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   6 <title>Option</title>
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  42 <li class="navBarCell1Rev">Class</li>
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  73 </div>
  74 <div>
  75 <ul class="subNavList">
  76 <li>Summary:&nbsp;</li>
  77 <li>Nested&nbsp;|&nbsp;</li>
  78 <li><a href="#field.summary">Field</a>&nbsp;|&nbsp;</li>
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  94 <div class="header">
  95 <div class="subTitle">compbio.metadata</div>
  96 <h2 title="Class Option" class="title">Class Option&lt;T&gt;</h2>
  97 </div>
  98 <div class="contentContainer">
  99 <ul class="inheritance">
 100 <li>java.lang.Object</li>
 101 <li>
 102 <ul class="inheritance">
 103 <li>compbio.metadata.Option&lt;T&gt;</li>
 104 </ul>
 105 </li>
 106 </ul>
 107 <div class="description">
 108 <ul class="blockList">
 109 <li class="blockList">
 110 <dl>
 111 <dt><span class="paramLabel">Type Parameters:</span></dt>
 112 <dd><code>T</code> - type of executable</dd>
 113 </dl>
 114 <dl>
 115 <dt>All Implemented Interfaces:</dt>
 116 <dd><a href="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</a>&lt;T&gt;</dd>
 117 </dl>
 118 <dl>
 119 <dt>Direct Known Subclasses:</dt>
 120 <dd><a href="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</a></dd>
 121 </dl>
 122 <hr>
 123 <br>
 124 <pre>public class <span class="typeNameLabel">Option&lt;T&gt;</span>
 125 extends java.lang.Object
 126 implements <a href="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</a>&lt;T&gt;</pre>
 127 <div class="block">Command line option/flag or multiple exclusive options with no value. Example
 128  -protein, -dna, -auto</div>
 129 <dl>
 130 <dt><span class="simpleTagLabel">Version:</span></dt>
 131 <dd>1.0 October 2009</dd>
 132 <dt><span class="simpleTagLabel">Author:</span></dt>
 133 <dd>pvtroshin</dd>
 134 </dl>
 135 </li>
 136 </ul>
 137 </div>
 138 <div class="summary">
 139 <ul class="blockList">
 140 <li class="blockList">
 141 <!-- =========== FIELD SUMMARY =========== -->
 142 <ul class="blockList">
 143 <li class="blockList"><a name="field.summary">
 144 <!--   -->
 145 </a>
 146 <h3>Field Summary</h3>
 147 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Field Summary table, listing fields, and an explanation">
 148 <caption><span>Fields</span><span class="tabEnd">&nbsp;</span></caption>
 149 <tr>
 150 <th class="colFirst" scope="col">Modifier and Type</th>
 151 <th class="colLast" scope="col">Field and Description</th>
 152 </tr>
 153 <tr class="altColor">
 154 <td class="colFirst"><code>private java.net.URL</code></td>
 155 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#basicURL">basicURL</a></span></code>&nbsp;</td>
 156 </tr>
 157 <tr class="rowColor">
 158 <td class="colFirst"><code>protected java.lang.String</code></td>
 159 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#defaultValue">defaultValue</a></span></code>&nbsp;</td>
 160 </tr>
 161 <tr class="altColor">
 162 <td class="colFirst"><code>protected java.lang.String</code></td>
 163 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#description">description</a></span></code>&nbsp;</td>
 164 </tr>
 165 <tr class="rowColor">
 166 <td class="colFirst"><code>protected java.lang.String</code></td>
 167 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#furtherDetails">furtherDetails</a></span></code>&nbsp;</td>
 168 </tr>
 169 <tr class="altColor">
 170 <td class="colFirst"><code>protected boolean</code></td>
 171 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#isRequired">isRequired</a></span></code>&nbsp;</td>
 172 </tr>
 173 <tr class="rowColor">
 174 <td class="colFirst"><code>protected java.lang.String</code></td>
 175 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#name">name</a></span></code>&nbsp;</td>
 176 </tr>
 177 <tr class="altColor">
 178 <td class="colFirst"><code>(package private) java.util.Set&lt;java.lang.String&gt;</code></td>
 179 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#optionNames">optionNames</a></span></code>&nbsp;</td>
 180 </tr>
 181 </table>
 182 </li>
 183 </ul>
 184 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
 185 <ul class="blockList">
 186 <li class="blockList"><a name="constructor.summary">
 187 <!--   -->
 188 </a>
 189 <h3>Constructor Summary</h3>
 190 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Constructor Summary table, listing constructors, and an explanation">
 191 <caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
 192 <tr>
 193 <th class="colOne" scope="col">Constructor and Description</th>
 194 </tr>
 195 <tr class="altColor">
 196 <td class="colOne"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#Option--">Option</a></span>()</code>&nbsp;</td>
 197 </tr>
 198 <tr class="rowColor">
 199 <td class="colOne"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#Option-java.lang.String-java.lang.String-">Option</a></span>(java.lang.String&nbsp;name,
 200       java.lang.String&nbsp;description)</code>&nbsp;</td>
 201 </tr>
 202 </table>
 203 </li>
 204 </ul>
 205 <!-- ========== METHOD SUMMARY =========== -->
 206 <ul class="blockList">
 207 <li class="blockList"><a name="method.summary">
 208 <!--   -->
 209 </a>
 210 <h3>Method Summary</h3>
 211 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Method Summary table, listing methods, and an explanation">
 212 <caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t1" class="tableTab"><span><a href="javascript:show(1);">Static Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
 213 <tr>
 214 <th class="colFirst" scope="col">Modifier and Type</th>
 215 <th class="colLast" scope="col">Method and Description</th>
 216 </tr>
 217 <tr id="i0" class="altColor">
 218 <td class="colFirst"><code>java.util.Set&lt;java.lang.String&gt;</code></td>
 219 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#addOptionNames-java.lang.String...-">addOptionNames</a></span>(java.lang.String...&nbsp;value)</code>
 220 <div class="block">Adds an option to the optionName list</div>
 221 </td>
 222 </tr>
 223 <tr id="i1" class="rowColor">
 224 <td class="colFirst"><code>boolean</code></td>
 225 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#equals-java.lang.Object-">equals</a></span>(java.lang.Object&nbsp;obj)</code>&nbsp;</td>
 226 </tr>
 227 <tr id="i2" class="altColor">
 228 <td class="colFirst"><code>java.net.URL</code></td>
 229 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#getBasicURL--">getBasicURL</a></span>()</code>&nbsp;</td>
 230 </tr>
 231 <tr id="i3" class="rowColor">
 232 <td class="colFirst"><code>java.lang.String</code></td>
 233 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#getDefaultValue--">getDefaultValue</a></span>()</code>
 234 <div class="block">A default value of the option.</div>
 235 </td>
 236 </tr>
 237 <tr id="i4" class="altColor">
 238 <td class="colFirst"><code>java.lang.String</code></td>
 239 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#getDescription--">getDescription</a></span>()</code>
 240 <div class="block">A long description of the Option</div>
 241 </td>
 242 </tr>
 243 <tr id="i5" class="rowColor">
 244 <td class="colFirst"><code>java.lang.String</code></td>
 245 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#getFurtherDetails--">getFurtherDetails</a></span>()</code>
 246 <div class="block">The URL where further details about the option can be found</div>
 247 </td>
 248 </tr>
 249 <tr id="i6" class="altColor">
 250 <td class="colFirst"><code>java.lang.String</code></td>
 251 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#getName--">getName</a></span>()</code>
 252 <div class="block">Human readable name of the option</div>
 253 </td>
 254 </tr>
 255 <tr id="i7" class="rowColor">
 256 <td class="colFirst"><code>java.util.List&lt;java.lang.String&gt;</code></td>
 257 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#getOptionNames--">getOptionNames</a></span>()</code>&nbsp;</td>
 258 </tr>
 259 <tr id="i8" class="altColor">
 260 <td class="colFirst"><code>java.util.List&lt;java.lang.String&gt;</code></td>
 261 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#getPossibleValues--">getPossibleValues</a></span>()</code>
 262 <div class="block">List of possible optionNames</div>
 263 </td>
 264 </tr>
 265 <tr id="i9" class="rowColor">
 266 <td class="colFirst"><code>int</code></td>
 267 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#hashCode--">hashCode</a></span>()</code>&nbsp;</td>
 268 </tr>
 269 <tr id="i10" class="altColor">
 270 <td class="colFirst"><code>boolean</code></td>
 271 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#isRequired--">isRequired</a></span>()</code>
 272 <div class="block">Flag that indicated that this option must be specified in the command
 273  line for an executable to run</div>
 274 </td>
 275 </tr>
 276 <tr id="i11" class="rowColor">
 277 <td class="colFirst"><code>void</code></td>
 278 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#setBasicURL-java.net.URL-">setBasicURL</a></span>(java.net.URL&nbsp;url)</code>&nbsp;</td>
 279 </tr>
 280 <tr id="i12" class="altColor">
 281 <td class="colFirst"><code>void</code></td>
 282 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#setDefaultValue-java.lang.String-">setDefaultValue</a></span>(java.lang.String&nbsp;defaultVal)</code>
 283 <div class="block">Sets one of the values defined in optionList as default.</div>
 284 </td>
 285 </tr>
 286 <tr id="i13" class="rowColor">
 287 <td class="colFirst"><code>void</code></td>
 288 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#setDescription-java.lang.String-">setDescription</a></span>(java.lang.String&nbsp;description)</code>&nbsp;</td>
 289 </tr>
 290 <tr id="i14" class="altColor">
 291 <td class="colFirst"><code>void</code></td>
 292 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#setFurtherDetails-java.lang.String-">setFurtherDetails</a></span>(java.lang.String&nbsp;furtherDetails)</code>&nbsp;</td>
 293 </tr>
 294 <tr id="i15" class="rowColor">
 295 <td class="colFirst"><code>void</code></td>
 296 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#setName-java.lang.String-">setName</a></span>(java.lang.String&nbsp;name)</code>&nbsp;</td>
 297 </tr>
 298 <tr id="i16" class="altColor">
 299 <td class="colFirst"><code>void</code></td>
 300 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#setOptionNames-java.util.Set-">setOptionNames</a></span>(java.util.Set&lt;java.lang.String&gt;&nbsp;optionNames)</code>&nbsp;</td>
 301 </tr>
 302 <tr id="i17" class="rowColor">
 303 <td class="colFirst"><code>void</code></td>
 304 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#setRequired-boolean-">setRequired</a></span>(boolean&nbsp;isRequired)</code>&nbsp;</td>
 305 </tr>
 306 <tr id="i18" class="altColor">
 307 <td class="colFirst"><code>void</code></td>
 308 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#setValue-java.lang.String-">setValue</a></span>(java.lang.String&nbsp;dValue)</code>
 309 <div class="block">Set default values for the parameter or an option</div>
 310 </td>
 311 </tr>
 312 <tr id="i19" class="rowColor">
 313 <td class="colFirst"><code>java.lang.String</code></td>
 314 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#toCommand-java.lang.String-">toCommand</a></span>(java.lang.String&nbsp;nameValueSeparator)</code>
 315 <div class="block">Convert the option to the command string.</div>
 316 </td>
 317 </tr>
 318 <tr id="i20" class="altColor">
 319 <td class="colFirst"><code>java.lang.String</code></td>
 320 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#toString--">toString</a></span>()</code>&nbsp;</td>
 321 </tr>
 322 <tr id="i21" class="rowColor">
 323 <td class="colFirst"><code>(package private) void</code></td>
 324 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#validate--">validate</a></span>()</code>
 325 <div class="block">Validate the option</div>
 326 </td>
 327 </tr>
 328 <tr id="i22" class="altColor">
 329 <td class="colFirst"><code>(package private) static boolean</code></td>
 330 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/metadata/Option.html#valueExist-java.lang.String-java.util.List-">valueExist</a></span>(java.lang.String&nbsp;testValue,
 331           java.util.List&lt;java.lang.String&gt;&nbsp;values)</code>&nbsp;</td>
 332 </tr>
 333 </table>
 334 <ul class="blockList">
 335 <li class="blockList"><a name="methods.inherited.from.class.java.lang.Object">
 336 <!--   -->
 337 </a>
 338 <h3>Methods inherited from class&nbsp;java.lang.Object</h3>
 339 <code>clone, finalize, getClass, notify, notifyAll, wait, wait, wait</code></li>
 340 </ul>
 341 </li>
 342 </ul>
 343 </li>
 344 </ul>
 345 </div>
 346 <div class="details">
 347 <ul class="blockList">
 348 <li class="blockList">
 349 <!-- ============ FIELD DETAIL =========== -->
 350 <ul class="blockList">
 351 <li class="blockList"><a name="field.detail">
 352 <!--   -->
 353 </a>
 354 <h3>Field Detail</h3>
 355 <a name="description">
 356 <!--   -->
 357 </a>
 358 <ul class="blockList">
 359 <li class="blockList">
 360 <h4>description</h4>
 361 <pre>protected&nbsp;java.lang.String description</pre>
 362 </li>
 363 </ul>
 364 <a name="optionNames">
 365 <!--   -->
 366 </a>
 367 <ul class="blockList">
 368 <li class="blockList">
 369 <h4>optionNames</h4>
 370 <pre>java.util.Set&lt;java.lang.String&gt; optionNames</pre>
 371 </li>
 372 </ul>
 373 <a name="name">
 374 <!--   -->
 375 </a>
 376 <ul class="blockList">
 377 <li class="blockList">
 378 <h4>name</h4>
 379 <pre>protected&nbsp;java.lang.String name</pre>
 380 </li>
 381 </ul>
 382 <a name="isRequired">
 383 <!--   -->
 384 </a>
 385 <ul class="blockList">
 386 <li class="blockList">
 387 <h4>isRequired</h4>
 388 <pre>protected&nbsp;boolean isRequired</pre>
 389 </li>
 390 </ul>
 391 <a name="furtherDetails">
 392 <!--   -->
 393 </a>
 394 <ul class="blockList">
 395 <li class="blockList">
 396 <h4>furtherDetails</h4>
 397 <pre>protected&nbsp;java.lang.String furtherDetails</pre>
 398 </li>
 399 </ul>
 400 <a name="defaultValue">
 401 <!--   -->
 402 </a>
 403 <ul class="blockList">
 404 <li class="blockList">
 405 <h4>defaultValue</h4>
 406 <pre>protected&nbsp;java.lang.String defaultValue</pre>
 407 </li>
 408 </ul>
 409 <a name="basicURL">
 410 <!--   -->
 411 </a>
 412 <ul class="blockListLast">
 413 <li class="blockList">
 414 <h4>basicURL</h4>
 415 <pre>private&nbsp;java.net.URL basicURL</pre>
 416 </li>
 417 </ul>
 418 </li>
 419 </ul>
 420 <!-- ========= CONSTRUCTOR DETAIL ======== -->
 421 <ul class="blockList">
 422 <li class="blockList"><a name="constructor.detail">
 423 <!--   -->
 424 </a>
 425 <h3>Constructor Detail</h3>
 426 <a name="Option--">
 427 <!--   -->
 428 </a>
 429 <ul class="blockList">
 430 <li class="blockList">
 431 <h4>Option</h4>
 432 <pre>Option()</pre>
 433 </li>
 434 </ul>
 435 <a name="Option-java.lang.String-java.lang.String-">
 436 <!--   -->
 437 </a>
 438 <ul class="blockListLast">
 439 <li class="blockList">
 440 <h4>Option</h4>
 441 <pre>public&nbsp;Option(java.lang.String&nbsp;name,
 442               java.lang.String&nbsp;description)</pre>
 443 </li>
 444 </ul>
 445 </li>
 446 </ul>
 447 <!-- ============ METHOD DETAIL ========== -->
 448 <ul class="blockList">
 449 <li class="blockList"><a name="method.detail">
 450 <!--   -->
 451 </a>
 452 <h3>Method Detail</h3>
 453 <a name="getName--">
 454 <!--   -->
 455 </a>
 456 <ul class="blockList">
 457 <li class="blockList">
 458 <h4>getName</h4>
 459 <pre>public&nbsp;java.lang.String&nbsp;getName()</pre>
 460 <div class="block">Human readable name of the option</div>
 461 <dl>
 462 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 463 <dd><code><a href="../../compbio/metadata/Argument.html#getName--">getName</a></code>&nbsp;in interface&nbsp;<code><a href="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</a>&lt;<a href="../../compbio/metadata/Option.html" title="type parameter in Option">T</a>&gt;</code></dd>
 464 </dl>
 465 </li>
 466 </ul>
 467 <a name="setName-java.lang.String-">
 468 <!--   -->
 469 </a>
 470 <ul class="blockList">
 471 <li class="blockList">
 472 <h4>setName</h4>
 473 <pre>public&nbsp;void&nbsp;setName(java.lang.String&nbsp;name)</pre>
 474 </li>
 475 </ul>
 476 <a name="setBasicURL-java.net.URL-">
 477 <!--   -->
 478 </a>
 479 <ul class="blockList">
 480 <li class="blockList">
 481 <h4>setBasicURL</h4>
 482 <pre>public&nbsp;void&nbsp;setBasicURL(java.net.URL&nbsp;url)</pre>
 483 </li>
 484 </ul>
 485 <a name="getBasicURL--">
 486 <!--   -->
 487 </a>
 488 <ul class="blockList">
 489 <li class="blockList">
 490 <h4>getBasicURL</h4>
 491 <pre>public&nbsp;java.net.URL&nbsp;getBasicURL()</pre>
 492 </li>
 493 </ul>
 494 <a name="getDescription--">
 495 <!--   -->
 496 </a>
 497 <ul class="blockList">
 498 <li class="blockList">
 499 <h4>getDescription</h4>
 500 <pre>public&nbsp;java.lang.String&nbsp;getDescription()</pre>
 501 <div class="block">A long description of the Option</div>
 502 <dl>
 503 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 504 <dd><code><a href="../../compbio/metadata/Argument.html#getDescription--">getDescription</a></code>&nbsp;in interface&nbsp;<code><a href="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</a>&lt;<a href="../../compbio/metadata/Option.html" title="type parameter in Option">T</a>&gt;</code></dd>
 505 </dl>
 506 </li>
 507 </ul>
 508 <a name="setDescription-java.lang.String-">
 509 <!--   -->
 510 </a>
 511 <ul class="blockList">
 512 <li class="blockList">
 513 <h4>setDescription</h4>
 514 <pre>public&nbsp;void&nbsp;setDescription(java.lang.String&nbsp;description)</pre>
 515 </li>
 516 </ul>
 517 <a name="getFurtherDetails--">
 518 <!--   -->
 519 </a>
 520 <ul class="blockList">
 521 <li class="blockList">
 522 <h4>getFurtherDetails</h4>
 523 <pre>public&nbsp;java.lang.String&nbsp;getFurtherDetails()</pre>
 524 <div class="block">The URL where further details about the option can be found</div>
 525 <dl>
 526 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 527 <dd><code><a href="../../compbio/metadata/Argument.html#getFurtherDetails--">getFurtherDetails</a></code>&nbsp;in interface&nbsp;<code><a href="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</a>&lt;<a href="../../compbio/metadata/Option.html" title="type parameter in Option">T</a>&gt;</code></dd>
 528 <dt><span class="throwsLabel">Throws:</span></dt>
 529 <dd><code>java.net.MalformedURLException</code></dd>
 530 </dl>
 531 </li>
 532 </ul>
 533 <a name="setFurtherDetails-java.lang.String-">
 534 <!--   -->
 535 </a>
 536 <ul class="blockList">
 537 <li class="blockList">
 538 <h4>setFurtherDetails</h4>
 539 <pre>public&nbsp;void&nbsp;setFurtherDetails(java.lang.String&nbsp;furtherDetails)</pre>
 540 </li>
 541 </ul>
 542 <a name="getDefaultValue--">
 543 <!--   -->
 544 </a>
 545 <ul class="blockList">
 546 <li class="blockList">
 547 <h4>getDefaultValue</h4>
 548 <pre>public&nbsp;java.lang.String&nbsp;getDefaultValue()</pre>
 549 <div class="block">A default value of the option. Defaults to command line argument name
 550  e.g. -auto</div>
 551 <dl>
 552 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 553 <dd><code><a href="../../compbio/metadata/Argument.html#getDefaultValue--">getDefaultValue</a></code>&nbsp;in interface&nbsp;<code><a href="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</a>&lt;<a href="../../compbio/metadata/Option.html" title="type parameter in Option">T</a>&gt;</code></dd>
 554 </dl>
 555 </li>
 556 </ul>
 557 <a name="setDefaultValue-java.lang.String-">
 558 <!--   -->
 559 </a>
 560 <ul class="blockList">
 561 <li class="blockList">
 562 <h4>setDefaultValue</h4>
 563 <pre>public&nbsp;void&nbsp;setDefaultValue(java.lang.String&nbsp;defaultVal)
 564                      throws <a href="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</a></pre>
 565 <div class="block">Sets one of the values defined in optionList as default. Attempting set
 566  the value not listed there will result in WrongParameter exception</div>
 567 <dl>
 568 <dt><span class="paramLabel">Parameters:</span></dt>
 569 <dd><code>defaultVal</code> - </dd>
 570 <dt><span class="throwsLabel">Throws:</span></dt>
 571 <dd><code><a href="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</a></code> - is thrown if the defaultValue is not found in optionList</dd>
 572 </dl>
 573 </li>
 574 </ul>
 575 <a name="valueExist-java.lang.String-java.util.List-">
 576 <!--   -->
 577 </a>
 578 <ul class="blockList">
 579 <li class="blockList">
 580 <h4>valueExist</h4>
 581 <pre>static&nbsp;boolean&nbsp;valueExist(java.lang.String&nbsp;testValue,
 582                           java.util.List&lt;java.lang.String&gt;&nbsp;values)</pre>
 583 </li>
 584 </ul>
 585 <a name="isRequired--">
 586 <!--   -->
 587 </a>
 588 <ul class="blockList">
 589 <li class="blockList">
 590 <h4>isRequired</h4>
 591 <pre>public&nbsp;boolean&nbsp;isRequired()</pre>
 592 <div class="block">Flag that indicated that this option must be specified in the command
 593  line for an executable to run</div>
 594 <dl>
 595 <dt><span class="returnLabel">Returns:</span></dt>
 596 <dd>true is the option is required, false otherwise</dd>
 597 </dl>
 598 </li>
 599 </ul>
 600 <a name="setRequired-boolean-">
 601 <!--   -->
 602 </a>
 603 <ul class="blockList">
 604 <li class="blockList">
 605 <h4>setRequired</h4>
 606 <pre>public&nbsp;void&nbsp;setRequired(boolean&nbsp;isRequired)</pre>
 607 </li>
 608 </ul>
 609 <a name="getOptionNames--">
 610 <!--   -->
 611 </a>
 612 <ul class="blockList">
 613 <li class="blockList">
 614 <h4>getOptionNames</h4>
 615 <pre>public&nbsp;java.util.List&lt;java.lang.String&gt;&nbsp;getOptionNames()</pre>
 616 <dl>
 617 <dt><span class="returnLabel">Returns:</span></dt>
 618 <dd>List of option names</dd>
 619 </dl>
 620 </li>
 621 </ul>
 622 <a name="setOptionNames-java.util.Set-">
 623 <!--   -->
 624 </a>
 625 <ul class="blockList">
 626 <li class="blockList">
 627 <h4>setOptionNames</h4>
 628 <pre>public&nbsp;void&nbsp;setOptionNames(java.util.Set&lt;java.lang.String&gt;&nbsp;optionNames)</pre>
 629 </li>
 630 </ul>
 631 <a name="addOptionNames-java.lang.String...-">
 632 <!--   -->
 633 </a>
 634 <ul class="blockList">
 635 <li class="blockList">
 636 <h4>addOptionNames</h4>
 637 <pre>public&nbsp;java.util.Set&lt;java.lang.String&gt;&nbsp;addOptionNames(java.lang.String...&nbsp;value)</pre>
 638 <div class="block">Adds an option to the optionName list</div>
 639 <dl>
 640 <dt><span class="paramLabel">Parameters:</span></dt>
 641 <dd><code>value</code> - </dd>
 642 <dt><span class="returnLabel">Returns:</span></dt>
 643 <dd>modified optionName list</dd>
 644 </dl>
 645 </li>
 646 </ul>
 647 <a name="toString--">
 648 <!--   -->
 649 </a>
 650 <ul class="blockList">
 651 <li class="blockList">
 652 <h4>toString</h4>
 653 <pre>public&nbsp;java.lang.String&nbsp;toString()</pre>
 654 <dl>
 655 <dt><span class="overrideSpecifyLabel">Overrides:</span></dt>
 656 <dd><code>toString</code>&nbsp;in class&nbsp;<code>java.lang.Object</code></dd>
 657 </dl>
 658 </li>
 659 </ul>
 660 <a name="toCommand-java.lang.String-">
 661 <!--   -->
 662 </a>
 663 <ul class="blockList">
 664 <li class="blockList">
 665 <h4>toCommand</h4>
 666 <pre>public&nbsp;java.lang.String&nbsp;toCommand(java.lang.String&nbsp;nameValueSeparator)</pre>
 667 <div class="block">Convert the option to the command string.</div>
 668 <dl>
 669 <dt><span class="returnLabel">Returns:</span></dt>
 670 <dd>If only one optionName is defined, than it is returned, if many
 671          option names are defined, then the defaultValue is returned.
 672          Option must have a default value if there are many optionNames to
 673          be valid.</dd>
 674 </dl>
 675 </li>
 676 </ul>
 677 <a name="equals-java.lang.Object-">
 678 <!--   -->
 679 </a>
 680 <ul class="blockList">
 681 <li class="blockList">
 682 <h4>equals</h4>
 683 <pre>public&nbsp;boolean&nbsp;equals(java.lang.Object&nbsp;obj)</pre>
 684 <dl>
 685 <dt><span class="overrideSpecifyLabel">Overrides:</span></dt>
 686 <dd><code>equals</code>&nbsp;in class&nbsp;<code>java.lang.Object</code></dd>
 687 </dl>
 688 </li>
 689 </ul>
 690 <a name="hashCode--">
 691 <!--   -->
 692 </a>
 693 <ul class="blockList">
 694 <li class="blockList">
 695 <h4>hashCode</h4>
 696 <pre>public&nbsp;int&nbsp;hashCode()</pre>
 697 <dl>
 698 <dt><span class="overrideSpecifyLabel">Overrides:</span></dt>
 699 <dd><code>hashCode</code>&nbsp;in class&nbsp;<code>java.lang.Object</code></dd>
 700 </dl>
 701 </li>
 702 </ul>
 703 <a name="getPossibleValues--">
 704 <!--   -->
 705 </a>
 706 <ul class="blockList">
 707 <li class="blockList">
 708 <h4>getPossibleValues</h4>
 709 <pre>public&nbsp;java.util.List&lt;java.lang.String&gt;&nbsp;getPossibleValues()</pre>
 710 <div class="block">List of possible optionNames</div>
 711 <dl>
 712 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 713 <dd><code><a href="../../compbio/metadata/Argument.html#getPossibleValues--">getPossibleValues</a></code>&nbsp;in interface&nbsp;<code><a href="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</a>&lt;<a href="../../compbio/metadata/Option.html" title="type parameter in Option">T</a>&gt;</code></dd>
 714 <dt><span class="returnLabel">Returns:</span></dt>
 715 <dd>List of values allowed for an Argument</dd>
 716 </dl>
 717 </li>
 718 </ul>
 719 <a name="setValue-java.lang.String-">
 720 <!--   -->
 721 </a>
 722 <ul class="blockList">
 723 <li class="blockList">
 724 <h4>setValue</h4>
 725 <pre>public&nbsp;void&nbsp;setValue(java.lang.String&nbsp;dValue)
 726               throws <a href="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</a></pre>
 727 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../compbio/metadata/Argument.html#setValue-java.lang.String-">Argument</a></code></span></div>
 728 <div class="block">Set default values for the parameter or an option</div>
 729 <dl>
 730 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 731 <dd><code><a href="../../compbio/metadata/Argument.html#setValue-java.lang.String-">setValue</a></code>&nbsp;in interface&nbsp;<code><a href="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</a>&lt;<a href="../../compbio/metadata/Option.html" title="type parameter in Option">T</a>&gt;</code></dd>
 732 <dt><span class="paramLabel">Parameters:</span></dt>
 733 <dd><code>dValue</code> - the value to be set</dd>
 734 <dt><span class="throwsLabel">Throws:</span></dt>
 735 <dd><code><a href="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</a></code> - - when the value to be set is illegal. Wrong value for
 736              numeric parameter is the value defined outside it , for
 737              string type parameter, wrong value is the one which is not
 738              listed in possible values list</dd>
 739 <dt><span class="seeLabel">See Also:</span></dt>
 740 <dd><a href="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><code>ValueConstrain</code></a></dd>
 741 </dl>
 742 </li>
 743 </ul>
 744 <a name="validate--">
 745 <!--   -->
 746 </a>
 747 <ul class="blockListLast">
 748 <li class="blockList">
 749 <h4>validate</h4>
 750 <pre>void&nbsp;validate()
 751        throws javax.xml.bind.ValidationException</pre>
 752 <div class="block">Validate the option</div>
 753 <dl>
 754 <dt><span class="throwsLabel">Throws:</span></dt>
 755 <dd><code>javax.xml.bind.ValidationException</code> - is the option is invalid. This happens if option does not
 756              have a default value but have multiple option names, or no
 757              option names is defined</dd>
 758 </dl>
 759 </li>
 760 </ul>
 761 </li>
 762 </ul>
 763 </li>
 764 </ul>
 765 </div>
 766 </div>
 767 <!-- ========= END OF CLASS DATA ========= -->
 768 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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 776 <ul class="navList" title="Navigation">
 777 <li><a href="../../overview-summary.html">Overview</a></li>
 778 <li><a href="package-summary.html">Package</a></li>
 779 <li class="navBarCell1Rev">Class</li>
 780 <li><a href="class-use/Option.html">Use</a></li>
 781 <li><a href="package-tree.html">Tree</a></li>
 782 <li><a href="../../deprecated-list.html">Deprecated</a></li>
 783 <li><a href="../../index-files/index-1.html">Index</a></li>
 784 <li><a href="../../help-doc.html">Help</a></li>
 785 </ul>
 786 </div>
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 790 <li><a href="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><span class="typeNameLink">Next&nbsp;Class</span></a></li>
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