code_ruby/Maasha/lib/doc/Filesys.html

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   8         <title>Class: Filesys</title>
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  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="./filesys_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
  42                                                         class="thickbox" title="filesys.rb">filesys.rb</a></li>
  43
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  47
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  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
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  61
  62
  63                         <!-- Namespace Contents -->
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  69                                 <h3 class="section-header">Methods</h3>
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  71
  72                                         <li><a href="#method-c-new">::new</a></li>
  73
  74                                         <li><a href="#method-c-open">::open</a></li>
  75
  76                                         <li><a href="#method-c-zopen">::zopen</a></li>
  77
  78                                         <li><a href="#method-i-close">#close</a></li>
  79
  80                                         <li><a href="#method-i-each">#each</a></li>
  81
  82                                 </ul>
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  84
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 147
 148                                         <li><a href="./FastqError.html">FastqError</a></li>
 149
 150                                         <li><a href="./Filesys.html">Filesys</a></li>
 151
 152                                         <li><a href="./FilesysError.html">FilesysError</a></li>
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 189                 </div>
 190         </div>
 191
 192         <div id="documentation">
 193                 <h1 class="class">Filesys</h1>
 194
 195                 <div id="description">
 196
 197                 </div>
 198
 199                 <!-- Constants -->
 200
 201
 202                 <!-- Attributes -->
 203
 204
 205                 <!-- Methods -->
 206
 207                 <div id="public-class-method-details" class="method-section section">
 208                         <h3 class="section-header">Public Class Methods</h3>
 209
 210
 211                         <div id="new-method" class="method-detail ">
 212                                 <a name="method-c-new"></a>
 213
 214                                 <div class="method-heading">
 215
 216                                         <span class="method-name">new</span><span
 217                                                 class="method-args">(io, type=nil)</span>
 218                                         <span class="method-click-advice">click to toggle source</span>
 219
 220                                 </div>
 221
 222                                 <div class="method-description">
 223
 224
 225
 226
 227
 228                                         <div class="method-source-code"
 229                                                 id="new-source">
 230 <pre>
 231     <span class="ruby-comment cmt"># File filesys.rb, line 58</span>
 232 58:   <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">io</span>, <span class="ruby-identifier">type</span>=<span class="ruby-keyword kw">nil</span>)
 233 59:     <span class="ruby-ivar">@io</span>   = <span class="ruby-identifier">io</span>
 234 60:     <span class="ruby-ivar">@type</span> = <span class="ruby-identifier">type</span>
 235 61:   <span class="ruby-keyword kw">end</span></pre>
 236                                         </div>
 237
 238                                 </div>
 239
 240
 241
 242
 243                         </div>
 244
 245
 246                         <div id="open-method" class="method-detail ">
 247                                 <a name="method-c-open"></a>
 248
 249                                 <div class="method-heading">
 250
 251                                         <span class="method-name">open</span><span
 252                                                 class="method-args">(*args)</span>
 253                                         <span class="method-click-advice">click to toggle source</span>
 254
 255                                 </div>
 256
 257                                 <div class="method-description">
 258
 259                                         <p>
 260 Class method allowing open to be used on (zipped) files. See File.open.
 261 </p>
 262
 263
 264
 265                                         <div class="method-source-code"
 266                                                 id="open-source">
 267 <pre>
 268     <span class="ruby-comment cmt"># File filesys.rb, line 35</span>
 269 35:   <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">open</span>(*<span class="ruby-identifier">args</span>)
 270 36:     <span class="ruby-identifier">args</span> = *<span class="ruby-identifier">args</span>
 271 37:     <span class="ruby-identifier">file</span> = <span class="ruby-identifier">args</span>.<span class="ruby-identifier">first</span>
 272 38:
 273 39:     <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">file</span> <span class="ruby-operator">==</span> <span class="ruby-value str">&quot;-&quot;</span>
 274 40:       <span class="ruby-identifier">ios</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">new</span>(<span class="ruby-constant">STDIN</span>)
 275 41:     <span class="ruby-keyword kw">elsif</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">pipe?</span> <span class="ruby-identifier">file</span>
 276 42:       <span class="ruby-identifier">ios</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">new</span>(<span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(*<span class="ruby-identifier">args</span>))
 277 43:     <span class="ruby-keyword kw">else</span>
 278 44:       <span class="ruby-identifier">ios</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">zopen</span>(*<span class="ruby-identifier">args</span>)
 279 45:     <span class="ruby-keyword kw">end</span>
 280 46:
 281 47:     <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">block_given?</span>
 282 48:       <span class="ruby-keyword kw">begin</span>
 283 49:         <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">ios</span>
 284 50:       <span class="ruby-keyword kw">ensure</span>
 285 51:         <span class="ruby-identifier">ios</span>.<span class="ruby-identifier">close</span>
 286 52:       <span class="ruby-keyword kw">end</span>
 287 53:     <span class="ruby-keyword kw">else</span>
 288 54:       <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">ios</span>
 289 55:     <span class="ruby-keyword kw">end</span>
 290 56:   <span class="ruby-keyword kw">end</span></pre>
 291                                         </div>
 292
 293                                 </div>
 294
 295
 296
 297
 298                         </div>
 299
 300
 301                 </div>
 302
 303                 <div id="private-class-method-details" class="method-section section">
 304                         <h3 class="section-header">Private Class Methods</h3>
 305
 306
 307                         <div id="zopen-method" class="method-detail ">
 308                                 <a name="method-c-zopen"></a>
 309
 310                                 <div class="method-heading">
 311
 312                                         <span class="method-name">zopen</span><span
 313                                                 class="method-args">(*args)</span>
 314                                         <span class="method-click-advice">click to toggle source</span>
 315
 316                                 </div>
 317
 318                                 <div class="method-description">
 319
 320                                         <p>
 321 Helper method to return an ios to a file that may be zipped in which case
 322 the ios is unzipped on the fly. See File.open.
 323 </p>
 324
 325
 326
 327                                         <div class="method-source-code"
 328                                                 id="zopen-source">
 329 <pre>
 330     <span class="ruby-comment cmt"># File filesys.rb, line 79</span>
 331 79:   <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">zopen</span>(*<span class="ruby-identifier">args</span>)
 332 80:     <span class="ruby-identifier">ios</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(*<span class="ruby-identifier">args</span>)
 333 81:
 334 82:     <span class="ruby-keyword kw">begin</span>
 335 83:       <span class="ruby-identifier">ios</span> = <span class="ruby-constant">Zlib</span><span class="ruby-operator">::</span><span class="ruby-constant">GzipReader</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">ios</span>)
 336 84:     <span class="ruby-keyword kw">rescue</span>
 337 85:       <span class="ruby-identifier">ios</span>.<span class="ruby-identifier">rewind</span>
 338 86:     <span class="ruby-keyword kw">end</span>
 339 87:
 340 88:     <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">ios</span>)
 341 89:   <span class="ruby-keyword kw">end</span></pre>
 342                                         </div>
 343
 344                                 </div>
 345
 346
 347
 348
 349                         </div>
 350
 351
 352                 </div>
 353
 354                 <div id="public-instance-method-details" class="method-section section">
 355                         <h3 class="section-header">Public Instance Methods</h3>
 356
 357
 358                         <div id="close-method" class="method-detail ">
 359                                 <a name="method-i-close"></a>
 360
 361                                 <div class="method-heading">
 362
 363                                         <span class="method-name">close</span><span
 364                                                 class="method-args">()</span>
 365                                         <span class="method-click-advice">click to toggle source</span>
 366
 367                                 </div>
 368
 369                                 <div class="method-description">
 370
 371                                         <p>
 372 Method to close ios.
 373 </p>
 374
 375
 376
 377                                         <div class="method-source-code"
 378                                                 id="close-source">
 379 <pre>
 380     <span class="ruby-comment cmt"># File filesys.rb, line 64</span>
 381 64:   <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">close</span>
 382 65:     <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">close</span>
 383 66:   <span class="ruby-keyword kw">end</span></pre>
 384                                         </div>
 385
 386                                 </div>
 387
 388
 389
 390
 391                         </div>
 392
 393
 394                         <div id="each-method" class="method-detail ">
 395                                 <a name="method-i-each"></a>
 396
 397                                 <div class="method-heading">
 398
 399                                         <span class="method-name">each</span><span
 400                                                 class="method-args">()</span>
 401                                         <span class="method-click-advice">click to toggle source</span>
 402
 403                                 </div>
 404
 405                                 <div class="method-description">
 406
 407                                         <p>
 408 Iterator method for parsing entries.
 409 </p>
 410
 411
 412
 413                                         <div class="method-source-code"
 414                                                 id="each-source">
 415 <pre>
 416     <span class="ruby-comment cmt"># File filesys.rb, line 69</span>
 417 69:   <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each</span>
 418 70:     <span class="ruby-keyword kw">while</span> <span class="ruby-identifier">entry</span> = <span class="ruby-identifier">get_entry</span> <span class="ruby-keyword kw">do</span>
 419 71:       <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">entry</span>
 420 72:     <span class="ruby-keyword kw">end</span>
 421 73:   <span class="ruby-keyword kw">end</span></pre>
 422                                         </div>
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