website/docs/full_javadoc/compbio/ws/server/WSUtil.html

   1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
   2 <!-- NewPage -->
   3 <html lang="en">
   4 <head>
   5 <!-- Generated by javadoc (1.8.0_121) on Fri Apr 21 15:32:50 BST 2017 -->
   6 <title>WSUtil</title>
   7 <meta name="date" content="2017-04-21">
   8 <link rel="stylesheet" type="text/css" href="../../../stylesheet.css" title="Style">
   9 <script type="text/javascript" src="../../../script.js"></script>
  10 </head>
  11 <body>
  12 <script type="text/javascript"><!--
  13     try {
  14         if (location.href.indexOf('is-external=true') == -1) {
  15             parent.document.title="WSUtil";
  16         }
  17     }
  18     catch(err) {
  19     }
  20 //-->
  21 var methods = {"i0":9,"i1":9,"i2":9,"i3":9,"i4":9,"i5":9,"i6":9,"i7":9,"i8":9,"i9":9,"i10":9,"i11":9,"i12":9,"i13":9};
  22 var tabs = {65535:["t0","All Methods"],1:["t1","Static Methods"],8:["t4","Concrete Methods"]};
  23 var altColor = "altColor";
  24 var rowColor = "rowColor";
  25 var tableTab = "tableTab";
  26 var activeTableTab = "activeTableTab";
  27 </script>
  28 <noscript>
  29 <div>JavaScript is disabled on your browser.</div>
  30 </noscript>
  31 <!-- ========= START OF TOP NAVBAR ======= -->
  32 <div class="topNav"><a name="navbar.top">
  33 <!--   -->
  34 </a>
  35 <div class="skipNav"><a href="#skip.navbar.top" title="Skip navigation links">Skip navigation links</a></div>
  36 <a name="navbar.top.firstrow">
  37 <!--   -->
  38 </a>
  39 <ul class="navList" title="Navigation">
  40 <li><a href="../../../overview-summary.html">Overview</a></li>
  41 <li><a href="package-summary.html">Package</a></li>
  42 <li class="navBarCell1Rev">Class</li>
  43 <li><a href="class-use/WSUtil.html">Use</a></li>
  44 <li><a href="package-tree.html">Tree</a></li>
  45 <li><a href="../../../deprecated-list.html">Deprecated</a></li>
  46 <li><a href="../../../index-files/index-1.html">Index</a></li>
  47 <li><a href="../../../help-doc.html">Help</a></li>
  48 </ul>
  49 </div>
  50 <div class="subNav">
  51 <ul class="navList">
  52 <li><a href="../../../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server"><span class="typeNameLink">Prev&nbsp;Class</span></a></li>
  53 <li>Next&nbsp;Class</li>
  54 </ul>
  55 <ul class="navList">
  56 <li><a href="../../../index.html?compbio/ws/server/WSUtil.html" target="_top">Frames</a></li>
  57 <li><a href="WSUtil.html" target="_top">No&nbsp;Frames</a></li>
  58 </ul>
  59 <ul class="navList" id="allclasses_navbar_top">
  60 <li><a href="../../../allclasses-noframe.html">All&nbsp;Classes</a></li>
  61 </ul>
  62 <div>
  63 <script type="text/javascript"><!--
  64   allClassesLink = document.getElementById("allclasses_navbar_top");
  65   if(window==top) {
  66     allClassesLink.style.display = "block";
  67   }
  68   else {
  69     allClassesLink.style.display = "none";
  70   }
  71   //-->
  72 </script>
  73 </div>
  74 <div>
  75 <ul class="subNavList">
  76 <li>Summary:&nbsp;</li>
  77 <li>Nested&nbsp;|&nbsp;</li>
  78 <li>Field&nbsp;|&nbsp;</li>
  79 <li><a href="#constructor.summary">Constr</a>&nbsp;|&nbsp;</li>
  80 <li><a href="#method.summary">Method</a></li>
  81 </ul>
  82 <ul class="subNavList">
  83 <li>Detail:&nbsp;</li>
  84 <li>Field&nbsp;|&nbsp;</li>
  85 <li><a href="#constructor.detail">Constr</a>&nbsp;|&nbsp;</li>
  86 <li><a href="#method.detail">Method</a></li>
  87 </ul>
  88 </div>
  89 <a name="skip.navbar.top">
  90 <!--   -->
  91 </a></div>
  92 <!-- ========= END OF TOP NAVBAR ========= -->
  93 <!-- ======== START OF CLASS DATA ======== -->
  94 <div class="header">
  95 <div class="subTitle">compbio.ws.server</div>
  96 <h2 title="Class WSUtil" class="title">Class WSUtil</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.ws.server.WSUtil</li>
 104 </ul>
 105 </li>
 106 </ul>
 107 <div class="description">
 108 <ul class="blockList">
 109 <li class="blockList">
 110 <hr>
 111 <br>
 112 <pre>public final class <span class="typeNameLabel">WSUtil</span>
 113 extends java.lang.Object</pre>
 114 </li>
 115 </ul>
 116 </div>
 117 <div class="summary">
 118 <ul class="blockList">
 119 <li class="blockList">
 120 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
 121 <ul class="blockList">
 122 <li class="blockList"><a name="constructor.summary">
 123 <!--   -->
 124 </a>
 125 <h3>Constructor Summary</h3>
 126 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Constructor Summary table, listing constructors, and an explanation">
 127 <caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
 128 <tr>
 129 <th class="colOne" scope="col">Constructor and Description</th>
 130 </tr>
 131 <tr class="altColor">
 132 <td class="colOne"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/WSUtil.html#WSUtil--">WSUtil</a></span>()</code>&nbsp;</td>
 133 </tr>
 134 </table>
 135 </li>
 136 </ul>
 137 <!-- ========== METHOD SUMMARY =========== -->
 138 <ul class="blockList">
 139 <li class="blockList"><a name="method.summary">
 140 <!--   -->
 141 </a>
 142 <h3>Method Summary</h3>
 143 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Method Summary table, listing methods, and an explanation">
 144 <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="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
 145 <tr>
 146 <th class="colFirst" scope="col">Modifier and Type</th>
 147 <th class="colLast" scope="col">Method and Description</th>
 148 </tr>
 149 <tr id="i0" class="altColor">
 150 <td class="colFirst"><code>static &lt;T&gt;&nbsp;java.lang.String</code></td>
 151 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/WSUtil.html#align-java.util.List-compbio.engine.client.ConfiguredExecutable-org.apache.log4j.Logger-java.lang.String-compbio.metadata.Limit-">align</a></span>(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 152      <a href="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;T&gt;&nbsp;confExec,
 153      org.apache.log4j.Logger&nbsp;logger,
 154      java.lang.String&nbsp;callingMethod,
 155      <a href="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a>&lt;T&gt;&nbsp;limit)</code>&nbsp;</td>
 156 </tr>
 157 <tr id="i1" class="rowColor">
 158 <td class="colFirst"><code>static &lt;T&gt;&nbsp;java.lang.String</code></td>
 159 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/WSUtil.html#analize-java.util.List-compbio.engine.client.ConfiguredExecutable-org.apache.log4j.Logger-java.lang.String-compbio.metadata.Limit-">analize</a></span>(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 160        <a href="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;T&gt;&nbsp;confExec,
 161        org.apache.log4j.Logger&nbsp;log,
 162        java.lang.String&nbsp;method,
 163        <a href="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a>&lt;T&gt;&nbsp;limit)</code>&nbsp;</td>
 164 </tr>
 165 <tr id="i2" class="altColor">
 166 <td class="colFirst"><code>static boolean</code></td>
 167 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/WSUtil.html#cancelJob-java.lang.String-">cancelJob</a></span>(java.lang.String&nbsp;jobId)</code>&nbsp;</td>
 168 </tr>
 169 <tr id="i3" class="rowColor">
 170 <td class="colFirst"><code>static &lt;T&gt;&nbsp;java.lang.String</code></td>
 171 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/WSUtil.html#fold-java.util.List-compbio.engine.client.ConfiguredExecutable-org.apache.log4j.Logger-java.lang.String-compbio.metadata.Limit-">fold</a></span>(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 172     <a href="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;T&gt;&nbsp;confExec,
 173     org.apache.log4j.Logger&nbsp;log,
 174     java.lang.String&nbsp;method,
 175     <a href="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a>&lt;T&gt;&nbsp;limit)</code>&nbsp;</td>
 176 </tr>
 177 <tr id="i4" class="altColor">
 178 <td class="colFirst"><code>static &lt;T&gt;&nbsp;<a href="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></code></td>
 179 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/WSUtil.html#getAnnotation-java.lang.String-org.apache.log4j.Logger-">getAnnotation</a></span>(java.lang.String&nbsp;jobId,
 180              org.apache.log4j.Logger&nbsp;log)</code>&nbsp;</td>
 181 </tr>
 182 <tr id="i5" class="rowColor">
 183 <td class="colFirst"><code>static &lt;T&gt;&nbsp;java.util.List&lt;java.lang.String&gt;</code></td>
 184 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/WSUtil.html#getCommands-java.util.List-java.lang.String-">getCommands</a></span>(java.util.List&lt;<a href="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;T&gt;&gt;&nbsp;options,
 185            java.lang.String&nbsp;keyValueSeparator)</code>&nbsp;</td>
 186 </tr>
 187 <tr id="i6" class="altColor">
 188 <td class="colFirst"><code>static <a href="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</a></code></td>
 189 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/WSUtil.html#getEngine-compbio.engine.client.ConfiguredExecutable-">getEngine</a></span>(<a href="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;?&gt;&nbsp;confClustal)</code>&nbsp;</td>
 190 </tr>
 191 <tr id="i7" class="rowColor">
 192 <td class="colFirst"><code>static <a href="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</a></code></td>
 193 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/WSUtil.html#getJobStatus-java.lang.String-">getJobStatus</a></span>(java.lang.String&nbsp;jobId)</code>&nbsp;</td>
 194 </tr>
 195 <tr id="i8" class="altColor">
 196 <td class="colFirst"><code>static byte</code></td>
 197 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/WSUtil.html#getProgress-java.lang.String-">getProgress</a></span>(java.lang.String&nbsp;jobId)</code>&nbsp;</td>
 198 </tr>
 199 <tr id="i9" class="rowColor">
 200 <td class="colFirst"><code>static <a href="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</a></code></td>
 201 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/WSUtil.html#pullFile-java.lang.String-long-">pullFile</a></span>(java.lang.String&nbsp;file,
 202         long&nbsp;position)</code>&nbsp;</td>
 203 </tr>
 204 <tr id="i10" class="altColor">
 205 <td class="colFirst"><code>(package private) static &lt;T&gt;&nbsp;void</code></td>
 206 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/WSUtil.html#reportUsage-compbio.engine.client.ConfiguredExecutable-org.apache.log4j.Logger-">reportUsage</a></span>(<a href="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;T&gt;&nbsp;confExec,
 207            org.apache.log4j.Logger&nbsp;logger)</code>&nbsp;</td>
 208 </tr>
 209 <tr id="i11" class="rowColor">
 210 <td class="colFirst"><code>static void</code></td>
 211 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/WSUtil.html#validateAAConInput-java.util.List-">validateAAConInput</a></span>(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)</code>&nbsp;</td>
 212 </tr>
 213 <tr id="i12" class="altColor">
 214 <td class="colFirst"><code>static void</code></td>
 215 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/WSUtil.html#validateFastaInput-java.util.List-">validateFastaInput</a></span>(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)</code>&nbsp;</td>
 216 </tr>
 217 <tr id="i13" class="rowColor">
 218 <td class="colFirst"><code>static void</code></td>
 219 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/WSUtil.html#validateJobId-java.lang.String-">validateJobId</a></span>(java.lang.String&nbsp;jobId)</code>&nbsp;</td>
 220 </tr>
 221 </table>
 222 <ul class="blockList">
 223 <li class="blockList"><a name="methods.inherited.from.class.java.lang.Object">
 224 <!--   -->
 225 </a>
 226 <h3>Methods inherited from class&nbsp;java.lang.Object</h3>
 227 <code>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</code></li>
 228 </ul>
 229 </li>
 230 </ul>
 231 </li>
 232 </ul>
 233 </div>
 234 <div class="details">
 235 <ul class="blockList">
 236 <li class="blockList">
 237 <!-- ========= CONSTRUCTOR DETAIL ======== -->
 238 <ul class="blockList">
 239 <li class="blockList"><a name="constructor.detail">
 240 <!--   -->
 241 </a>
 242 <h3>Constructor Detail</h3>
 243 <a name="WSUtil--">
 244 <!--   -->
 245 </a>
 246 <ul class="blockListLast">
 247 <li class="blockList">
 248 <h4>WSUtil</h4>
 249 <pre>public&nbsp;WSUtil()</pre>
 250 </li>
 251 </ul>
 252 </li>
 253 </ul>
 254 <!-- ============ METHOD DETAIL ========== -->
 255 <ul class="blockList">
 256 <li class="blockList"><a name="method.detail">
 257 <!--   -->
 258 </a>
 259 <h3>Method Detail</h3>
 260 <a name="validateJobId-java.lang.String-">
 261 <!--   -->
 262 </a>
 263 <ul class="blockList">
 264 <li class="blockList">
 265 <h4>validateJobId</h4>
 266 <pre>public static final&nbsp;void&nbsp;validateJobId(java.lang.String&nbsp;jobId)
 267                                 throws java.security.InvalidParameterException</pre>
 268 <dl>
 269 <dt><span class="throwsLabel">Throws:</span></dt>
 270 <dd><code>java.security.InvalidParameterException</code></dd>
 271 </dl>
 272 </li>
 273 </ul>
 274 <a name="validateFastaInput-java.util.List-">
 275 <!--   -->
 276 </a>
 277 <ul class="blockList">
 278 <li class="blockList">
 279 <h4>validateFastaInput</h4>
 280 <pre>public static final&nbsp;void&nbsp;validateFastaInput(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)
 281                                      throws <a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></pre>
 282 <dl>
 283 <dt><span class="throwsLabel">Throws:</span></dt>
 284 <dd><code><a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></code></dd>
 285 </dl>
 286 </li>
 287 </ul>
 288 <a name="getJobStatus-java.lang.String-">
 289 <!--   -->
 290 </a>
 291 <ul class="blockList">
 292 <li class="blockList">
 293 <h4>getJobStatus</h4>
 294 <pre>public static&nbsp;<a href="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</a>&nbsp;getJobStatus(java.lang.String&nbsp;jobId)</pre>
 295 </li>
 296 </ul>
 297 <a name="pullFile-java.lang.String-long-">
 298 <!--   -->
 299 </a>
 300 <ul class="blockList">
 301 <li class="blockList">
 302 <h4>pullFile</h4>
 303 <pre>public static&nbsp;<a href="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</a>&nbsp;pullFile(java.lang.String&nbsp;file,
 304                                    long&nbsp;position)</pre>
 305 </li>
 306 </ul>
 307 <a name="getProgress-java.lang.String-">
 308 <!--   -->
 309 </a>
 310 <ul class="blockList">
 311 <li class="blockList">
 312 <h4>getProgress</h4>
 313 <pre>public static&nbsp;byte&nbsp;getProgress(java.lang.String&nbsp;jobId)</pre>
 314 </li>
 315 </ul>
 316 <a name="getEngine-compbio.engine.client.ConfiguredExecutable-">
 317 <!--   -->
 318 </a>
 319 <ul class="blockList">
 320 <li class="blockList">
 321 <h4>getEngine</h4>
 322 <pre>public static&nbsp;<a href="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</a>&nbsp;getEngine(<a href="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;?&gt;&nbsp;confClustal)</pre>
 323 </li>
 324 </ul>
 325 <a name="cancelJob-java.lang.String-">
 326 <!--   -->
 327 </a>
 328 <ul class="blockList">
 329 <li class="blockList">
 330 <h4>cancelJob</h4>
 331 <pre>public static&nbsp;boolean&nbsp;cancelJob(java.lang.String&nbsp;jobId)</pre>
 332 </li>
 333 </ul>
 334 <a name="align-java.util.List-compbio.engine.client.ConfiguredExecutable-org.apache.log4j.Logger-java.lang.String-compbio.metadata.Limit-">
 335 <!--   -->
 336 </a>
 337 <ul class="blockList">
 338 <li class="blockList">
 339 <h4>align</h4>
 340 <pre>public static&nbsp;&lt;T&gt;&nbsp;java.lang.String&nbsp;align(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 341                                          <a href="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;T&gt;&nbsp;confExec,
 342                                          org.apache.log4j.Logger&nbsp;logger,
 343                                          java.lang.String&nbsp;callingMethod,
 344                                          <a href="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a>&lt;T&gt;&nbsp;limit)
 345                                   throws <a href="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a>,
 346                                          <a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></pre>
 347 <dl>
 348 <dt><span class="throwsLabel">Throws:</span></dt>
 349 <dd><code><a href="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a></code></dd>
 350 <dd><code><a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></code></dd>
 351 </dl>
 352 </li>
 353 </ul>
 354 <a name="reportUsage-compbio.engine.client.ConfiguredExecutable-org.apache.log4j.Logger-">
 355 <!--   -->
 356 </a>
 357 <ul class="blockList">
 358 <li class="blockList">
 359 <h4>reportUsage</h4>
 360 <pre>static&nbsp;&lt;T&gt;&nbsp;void&nbsp;reportUsage(<a href="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;T&gt;&nbsp;confExec,
 361                             org.apache.log4j.Logger&nbsp;logger)</pre>
 362 </li>
 363 </ul>
 364 <a name="analize-java.util.List-compbio.engine.client.ConfiguredExecutable-org.apache.log4j.Logger-java.lang.String-compbio.metadata.Limit-">
 365 <!--   -->
 366 </a>
 367 <ul class="blockList">
 368 <li class="blockList">
 369 <h4>analize</h4>
 370 <pre>public static&nbsp;&lt;T&gt;&nbsp;java.lang.String&nbsp;analize(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 371                                            <a href="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;T&gt;&nbsp;confExec,
 372                                            org.apache.log4j.Logger&nbsp;log,
 373                                            java.lang.String&nbsp;method,
 374                                            <a href="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a>&lt;T&gt;&nbsp;limit)
 375                                     throws <a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></pre>
 376 <dl>
 377 <dt><span class="throwsLabel">Throws:</span></dt>
 378 <dd><code><a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></code></dd>
 379 </dl>
 380 </li>
 381 </ul>
 382 <a name="fold-java.util.List-compbio.engine.client.ConfiguredExecutable-org.apache.log4j.Logger-java.lang.String-compbio.metadata.Limit-">
 383 <!--   -->
 384 </a>
 385 <ul class="blockList">
 386 <li class="blockList">
 387 <h4>fold</h4>
 388 <pre>public static&nbsp;&lt;T&gt;&nbsp;java.lang.String&nbsp;fold(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 389                                         <a href="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;T&gt;&nbsp;confExec,
 390                                         org.apache.log4j.Logger&nbsp;log,
 391                                         java.lang.String&nbsp;method,
 392                                         <a href="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a>&lt;T&gt;&nbsp;limit)
 393                                  throws <a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></pre>
 394 <dl>
 395 <dt><span class="throwsLabel">Throws:</span></dt>
 396 <dd><code><a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></code></dd>
 397 </dl>
 398 </li>
 399 </ul>
 400 <a name="getCommands-java.util.List-java.lang.String-">
 401 <!--   -->
 402 </a>
 403 <ul class="blockList">
 404 <li class="blockList">
 405 <h4>getCommands</h4>
 406 <pre>public static final&nbsp;&lt;T&gt;&nbsp;java.util.List&lt;java.lang.String&gt;&nbsp;getCommands(java.util.List&lt;<a href="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;T&gt;&gt;&nbsp;options,
 407                                                                      java.lang.String&nbsp;keyValueSeparator)</pre>
 408 </li>
 409 </ul>
 410 <a name="validateAAConInput-java.util.List-">
 411 <!--   -->
 412 </a>
 413 <ul class="blockList">
 414 <li class="blockList">
 415 <h4>validateAAConInput</h4>
 416 <pre>public static&nbsp;void&nbsp;validateAAConInput(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)
 417                                throws <a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></pre>
 418 <dl>
 419 <dt><span class="throwsLabel">Throws:</span></dt>
 420 <dd><code><a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></code></dd>
 421 </dl>
 422 </li>
 423 </ul>
 424 <a name="getAnnotation-java.lang.String-org.apache.log4j.Logger-">
 425 <!--   -->
 426 </a>
 427 <ul class="blockListLast">
 428 <li class="blockList">
 429 <h4>getAnnotation</h4>
 430 <pre>public static&nbsp;&lt;T&gt;&nbsp;<a href="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a>&nbsp;getAnnotation(java.lang.String&nbsp;jobId,
 431                                              org.apache.log4j.Logger&nbsp;log)
 432                                       throws <a href="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</a></pre>
 433 <dl>
 434 <dt><span class="throwsLabel">Throws:</span></dt>
 435 <dd><code><a href="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</a></code></dd>
 436 </dl>
 437 </li>
 438 </ul>
 439 </li>
 440 </ul>
 441 </li>
 442 </ul>
 443 </div>
 444 </div>
 445 <!-- ========= END OF CLASS DATA ========= -->
 446 <!-- ======= START OF BOTTOM NAVBAR ====== -->
 447 <div class="bottomNav"><a name="navbar.bottom">
 448 <!--   -->
 449 </a>
 450 <div class="skipNav"><a href="#skip.navbar.bottom" title="Skip navigation links">Skip navigation links</a></div>
 451 <a name="navbar.bottom.firstrow">
 452 <!--   -->
 453 </a>
 454 <ul class="navList" title="Navigation">
 455 <li><a href="../../../overview-summary.html">Overview</a></li>
 456 <li><a href="package-summary.html">Package</a></li>
 457 <li class="navBarCell1Rev">Class</li>
 458 <li><a href="class-use/WSUtil.html">Use</a></li>
 459 <li><a href="package-tree.html">Tree</a></li>
 460 <li><a href="../../../deprecated-list.html">Deprecated</a></li>
 461 <li><a href="../../../index-files/index-1.html">Index</a></li>
 462 <li><a href="../../../help-doc.html">Help</a></li>
 463 </ul>
 464 </div>
 465 <div class="subNav">
 466 <ul class="navList">
 467 <li><a href="../../../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server"><span class="typeNameLink">Prev&nbsp;Class</span></a></li>
 468 <li>Next&nbsp;Class</li>
 469 </ul>
 470 <ul class="navList">
 471 <li><a href="../../../index.html?compbio/ws/server/WSUtil.html" target="_top">Frames</a></li>
 472 <li><a href="WSUtil.html" target="_top">No&nbsp;Frames</a></li>
 473 </ul>
 474 <ul class="navList" id="allclasses_navbar_bottom">
 475 <li><a href="../../../allclasses-noframe.html">All&nbsp;Classes</a></li>
 476 </ul>
 477 <div>
 478 <script type="text/javascript"><!--
 479   allClassesLink = document.getElementById("allclasses_navbar_bottom");
 480   if(window==top) {
 481     allClassesLink.style.display = "block";
 482   }
 483   else {
 484     allClassesLink.style.display = "none";
 485   }
 486   //-->
 487 </script>
 488 </div>
 489 <div>
 490 <ul class="subNavList">
 491 <li>Summary:&nbsp;</li>
 492 <li>Nested&nbsp;|&nbsp;</li>
 493 <li>Field&nbsp;|&nbsp;</li>
 494 <li><a href="#constructor.summary">Constr</a>&nbsp;|&nbsp;</li>
 495 <li><a href="#method.summary">Method</a></li>
 496 </ul>
 497 <ul class="subNavList">
 498 <li>Detail:&nbsp;</li>
 499 <li>Field&nbsp;|&nbsp;</li>
 500 <li><a href="#constructor.detail">Constr</a>&nbsp;|&nbsp;</li>
 501 <li><a href="#method.detail">Method</a></li>
 502 </ul>
 503 </div>
 504 <a name="skip.navbar.bottom">
 505 <!--   -->
 506 </a></div>
 507 <!-- ======== END OF BOTTOM NAVBAR ======= -->
 508 </body>
 509 </html>