1.0f && g!=null)\r
 282         {\r
 283           Graphics2D g2 = (Graphics2D) g;\r
 284           g2.setComposite(\r
 285               AlphaComposite.getInstance(\r
 286                   AlphaComposite.SRC_OVER, 1.0f));\r
 287         }\r
 288     }\r
 289 \r
 290 \r
 291     char s;\r
 292     int i;\r
 293     void renderFeature(Graphics g, SequenceI seq,\r
 294                        int fstart, int fend, Color featureColour, int start, int end,  int y1)\r
 295     {\r
 296 \r
 297       if (((fstart <= end) && (fend >= start)))\r
 298       {\r
 299         if (fstart < start)\r
 300         { // fix for if the feature we have starts before the sequence start,\r
 301           fstart = start; // but the feature end is still valid!!\r
 302         }\r
 303 \r
 304         if (fend >= end)\r
 305         {\r
 306           fend = end;\r
 307         }\r
 308           int pady = (y1 + av.charHeight) - av.charHeight / 5;\r
 309           for (i = fstart; i <= fend; i++)\r
 310           {\r
 311             s = seq.getSequence().charAt(i);\r
 312 \r
 313             if (jalview.util.Comparison.isGap(s))\r
 314             {\r
 315               continue;\r
 316             }\r
 317 \r
 318             g.setColor(featureColour);\r
 319 \r
 320             g.fillRect( (i - start) * av.charWidth, y1, av.charWidth,av.charHeight);\r
 321 \r
 322             if(offscreenRender || !av.validCharWidth)\r
 323               continue;\r
 324 \r
 325             g.setColor(Color.white);\r
 326             charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
 327             g.drawString(String.valueOf(s),\r
 328                          charOffset + (av.charWidth * (i - start)),\r
 329                          pady);\r
 330 \r
 331           }\r
 332       }\r
 333     }\r
 334 \r
 335 \r
 336     boolean newFeatureAdded = false;\r
 337 \r
 338     public void featuresAdded()\r
 339     {\r
 340       findAllFeatures();\r
 341     }\r
 342 \r
 343    boolean findingFeatures = false;\r
 344    synchronized void findAllFeatures()\r
 345    {\r
 346       newFeatureAdded = false;\r
 347 \r
 348       if(findingFeatures)\r
 349       {\r
 350         newFeatureAdded = true;\r
 351         return;\r
 352       }\r
 353 \r
 354       findingFeatures = true;\r
 355       jalview.schemes.UserColourScheme ucs = new\r
 356           jalview.schemes.UserColourScheme();\r
 357 \r
 358       if(av.featuresDisplayed==null)\r
 359         av.featuresDisplayed = new Hashtable();\r
 360 \r
 361       av.featuresDisplayed.clear();\r
 362 \r
 363       Vector allfeatures = new Vector();\r
 364       for (int i = 0; i < av.alignment.getHeight(); i++)\r
 365       {\r
 366         SequenceFeature [] features\r
 367             = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
 368 \r
 369         if (features == null)\r
 370           continue;\r
 371 \r
 372         int index = 0;\r
 373         while (index < features.length)\r
 374         {\r
 375           if (!av.featuresDisplayed.containsKey(features[index].getType()))\r
 376           {\r
 377             if(!(features[index].begin == 0 && features[index].end ==0))\r
 378             {\r
 379               // If beginning and end are 0, the feature is for the whole sequence\r
 380               // and we don't want to render the feature in the normal way\r
 381 \r
 382               if (getColour(features[index].getType()) == null)\r
 383               {\r
 384                  featureColours.put(features[index].getType(),\r
 385                                    ucs.createColourFromName(features[index].\r
 386                     getType()));\r
 387               }\r
 388 \r
 389               av.featuresDisplayed.put(features[index].getType(),\r
 390                                        new Integer(getColour(features[index].\r
 391                   getType()).getRGB()));\r
 392               allfeatures.addElement(features[index].getType());\r
 393             }\r
 394           }\r
 395           index++;\r
 396         }\r
 397       }\r
 398 \r
 399       renderOrder = new String[allfeatures.size()];\r
 400       Enumeration en = allfeatures.elements();\r
 401       int i = allfeatures.size()-1;\r
 402       while(en.hasMoreElements())\r
 403       {\r
 404         renderOrder[i] = en.nextElement().toString();\r
 405         i--;\r
 406       }\r
 407 \r
 408       findingFeatures = false;\r
 409     }\r
 410 \r
 411     public Color getColour(String featureType)\r
 412     {\r
 413       Color colour = (Color)featureColours.get(featureType);\r
 414       return colour;\r
 415     }\r
 416 \r
 417 \r
 418     static String lastFeatureAdded;\r
 419     static String lastFeatureGroupAdded;\r
 420     static String lastDescriptionAdded;\r
 421 \r
 422     public boolean createNewFeatures(SequenceI[] sequences,\r
 423                                   SequenceFeature [] features)\r
 424     {\r
 425 \r
 426       JPanel bigPanel = new JPanel(new BorderLayout());\r
 427       JComboBox name = new JComboBox();\r
 428       JComboBox source = new JComboBox();\r
 429       JTextArea description = new JTextArea(3,25);\r
 430 \r
 431       JPanel panel = new JPanel(new GridLayout(2, 2));\r
 432       panel.add(new JLabel("New Sequence Feature Name: ",JLabel.RIGHT));\r
 433       panel.add(name);\r
 434       panel.add(new JLabel("Feature Group: ", JLabel.RIGHT));\r
 435       panel.add(source);\r
 436       name.setEditable(true);\r
 437       source.setEditable(true);\r
 438 \r
 439       bigPanel.add(panel, BorderLayout.NORTH);\r
 440       panel = new JPanel();\r
 441       panel.add(new JLabel("Description: ", JLabel.RIGHT));\r
 442       description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
 443       description.setLineWrap(true);\r
 444       panel.add(new JScrollPane(description));\r
 445       bigPanel.add(panel, BorderLayout.CENTER);\r
 446 \r
 447 \r
 448       Enumeration en;\r
 449       if (av.featuresDisplayed != null)\r
 450       {\r
 451         en = av.featuresDisplayed.keys();\r
 452         while (en.hasMoreElements())\r
 453         {\r
 454           name.addItem(en.nextElement().toString());\r
 455         }\r
 456       }\r
 457 \r
 458       if (featureGroups != null)\r
 459       {\r
 460         en = featureGroups.keys();\r
 461         while (en.hasMoreElements())\r
 462         {\r
 463           source.addItem(en.nextElement().toString());\r
 464         }\r
 465       }\r
 466 \r
 467       if (lastFeatureAdded == null)\r
 468         if (features[0].type != null)\r
 469           lastFeatureAdded = features[0].type;\r
 470         else\r
 471           lastFeatureAdded = "feature_1";\r
 472 \r
 473       if (lastFeatureGroupAdded == null)\r
 474         if (features[0].featureGroup != null)\r
 475           lastFeatureGroupAdded = features[0].featureGroup;\r
 476         else\r
 477           lastFeatureAdded = "Jalview";\r
 478 \r
 479 \r
 480       name.setSelectedItem(lastFeatureAdded);\r
 481       source.setSelectedItem(lastFeatureGroupAdded);\r
 482       description.setText(\r
 483           lastDescriptionAdded == null ?\r
 484           features[0].description : lastDescriptionAdded);\r
 485 \r
 486 \r
 487       int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
 488           bigPanel, "Create New Sequence Feature(s)",\r
 489           JOptionPane.OK_CANCEL_OPTION);\r
 490 \r
 491 \r
 492       if(reply==JOptionPane.OK_OPTION\r
 493          && name.getSelectedItem()!=null\r
 494          && source.getSelectedItem()!=null)\r
 495       {\r
 496         lastFeatureAdded = name.getSelectedItem().toString();\r
 497         lastFeatureGroupAdded = source.getSelectedItem().toString();\r
 498         lastDescriptionAdded = description.getText().replaceAll("\n"," ");\r
 499 \r
 500         jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();\r
 501 \r
 502 \r
 503         for(int i=0; i<sequences.length; i++)\r
 504         {\r
 505           features[i].type = lastFeatureAdded;\r
 506           features[i].featureGroup = lastFeatureGroupAdded;\r
 507           features[i].description = lastDescriptionAdded;\r
 508           sequences[i].addSequenceFeature(features[i]);\r
 509           ffile.parseDescriptionHTML(features[i], false);\r
 510         }\r
 511 \r
 512         if (av.featuresDisplayed == null)\r
 513           av.featuresDisplayed = new Hashtable();\r
 514 \r
 515         if(featureGroups==null)\r
 516           featureGroups = new Hashtable();\r
 517 \r
 518         featureGroups.put(lastFeatureGroupAdded, new Boolean(true));\r
 519 \r
 520         Color col = getColour(lastFeatureAdded);\r
 521         if(col==null)\r
 522         {\r
 523           col = new Color(60, 160, 115);\r
 524           setColour(lastFeatureAdded, col);\r
 525         }\r
 526 \r
 527         av.featuresDisplayed.put(lastFeatureGroupAdded, new Integer(col.getRGB()));\r
 528         findAllFeatures();\r
 529         return true;\r
 530       }\r
 531       else\r
 532         return false;\r
 533 \r
 534     }\r
 535 \r
 536     public void setColour(String featureType, Color col)\r
 537     {\r
 538       featureColours.put(featureType, col);\r
 539     }\r
 540 \r
 541     public void setTransparency(float value)\r
 542     {\r
 543       transparency = value;\r
 544     }\r
 545 \r
 546     public float getTransparency()\r
 547     {\r
 548       return transparency;\r
 549     }\r
 550 \r
 551     public void setFeaturePriority(Object [][] data)\r
 552     {\r
 553       // The feature table will display high priority\r
 554       // features at the top, but theses are the ones\r
 555       // we need to render last, so invert the data\r
 556       if(av.featuresDisplayed!=null)\r
 557         av.featuresDisplayed.clear();\r
 558       else\r
 559         av.featuresDisplayed = new Hashtable();\r
 560 \r
 561       renderOrder = new String[data.length];\r
 562 \r
 563       if (data.length > 0)\r
 564         for (int i = 0; i < data.length; i++)\r
 565         {\r
 566           String type = data[i][0].toString();\r
 567           setColour(type, (Color) data[i][1]);\r
 568           if ( ( (Boolean) data[i][2]).booleanValue())\r
 569           {\r
 570             av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));\r
 571           }\r
 572 \r
 573           renderOrder[data.length - i - 1] = type;\r
 574         }\r
 575 \r
 576     }\r
 577 \r
 578 \r
 579 \r
 580 \r
 581 }\r