code_ruby/Maasha/lib/doc/classes/Seq.html

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   4 <head>
   5   <title>Class: Seq [RDoc Documentation]</title>
   6   <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
   7   <meta http-equiv="Content-Script-Type" content="text/javascript" />
   8   <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
   9   <script type="text/javascript">
  10   // <![CDATA[
  11
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  35   // Make codeblocks hidden by default
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  37
  38   // ]]>
  39   </script>
  40
  41 </head>
  42 <body>
  43
  44
  45     <div id="classHeader">
  46         <table class="header-table">
  47         <tr class="top-aligned-row">
  48           <td><strong>Class</strong></td>
  49           <td class="class-name-in-header">Seq</td>
  50         </tr>
  51         <tr class="top-aligned-row">
  52             <td><strong>In:</strong></td>
  53             <td>
  54
  55
  56                 <a href="../files/seq_rb.html">
  57
  58                 seq.rb
  59
  60                 </a>
  61
  62
  63         <br />
  64
  65             </td>
  66         </tr>
  67
  68
  69         <tr class="top-aligned-row">
  70             <td><strong>Parent:</strong></td>
  71             <td>
  72
  73                 Object
  74
  75             </td>
  76         </tr>
  77
  78         </table>
  79     </div>
  80   <!-- banner header -->
  81
  82   <div id="bodyContent">
  83
  84   <div id="contextContent">
  85
  86    </div>
  87
  88
  89     <div id="method-list">
  90       <h3 class="section-bar">Methods</h3>
  91
  92       <div class="name-list">
  93
  94         <a href="#M000043">complement</a>&nbsp;&nbsp;
  95
  96         <a href="#M000044">generate</a>&nbsp;&nbsp;
  97
  98         <a href="#M000037">is_dna</a>&nbsp;&nbsp;
  99
 100         <a href="#M000039">is_protein</a>&nbsp;&nbsp;
 101
 102         <a href="#M000038">is_rna</a>&nbsp;&nbsp;
 103
 104         <a href="#M000036">len</a>&nbsp;&nbsp;
 105
 106         <a href="#M000035">length</a>&nbsp;&nbsp;
 107
 108         <a href="#M000042">to_bp</a>&nbsp;&nbsp;
 109
 110         <a href="#M000041">to_dna</a>&nbsp;&nbsp;
 111
 112         <a href="#M000040">to_rna</a>&nbsp;&nbsp;
 113
 114       </div>
 115     </div>
 116
 117   </div>
 118
 119     <!-- if includes -->
 120
 121     <div id="section">
 122
 123
 124
 125     <div id="attribute-list">
 126       <h3 class="section-bar">Attributes</h3>
 127
 128       <div class="name-list">
 129         <table>
 130
 131         <tr class="top-aligned-row context-row">
 132           <td class="context-item-name">qual</td>
 133
 134           <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
 135
 136           <td class="context-item-desc"></td>
 137         </tr>
 138
 139         <tr class="top-aligned-row context-row">
 140           <td class="context-item-name">seq</td>
 141
 142           <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
 143
 144           <td class="context-item-desc"></td>
 145         </tr>
 146
 147         <tr class="top-aligned-row context-row">
 148           <td class="context-item-name">seq_name</td>
 149
 150           <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
 151
 152           <td class="context-item-desc"></td>
 153         </tr>
 154
 155         <tr class="top-aligned-row context-row">
 156           <td class="context-item-name">type</td>
 157
 158           <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
 159
 160           <td class="context-item-desc"></td>
 161         </tr>
 162
 163         </table>
 164       </div>
 165     </div>
 166
 167
 168     <!-- if method_list -->
 169
 170     <div id="methods">
 171
 172       <h3 class="section-bar">Public Instance methods</h3>
 173
 174
 175       <div id="method-M000043" class="method-detail">
 176         <a name="M000043"></a>
 177
 178         <div class="method-heading">
 179
 180           <a href="Seq.src/M000043.html" target="Code" class="method-signature"
 181             onclick="popupCode('Seq.src/M000043.html');return false;">
 182
 183           <span class="method-name">complement</span><span class="method-args">()</span>
 184
 185           </a>
 186
 187         </div>
 188
 189         <div class="method-description">
 190
 191           <p>
 192 Method that complements sequence including ambiguity codes.
 193 </p>
 194
 195         </div>
 196       </div>
 197
 198
 199       <div id="method-M000044" class="method-detail">
 200         <a name="M000044"></a>
 201
 202         <div class="method-heading">
 203
 204           <a href="Seq.src/M000044.html" target="Code" class="method-signature"
 205             onclick="popupCode('Seq.src/M000044.html');return false;">
 206
 207           <span class="method-name">generate</span><span class="method-args">(length,type)</span>
 208
 209           </a>
 210
 211         </div>
 212
 213         <div class="method-description">
 214
 215           <p>
 216 Method that generates a random sequence of a given length.
 217 </p>
 218
 219         </div>
 220       </div>
 221
 222
 223       <div id="method-M000037" class="method-detail">
 224         <a name="M000037"></a>
 225
 226         <div class="method-heading">
 227
 228           <a href="Seq.src/M000037.html" target="Code" class="method-signature"
 229             onclick="popupCode('Seq.src/M000037.html');return false;">
 230
 231           <span class="method-name">is_dna</span><span class="method-args">()</span>
 232
 233           </a>
 234
 235         </div>
 236
 237         <div class="method-description">
 238
 239           <p>
 240 Method that returns true is a given sequence type is DNA.
 241 </p>
 242
 243         </div>
 244       </div>
 245
 246
 247       <div id="method-M000039" class="method-detail">
 248         <a name="M000039"></a>
 249
 250         <div class="method-heading">
 251
 252           <a href="Seq.src/M000039.html" target="Code" class="method-signature"
 253             onclick="popupCode('Seq.src/M000039.html');return false;">
 254
 255           <span class="method-name">is_protein</span><span class="method-args">()</span>
 256
 257           </a>
 258
 259         </div>
 260
 261         <div class="method-description">
 262
 263         </div>
 264       </div>
 265
 266
 267       <div id="method-M000038" class="method-detail">
 268         <a name="M000038"></a>
 269
 270         <div class="method-heading">
 271
 272           <a href="Seq.src/M000038.html" target="Code" class="method-signature"
 273             onclick="popupCode('Seq.src/M000038.html');return false;">
 274
 275           <span class="method-name">is_rna</span><span class="method-args">()</span>
 276
 277           </a>
 278
 279         </div>
 280
 281         <div class="method-description">
 282
 283         </div>
 284       </div>
 285
 286
 287       <div id="method-M000036" class="method-detail">
 288         <a name="M000036"></a>
 289
 290         <div class="method-heading">
 291
 292           <span class="method-name">len</span><span class="method-args">()</span>
 293
 294         </div>
 295
 296         <div class="method-description">
 297
 298           <p>
 299 Alias for <a href="Seq.html#M000035">length</a>
 300 </p>
 301
 302         </div>
 303       </div>
 304
 305
 306       <div id="method-M000035" class="method-detail">
 307         <a name="M000035"></a>
 308
 309         <div class="method-heading">
 310
 311           <a href="Seq.src/M000035.html" target="Code" class="method-signature"
 312             onclick="popupCode('Seq.src/M000035.html');return false;">
 313
 314           <span class="method-name">length</span><span class="method-args">()</span>
 315
 316           </a>
 317
 318         </div>
 319
 320         <div class="method-description">
 321
 322         </div>
 323       </div>
 324
 325
 326       <div id="method-M000042" class="method-detail">
 327         <a name="M000042"></a>
 328
 329         <div class="method-heading">
 330
 331           <a href="Seq.src/M000042.html" target="Code" class="method-signature"
 332             onclick="popupCode('Seq.src/M000042.html');return false;">
 333
 334           <span class="method-name">to_bp</span><span class="method-args">()</span>
 335
 336           </a>
 337
 338         </div>
 339
 340         <div class="method-description">
 341
 342           <p>
 343 Method that given a <a href="Seq.html">Seq</a> entry returns a <a
 344 href="Biopieces.html">Biopieces</a> record (a hash).
 345 </p>
 346
 347         </div>
 348       </div>
 349
 350
 351       <div id="method-M000041" class="method-detail">
 352         <a name="M000041"></a>
 353
 354         <div class="method-heading">
 355
 356           <a href="Seq.src/M000041.html" target="Code" class="method-signature"
 357             onclick="popupCode('Seq.src/M000041.html');return false;">
 358
 359           <span class="method-name">to_dna</span><span class="method-args">()</span>
 360
 361           </a>
 362
 363         </div>
 364
 365         <div class="method-description">
 366
 367           <p>
 368 Method to reverse-transcribe RNA to DNA.
 369 </p>
 370
 371         </div>
 372       </div>
 373
 374
 375       <div id="method-M000040" class="method-detail">
 376         <a name="M000040"></a>
 377
 378         <div class="method-heading">
 379
 380           <a href="Seq.src/M000040.html" target="Code" class="method-signature"
 381             onclick="popupCode('Seq.src/M000040.html');return false;">
 382
 383           <span class="method-name">to_rna</span><span class="method-args">()</span>
 384
 385           </a>
 386
 387         </div>
 388
 389         <div class="method-description">
 390
 391           <p>
 392 Method to transcribe DNA to RNA.
 393 </p>
 394
 395         </div>
 396       </div>
 397
 398
 399
 400     </div>
 401
 402
 403
 404
 405   </div>
 406
 407 <div id="validator-badges">
 408   <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
 409 </div>
 410
 411 </body>
 412 </html>