code_ruby/Maasha/lib/doc/Read.html

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   7
   8         <title>Class: Read</title>
   9
  10         <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
  11
  12         <script src="./js/jquery.js" type="text/javascript"
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  18         <script src="./js/darkfish.js" type="text/javascript"
  19                 charset="utf-8"></script>
  20
  21 </head>
  22 <body class="class">
  23
  24         <div id="metadata">
  25                 <div id="home-metadata">
  26                         <div id="home-section" class="section">
  27         <h3 class="section-header">
  28           <a href="./index.html">Home</a>
  29           <a href="./index.html#classes">Classes</a>
  30           <a href="./index.html#methods">Methods</a>
  31         </h3>
  32                         </div>
  33                 </div>
  34
  35                 <div id="file-metadata">
  36                         <div id="file-list-section" class="section">
  37                                 <h3 class="section-header">In Files</h3>
  38                                 <div class="section-body">
  39                                         <ul>
  40
  41                                                 <li><a href="./sff_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
  42                                                         class="thickbox" title="sff.rb">sff.rb</a></li>
  43
  44                                         </ul>
  45                                 </div>
  46                         </div>
  47
  48
  49                 </div>
  50
  51                 <div id="class-metadata">
  52
  53                         <!-- Parent Class -->
  54
  55                         <div id="parent-class-section" class="section">
  56                                 <h3 class="section-header">Parent</h3>
  57
  58                                 <p class="link">Object</p>
  59
  60                         </div>
  61
  62
  63                         <!-- Namespace Contents -->
  64
  65
  66                         <!-- Method Quickref -->
  67
  68                         <div id="method-list-section" class="section">
  69                                 <h3 class="section-header">Methods</h3>
  70                                 <ul class="link-list">
  71
  72                                         <li><a href="#method-i-clip">#clip</a></li>
  73
  74                                         <li><a href="#method-i-coordinates_get">#coordinates_get</a></li>
  75
  76                                         <li><a href="#method-i-mask">#mask</a></li>
  77
  78                                         <li><a href="#method-i-to_bp">#to_bp</a></li>
  79
  80                                 </ul>
  81                         </div>
  82
  83
  84                         <!-- Included Modules -->
  85
  86                 </div>
  87
  88                 <div id="project-metadata">
  89
  90
  91
  92                         <div id="classindex-section" class="section project-section">
  93                                 <h3 class="section-header">Class Index
  94                                         <span class="search-toggle"><img src="./images/find.png"
  95                                                 height="16" width="16" alt="[+]"
  96                                                 title="show/hide quicksearch" /></span></h3>
  97                                 <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
  98                                 <fieldset>
  99                                         <legend>Quicksearch</legend>
 100                                         <input type="text" name="quicksearch" value=""
 101                                                 class="quicksearch-field" />
 102                                 </fieldset>
 103                                 </form>
 104
 105                                 <ul class="link-list">
 106
 107                                         <li><a href="./Base36.html">Base36</a></li>
 108
 109                                         <li><a href="./Base36Error.html">Base36Error</a></li>
 110
 111                                         <li><a href="./Biopieces.html">Biopieces</a></li>
 112
 113                                         <li><a href="./BitArray.html">BitArray</a></li>
 114
 115                                         <li><a href="./BitArrayError.html">BitArrayError</a></li>
 116
 117                                         <li><a href="./Boulder.html">Boulder</a></li>
 118
 119                                         <li><a href="./BoulderError.html">BoulderError</a></li>
 120
 121                                         <li><a href="./CastError.html">CastError</a></li>
 122
 123                                         <li><a href="./Casts.html">Casts</a></li>
 124
 125                                         <li><a href="./Digest.html">Digest</a></li>
 126
 127                                         <li><a href="./DigestError.html">DigestError</a></li>
 128
 129                                         <li><a href="./Fasta.html">Fasta</a></li>
 130
 131                                         <li><a href="./FastaError.html">FastaError</a></li>
 132
 133                                         <li><a href="./Fastq.html">Fastq</a></li>
 134
 135                                         <li><a href="./FastqError.html">FastqError</a></li>
 136
 137                                         <li><a href="./Filesys.html">Filesys</a></li>
 138
 139                                         <li><a href="./FilesysError.html">FilesysError</a></li>
 140
 141                                         <li><a href="./Genbank.html">Genbank</a></li>
 142
 143                                         <li><a href="./GenbankError.html">GenbankError</a></li>
 144
 145                                         <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
 146
 147                                         <li><a href="./Locator.html">Locator</a></li>
 148
 149                                         <li><a href="./LocatorError.html">LocatorError</a></li>
 150
 151                                         <li><a href="./OptionHandler.html">OptionHandler</a></li>
 152
 153                                         <li><a href="./Read.html">Read</a></li>
 154
 155                                         <li><a href="./SFF.html">SFF</a></li>
 156
 157                                         <li><a href="./SFFError.html">SFFError</a></li>
 158
 159                                         <li><a href="./Seq.html">Seq</a></li>
 160
 161                                         <li><a href="./SeqError.html">SeqError</a></li>
 162
 163                                         <li><a href="./Status.html">Status</a></li>
 164
 165                                         <li><a href="./Stream.html">Stream</a></li>
 166
 167                                         <li><a href="./String.html">String</a></li>
 168
 169                                         <li><a href="./StringError.html">StringError</a></li>
 170
 171                                 </ul>
 172                                 <div id="no-class-search-results" style="display: none;">No matching classes.</div>
 173                         </div>
 174
 175
 176                 </div>
 177         </div>
 178
 179         <div id="documentation">
 180                 <h1 class="class">Read</h1>
 181
 182                 <div id="description">
 183                         <p>
 184 Class containing data accessor methods for an <a href="SFF.html">SFF</a>
 185 entry and methods for manipulating this entry.
 186 </p>
 187
 188                 </div>
 189
 190                 <!-- Constants -->
 191
 192
 193                 <!-- Attributes -->
 194
 195                 <div id="attribute-method-details" class="method-section section">
 196                         <h3 class="section-header">Attributes</h3>
 197
 198
 199                         <div id="read-header-length-attribute-method" class="method-detail">
 200                                 <a name="read_header_length"></a>
 201
 202                                 <a name="read_header_length="></a>
 203
 204                                 <div class="method-heading attribute-method-heading">
 205                                         <span class="method-name">read_header_length</span><span
 206                                                 class="attribute-access-type">[RW]</span>
 207                                 </div>
 208
 209                                 <div class="method-description">
 210
 211
 212
 213                                 </div>
 214                         </div>
 215
 216                         <div id="name-length-attribute-method" class="method-detail">
 217                                 <a name="name_length"></a>
 218
 219                                 <a name="name_length="></a>
 220
 221                                 <div class="method-heading attribute-method-heading">
 222                                         <span class="method-name">name_length</span><span
 223                                                 class="attribute-access-type">[RW]</span>
 224                                 </div>
 225
 226                                 <div class="method-description">
 227
 228
 229
 230                                 </div>
 231                         </div>
 232
 233                         <div id="number-of-bases-attribute-method" class="method-detail">
 234                                 <a name="number_of_bases"></a>
 235
 236                                 <a name="number_of_bases="></a>
 237
 238                                 <div class="method-heading attribute-method-heading">
 239                                         <span class="method-name">number_of_bases</span><span
 240                                                 class="attribute-access-type">[RW]</span>
 241                                 </div>
 242
 243                                 <div class="method-description">
 244
 245
 246
 247                                 </div>
 248                         </div>
 249
 250                         <div id="clip-qual-left-attribute-method" class="method-detail">
 251                                 <a name="clip_qual_left"></a>
 252
 253                                 <a name="clip_qual_left="></a>
 254
 255                                 <div class="method-heading attribute-method-heading">
 256                                         <span class="method-name">clip_qual_left</span><span
 257                                                 class="attribute-access-type">[RW]</span>
 258                                 </div>
 259
 260                                 <div class="method-description">
 261
 262
 263
 264                                 </div>
 265                         </div>
 266
 267                         <div id="clip-qual-right-attribute-method" class="method-detail">
 268                                 <a name="clip_qual_right"></a>
 269
 270                                 <a name="clip_qual_right="></a>
 271
 272                                 <div class="method-heading attribute-method-heading">
 273                                         <span class="method-name">clip_qual_right</span><span
 274                                                 class="attribute-access-type">[RW]</span>
 275                                 </div>
 276
 277                                 <div class="method-description">
 278
 279
 280
 281                                 </div>
 282                         </div>
 283
 284                         <div id="clip-adapter-left-attribute-method" class="method-detail">
 285                                 <a name="clip_adapter_left"></a>
 286
 287                                 <a name="clip_adapter_left="></a>
 288
 289                                 <div class="method-heading attribute-method-heading">
 290                                         <span class="method-name">clip_adapter_left</span><span
 291                                                 class="attribute-access-type">[RW]</span>
 292                                 </div>
 293
 294                                 <div class="method-description">
 295
 296
 297
 298                                 </div>
 299                         </div>
 300
 301                         <div id="clip-adaptor-right-attribute-method" class="method-detail">
 302                                 <a name="clip_adaptor_right"></a>
 303
 304                                 <a name="clip_adaptor_right="></a>
 305
 306                                 <div class="method-heading attribute-method-heading">
 307                                         <span class="method-name">clip_adaptor_right</span><span
 308                                                 class="attribute-access-type">[RW]</span>
 309                                 </div>
 310
 311                                 <div class="method-description">
 312
 313
 314
 315                                 </div>
 316                         </div>
 317
 318                         <div id="name-attribute-method" class="method-detail">
 319                                 <a name="name"></a>
 320
 321                                 <a name="name="></a>
 322
 323                                 <div class="method-heading attribute-method-heading">
 324                                         <span class="method-name">name</span><span
 325                                                 class="attribute-access-type">[RW]</span>
 326                                 </div>
 327
 328                                 <div class="method-description">
 329
 330
 331
 332                                 </div>
 333                         </div>
 334
 335                         <div id="flowgram-values-attribute-method" class="method-detail">
 336                                 <a name="flowgram_values"></a>
 337
 338                                 <a name="flowgram_values="></a>
 339
 340                                 <div class="method-heading attribute-method-heading">
 341                                         <span class="method-name">flowgram_values</span><span
 342                                                 class="attribute-access-type">[RW]</span>
 343                                 </div>
 344
 345                                 <div class="method-description">
 346
 347
 348
 349                                 </div>
 350                         </div>
 351
 352                         <div id="flow-index-per-base-attribute-method" class="method-detail">
 353                                 <a name="flow_index_per_base"></a>
 354
 355                                 <a name="flow_index_per_base="></a>
 356
 357                                 <div class="method-heading attribute-method-heading">
 358                                         <span class="method-name">flow_index_per_base</span><span
 359                                                 class="attribute-access-type">[RW]</span>
 360                                 </div>
 361
 362                                 <div class="method-description">
 363
 364
 365
 366                                 </div>
 367                         </div>
 368
 369                         <div id="bases-attribute-method" class="method-detail">
 370                                 <a name="bases"></a>
 371
 372                                 <a name="bases="></a>
 373
 374                                 <div class="method-heading attribute-method-heading">
 375                                         <span class="method-name">bases</span><span
 376                                                 class="attribute-access-type">[RW]</span>
 377                                 </div>
 378
 379                                 <div class="method-description">
 380
 381
 382
 383                                 </div>
 384                         </div>
 385
 386                         <div id="quality-scores-attribute-method" class="method-detail">
 387                                 <a name="quality_scores"></a>
 388
 389                                 <a name="quality_scores="></a>
 390
 391                                 <div class="method-heading attribute-method-heading">
 392                                         <span class="method-name">quality_scores</span><span
 393                                                 class="attribute-access-type">[RW]</span>
 394                                 </div>
 395
 396                                 <div class="method-description">
 397
 398
 399
 400                                 </div>
 401                         </div>
 402
 403                         <div id="x-pos-attribute-method" class="method-detail">
 404                                 <a name="x_pos"></a>
 405
 406                                 <a name="x_pos="></a>
 407
 408                                 <div class="method-heading attribute-method-heading">
 409                                         <span class="method-name">x_pos</span><span
 410                                                 class="attribute-access-type">[RW]</span>
 411                                 </div>
 412
 413                                 <div class="method-description">
 414
 415
 416
 417                                 </div>
 418                         </div>
 419
 420                         <div id="y-pos-attribute-method" class="method-detail">
 421                                 <a name="y_pos"></a>
 422
 423                                 <a name="y_pos="></a>
 424
 425                                 <div class="method-heading attribute-method-heading">
 426                                         <span class="method-name">y_pos</span><span
 427                                                 class="attribute-access-type">[RW]</span>
 428                                 </div>
 429
 430                                 <div class="method-description">
 431
 432
 433
 434                                 </div>
 435                         </div>
 436
 437                 </div>
 438
 439
 440                 <!-- Methods -->
 441
 442                 <div id="public-instance-method-details" class="method-section section">
 443                         <h3 class="section-header">Public Instance Methods</h3>
 444
 445
 446                         <div id="clip-method" class="method-detail ">
 447                                 <a name="method-i-clip"></a>
 448
 449                                 <div class="method-heading">
 450
 451                                         <span class="method-name">clip</span><span
 452                                                 class="method-args">()</span>
 453                                         <span class="method-click-advice">click to toggle source</span>
 454
 455                                 </div>
 456
 457                                 <div class="method-description">
 458
 459                                         <p>
 460 Method that clips sequence (i.e. trims) according to <a
 461 href="Read.html#clip_qual_left">clip_qual_left</a> and <a
 462 href="Read.html#clip_qual_right">clip_qual_right</a> information.
 463 </p>
 464
 465
 466
 467                                         <div class="method-source-code"
 468                                                 id="clip-source">
 469 <pre>
 470      <span class="ruby-comment cmt"># File sff.rb, line 228</span>
 471 228:   <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">clip</span>
 472 229:     <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span>          = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span>[<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_left</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span> <span class="ruby-operator">...</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_right</span>]
 473 230:     <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">quality_scores</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">quality_scores</span>[<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_left</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span> <span class="ruby-operator">...</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_right</span>]
 474 231:   <span class="ruby-keyword kw">end</span></pre>
 475                                         </div>
 476
 477                                 </div>
 478
 479
 480
 481
 482                         </div>
 483
 484
 485                         <div id="mask-method" class="method-detail ">
 486                                 <a name="method-i-mask"></a>
 487
 488                                 <div class="method-heading">
 489
 490                                         <span class="method-name">mask</span><span
 491                                                 class="method-args">()</span>
 492                                         <span class="method-click-advice">click to toggle source</span>
 493
 494                                 </div>
 495
 496                                 <div class="method-description">
 497
 498                                         <p>
 499 Method that soft masks the sequence (i.e. lowercases sequence) according to
 500 <a href="Read.html#clip_qual_left">clip_qual_left</a> and <a
 501 href="Read.html#clip_qual_right">clip_qual_right</a> information.
 502 </p>
 503
 504
 505
 506                                         <div class="method-source-code"
 507                                                 id="mask-source">
 508 <pre>
 509      <span class="ruby-comment cmt"># File sff.rb, line 218</span>
 510 218:   <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">mask</span>
 511 219:     <span class="ruby-identifier">left</span>   = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span>[<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_left</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>].<span class="ruby-identifier">downcase</span>
 512 220:     <span class="ruby-identifier">middle</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span>[<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_left</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span> <span class="ruby-operator">...</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_right</span>]
 513 221:     <span class="ruby-identifier">right</span>  = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span>[<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_right</span> <span class="ruby-operator">...</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span>.<span class="ruby-identifier">length</span>].<span class="ruby-identifier">downcase</span>
 514 222:
 515 223:     <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span> = <span class="ruby-identifier">left</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">middle</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">right</span>
 516 224:   <span class="ruby-keyword kw">end</span></pre>
 517                                         </div>
 518
 519                                 </div>
 520
 521
 522
 523
 524                         </div>
 525
 526
 527                         <div id="to-bp-method" class="method-detail ">
 528                                 <a name="method-i-to_bp"></a>
 529
 530                                 <div class="method-heading">
 531
 532                                         <span class="method-name">to_bp</span><span
 533                                                 class="method-args">()</span>
 534                                         <span class="method-click-advice">click to toggle source</span>
 535
 536                                 </div>
 537
 538                                 <div class="method-description">
 539
 540                                         <p>
 541 Method that converts a <a href="Read.html">Read</a> object&#8217;s data to
 542 a Biopiece record (a hash).
 543 </p>
 544
 545
 546
 547                                         <div class="method-source-code"
 548                                                 id="to-bp-source">
 549 <pre>
 550      <span class="ruby-comment cmt"># File sff.rb, line 197</span>
 551 197:   <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_bp</span>
 552 198:     <span class="ruby-identifier">coordinates_get</span>
 553 199:
 554 200:     <span class="ruby-identifier">hash</span> = {}
 555 201:
 556 202:     <span class="ruby-identifier">hash</span>[<span class="ruby-value">:SEQ_NAME</span>]           = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">name</span>
 557 203:     <span class="ruby-identifier">hash</span>[<span class="ruby-value">:SEQ</span>]                = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span>
 558 204:     <span class="ruby-identifier">hash</span>[<span class="ruby-value">:SEQ_LEN</span>]            = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span>.<span class="ruby-identifier">length</span>
 559 205:     <span class="ruby-identifier">hash</span>[<span class="ruby-value">:CLIP_QUAL_LEFT</span>]     = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_left</span>     <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
 560 206:     <span class="ruby-identifier">hash</span>[<span class="ruby-value">:CLIP_QUAL_RIGHT</span>]    = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_right</span>    <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
 561 207:     <span class="ruby-identifier">hash</span>[<span class="ruby-value">:CLIP_ADAPTOR_LEFT</span>]  = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_adapter_left</span>  <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
 562 208:     <span class="ruby-identifier">hash</span>[<span class="ruby-value">:CLIP_ADAPTOR_RIGHT</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_adaptor_right</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
 563 209:     <span class="ruby-identifier">hash</span>[<span class="ruby-value">:SCORES</span>]             = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">quality_scores</span>.<span class="ruby-identifier">map</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span> (<span class="ruby-identifier">i</span> <span class="ruby-operator">+=</span> <span class="ruby-value">64</span>).<span class="ruby-identifier">chr</span> }.<span class="ruby-identifier">join</span> <span class="ruby-value str">&quot;&quot;</span>
 564 210:     <span class="ruby-identifier">hash</span>[<span class="ruby-value">:X_POS</span>]              = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">x_pos</span>
 565 211:     <span class="ruby-identifier">hash</span>[<span class="ruby-value">:Y_POS</span>]              = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">y_pos</span>
 566 212:
 567 213:     <span class="ruby-identifier">hash</span>
 568 214:   <span class="ruby-keyword kw">end</span></pre>
 569                                         </div>
 570
 571                                 </div>
 572
 573
 574
 575
 576                         </div>
 577
 578
 579                 </div>
 580
 581                 <div id="private-instance-method-details" class="method-section section">
 582                         <h3 class="section-header">Private Instance Methods</h3>
 583
 584
 585                         <div id="coordinates-get-method" class="method-detail ">
 586                                 <a name="method-i-coordinates_get"></a>
 587
 588                                 <div class="method-heading">
 589
 590                                         <span class="method-name">coordinates_get</span><span
 591                                                 class="method-args">()</span>
 592                                         <span class="method-click-advice">click to toggle source</span>
 593
 594                                 </div>
 595
 596                                 <div class="method-description">
 597
 598                                         <p>
 599 Method that extracts the X/Y coordinates from an <a href="SFF.html">SFF</a>
 600 read name encoded with base36.
 601 </p>
 602
 603
 604
 605                                         <div class="method-source-code"
 606                                                 id="coordinates-get-source">
 607 <pre>
 608      <span class="ruby-comment cmt"># File sff.rb, line 237</span>
 609 237:   <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">coordinates_get</span>
 610 238:     <span class="ruby-identifier">base36</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">name</span>[<span class="ruby-value">5</span>, <span class="ruby-value">5</span>]
 611 239:     <span class="ruby-identifier">num</span>    = <span class="ruby-constant">Base36</span>.<span class="ruby-identifier">decode</span>(<span class="ruby-identifier">base36</span>)
 612 240:
 613 241:     <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">x_pos</span> = <span class="ruby-identifier">num</span> <span class="ruby-operator">&gt;&gt;</span> <span class="ruby-constant">BIT_SHIFT</span>
 614 242:     <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">y_pos</span> = <span class="ruby-identifier">num</span> &amp;  <span class="ruby-constant">BIT_MASK</span>
 615 243:   <span class="ruby-keyword kw">end</span></pre>
 616                                         </div>
 617
 618                                 </div>
 619
 620
 621
 622
 623                         </div>
 624
 625
 626                 </div>
 627
 628
 629         </div>
 630
 631
 632         <div id="rdoc-debugging-section-dump" class="debugging-section">
 633
 634                 <p>Disabled; run with --debug to generate this.</p>
 635
 636         </div>
 637
 638         <div id="validator-badges">
 639                 <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
 640                 <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
 641                         Rdoc Generator</a> 1.1.6</small>.</p>
 642         </div>
 643
 644 </body>
 645 </html>
 646