website/docs/full_javadoc/compbio/ws/server/MSAprobsWS.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>MSAprobsWS</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="MSAprobsWS";
  16         }
  17     }
  18     catch(err) {
  19     }
  20 //-->
  21 var methods = {"i0":10,"i1":10,"i2":10,"i3":10,"i4":10,"i5":10,"i6":10,"i7":10,"i8":10,"i9":10,"i10":10,"i11":10};
  22 var tabs = {65535:["t0","All Methods"],2:["t2","Instance 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/MSAprobsWS.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/MainManager.html" title="class in compbio.ws.server"><span class="typeNameLink">Prev&nbsp;Class</span></a></li>
  53 <li><a href="../../../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server"><span class="typeNameLink">Next&nbsp;Class</span></a></li>
  54 </ul>
  55 <ul class="navList">
  56 <li><a href="../../../index.html?compbio/ws/server/MSAprobsWS.html" target="_top">Frames</a></li>
  57 <li><a href="MSAprobsWS.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><a href="#field.summary">Field</a>&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><a href="#field.detail">Field</a>&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 MSAprobsWS" class="title">Class MSAprobsWS</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.MSAprobsWS</li>
 104 </ul>
 105 </li>
 106 </ul>
 107 <div class="description">
 108 <ul class="blockList">
 109 <li class="blockList">
 110 <dl>
 111 <dt>All Implemented Interfaces:</dt>
 112 <dd><a href="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</a>, <a href="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</a>, <a href="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;, <a href="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;</dd>
 113 </dl>
 114 <hr>
 115 <br>
 116 <pre>public class <span class="typeNameLabel">MSAprobsWS</span>
 117 extends java.lang.Object
 118 implements <a href="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;</pre>
 119 </li>
 120 </ul>
 121 </div>
 122 <div class="summary">
 123 <ul class="blockList">
 124 <li class="blockList">
 125 <!-- =========== FIELD SUMMARY =========== -->
 126 <ul class="blockList">
 127 <li class="blockList"><a name="field.summary">
 128 <!--   -->
 129 </a>
 130 <h3>Field Summary</h3>
 131 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Field Summary table, listing fields, and an explanation">
 132 <caption><span>Fields</span><span class="tabEnd">&nbsp;</span></caption>
 133 <tr>
 134 <th class="colFirst" scope="col">Modifier and Type</th>
 135 <th class="colLast" scope="col">Field and Description</th>
 136 </tr>
 137 <tr class="altColor">
 138 <td class="colFirst"><code>private static <a href="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;</code></td>
 139 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MSAprobsWS.html#limitMan">limitMan</a></span></code>&nbsp;</td>
 140 </tr>
 141 <tr class="rowColor">
 142 <td class="colFirst"><code>private static org.apache.log4j.Logger</code></td>
 143 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MSAprobsWS.html#log">log</a></span></code>&nbsp;</td>
 144 </tr>
 145 <tr class="altColor">
 146 <td class="colFirst"><code>private static <a href="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;</code></td>
 147 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MSAprobsWS.html#MSAprobsOptions">MSAprobsOptions</a></span></code>&nbsp;</td>
 148 </tr>
 149 </table>
 150 <ul class="blockList">
 151 <li class="blockList"><a name="fields.inherited.from.class.compbio.data.msa.JABAService">
 152 <!--   -->
 153 </a>
 154 <h3>Fields inherited from interface&nbsp;compbio.data.msa.<a href="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</a></h3>
 155 <code><a href="../../../compbio/data/msa/JABAService.html#JABAWS_VERSION">JABAWS_VERSION</a>, <a href="../../../compbio/data/msa/JABAService.html#SERVICE_NAMESPACE">SERVICE_NAMESPACE</a>, <a href="../../../compbio/data/msa/JABAService.html#V2_SERVICE_NAMESPACE">V2_SERVICE_NAMESPACE</a>, <a href="../../../compbio/data/msa/JABAService.html#V3_SERVICE_NAMESPACE">V3_SERVICE_NAMESPACE</a></code></li>
 156 </ul>
 157 </li>
 158 </ul>
 159 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
 160 <ul class="blockList">
 161 <li class="blockList"><a name="constructor.summary">
 162 <!--   -->
 163 </a>
 164 <h3>Constructor Summary</h3>
 165 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Constructor Summary table, listing constructors, and an explanation">
 166 <caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
 167 <tr>
 168 <th class="colOne" scope="col">Constructor and Description</th>
 169 </tr>
 170 <tr class="altColor">
 171 <td class="colOne"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MSAprobsWS.html#MSAprobsWS--">MSAprobsWS</a></span>()</code>&nbsp;</td>
 172 </tr>
 173 </table>
 174 </li>
 175 </ul>
 176 <!-- ========== METHOD SUMMARY =========== -->
 177 <ul class="blockList">
 178 <li class="blockList"><a name="method.summary">
 179 <!--   -->
 180 </a>
 181 <h3>Method Summary</h3>
 182 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Method Summary table, listing methods, and an explanation">
 183 <caption><span id="t0" class="activeTableTab"><span>All Methods</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>
 184 <tr>
 185 <th class="colFirst" scope="col">Modifier and Type</th>
 186 <th class="colLast" scope="col">Method and Description</th>
 187 </tr>
 188 <tr id="i0" class="altColor">
 189 <td class="colFirst"><code>java.lang.String</code></td>
 190 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MSAprobsWS.html#align-java.util.List-">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)</code>
 191 <div class="block">Align a list of sequences with default settings.</div>
 192 </td>
 193 </tr>
 194 <tr id="i1" class="rowColor">
 195 <td class="colFirst"><code>boolean</code></td>
 196 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MSAprobsWS.html#cancelJob-java.lang.String-">cancelJob</a></span>(java.lang.String&nbsp;jobId)</code>
 197 <div class="block">Stop running the job <code>jobId</code> but leave its output untouched</div>
 198 </td>
 199 </tr>
 200 <tr id="i2" class="altColor">
 201 <td class="colFirst"><code>java.lang.String</code></td>
 202 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MSAprobsWS.html#customAlign-java.util.List-java.util.List-">customAlign</a></span>(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 203            java.util.List&lt;<a href="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;&gt;&nbsp;options)</code>
 204 <div class="block">Align a list of sequences with options.</div>
 205 </td>
 206 </tr>
 207 <tr id="i3" class="rowColor">
 208 <td class="colFirst"><code><a href="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</a></code></td>
 209 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MSAprobsWS.html#getJobStatus-java.lang.String-">getJobStatus</a></span>(java.lang.String&nbsp;jobId)</code>
 210 <div class="block">Return the status of the job.</div>
 211 </td>
 212 </tr>
 213 <tr id="i4" class="altColor">
 214 <td class="colFirst"><code><a href="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;</code></td>
 215 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MSAprobsWS.html#getLimit-java.lang.String-">getLimit</a></span>(java.lang.String&nbsp;presetName)</code>
 216 <div class="block">Get a Limit for a preset.</div>
 217 </td>
 218 </tr>
 219 <tr id="i5" class="rowColor">
 220 <td class="colFirst"><code><a href="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;</code></td>
 221 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MSAprobsWS.html#getLimits--">getLimits</a></span>()</code>
 222 <div class="block">List Limits supported by a web service.</div>
 223 </td>
 224 </tr>
 225 <tr id="i6" class="altColor">
 226 <td class="colFirst"><code><a href="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;</code></td>
 227 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MSAprobsWS.html#getPresets--">getPresets</a></span>()</code>
 228 <div class="block">Get presets supported by a web service</div>
 229 </td>
 230 </tr>
 231 <tr id="i7" class="rowColor">
 232 <td class="colFirst"><code><a href="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 233 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MSAprobsWS.html#getResult-java.lang.String-">getResult</a></span>(java.lang.String&nbsp;jobId)</code>
 234 <div class="block">Return the result of the job.</div>
 235 </td>
 236 </tr>
 237 <tr id="i8" class="altColor">
 238 <td class="colFirst"><code><a href="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;</code></td>
 239 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MSAprobsWS.html#getRunnerOptions--">getRunnerOptions</a></span>()</code>
 240 <div class="block">Get options supported by a web service</div>
 241 </td>
 242 </tr>
 243 <tr id="i9" class="rowColor">
 244 <td class="colFirst"><code>(package private) <a href="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;</code></td>
 245 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MSAprobsWS.html#init-java.util.List-">init</a></span>(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;dataSet)</code>&nbsp;</td>
 246 </tr>
 247 <tr id="i10" class="altColor">
 248 <td class="colFirst"><code>java.lang.String</code></td>
 249 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MSAprobsWS.html#presetAlign-java.util.List-compbio.metadata.Preset-">presetAlign</a></span>(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 250            <a href="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;&nbsp;preset)</code>
 251 <div class="block">Align a list of sequences with preset.</div>
 252 </td>
 253 </tr>
 254 <tr id="i11" class="rowColor">
 255 <td class="colFirst"><code><a href="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</a></code></td>
 256 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MSAprobsWS.html#pullExecStatistics-java.lang.String-long-">pullExecStatistics</a></span>(java.lang.String&nbsp;jobId,
 257                   long&nbsp;position)</code>
 258 <div class="block">Reads 1kb chunk from the statistics file which is specific to a given web
 259  service from the <code>position</code>.</div>
 260 </td>
 261 </tr>
 262 </table>
 263 <ul class="blockList">
 264 <li class="blockList"><a name="methods.inherited.from.class.java.lang.Object">
 265 <!--   -->
 266 </a>
 267 <h3>Methods inherited from class&nbsp;java.lang.Object</h3>
 268 <code>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</code></li>
 269 </ul>
 270 </li>
 271 </ul>
 272 </li>
 273 </ul>
 274 </div>
 275 <div class="details">
 276 <ul class="blockList">
 277 <li class="blockList">
 278 <!-- ============ FIELD DETAIL =========== -->
 279 <ul class="blockList">
 280 <li class="blockList"><a name="field.detail">
 281 <!--   -->
 282 </a>
 283 <h3>Field Detail</h3>
 284 <a name="log">
 285 <!--   -->
 286 </a>
 287 <ul class="blockList">
 288 <li class="blockList">
 289 <h4>log</h4>
 290 <pre>private static&nbsp;org.apache.log4j.Logger log</pre>
 291 </li>
 292 </ul>
 293 <a name="MSAprobsOptions">
 294 <!--   -->
 295 </a>
 296 <ul class="blockList">
 297 <li class="blockList">
 298 <h4>MSAprobsOptions</h4>
 299 <pre>private static final&nbsp;<a href="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt; MSAprobsOptions</pre>
 300 </li>
 301 </ul>
 302 <a name="limitMan">
 303 <!--   -->
 304 </a>
 305 <ul class="blockListLast">
 306 <li class="blockList">
 307 <h4>limitMan</h4>
 308 <pre>private static final&nbsp;<a href="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt; limitMan</pre>
 309 </li>
 310 </ul>
 311 </li>
 312 </ul>
 313 <!-- ========= CONSTRUCTOR DETAIL ======== -->
 314 <ul class="blockList">
 315 <li class="blockList"><a name="constructor.detail">
 316 <!--   -->
 317 </a>
 318 <h3>Constructor Detail</h3>
 319 <a name="MSAprobsWS--">
 320 <!--   -->
 321 </a>
 322 <ul class="blockListLast">
 323 <li class="blockList">
 324 <h4>MSAprobsWS</h4>
 325 <pre>public&nbsp;MSAprobsWS()</pre>
 326 </li>
 327 </ul>
 328 </li>
 329 </ul>
 330 <!-- ============ METHOD DETAIL ========== -->
 331 <ul class="blockList">
 332 <li class="blockList"><a name="method.detail">
 333 <!--   -->
 334 </a>
 335 <h3>Method Detail</h3>
 336 <a name="align-java.util.List-">
 337 <!--   -->
 338 </a>
 339 <ul class="blockList">
 340 <li class="blockList">
 341 <h4>align</h4>
 342 <pre>public&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)
 343                        throws <a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></pre>
 344 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../compbio/data/msa/MsaWS.html#align-java.util.List-">MsaWS</a></code></span></div>
 345 <div class="block">Align a list of sequences with default settings.
 346
 347  Any dataset containing a greater number of sequences or when the average
 348  length of the sequences are greater then defined in the default Limit,
 349  will not be accepted for an alignment operation and
 350  JobSubmissionException will be thrown.</div>
 351 <dl>
 352 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 353 <dd><code><a href="../../../compbio/data/msa/MsaWS.html#align-java.util.List-">align</a></code>&nbsp;in interface&nbsp;<code><a href="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;</code></dd>
 354 <dt><span class="paramLabel">Parameters:</span></dt>
 355 <dd><code>sequences</code> - List of FastaSequence objects. The program does not perform
 356             any sequence validity checks. Nor does it checks whether the
 357             sequences names are unique. It is responsibility of the caller
 358             to make sure of this</dd>
 359 <dt><span class="returnLabel">Returns:</span></dt>
 360 <dd>jobId - unique identifier for the job</dd>
 361 <dt><span class="throwsLabel">Throws:</span></dt>
 362 <dd><code><a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></code> - is thrown when the job could not be submitted due to the
 363              following reasons: 1) The number of sequences in the
 364              submission or their average length is greater then defined by
 365              the default Limit. 2) Any problems on the server side e.g. it
 366              is misconfigured or malfunction, is reported via this
 367              exception. In the first case the information on the limit
 368              could be obtained from an exception.</dd>
 369 <dd><code><a href="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</a></code> - thrown if server OS does not support native executables for a
 370              given web service, e.g. JABAWS is deployed on Windows and
 371              Mafft service is called</dd>
 372 <dd><code><a href="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a></code> - is throw if the input sequences number or their average
 373              length exceeds what is defined by the limit</dd>
 374 </dl>
 375 </li>
 376 </ul>
 377 <a name="init-java.util.List-">
 378 <!--   -->
 379 </a>
 380 <ul class="blockList">
 381 <li class="blockList">
 382 <h4>init</h4>
 383 <pre><a href="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;&nbsp;init(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;dataSet)
 384                              throws <a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></pre>
 385 <dl>
 386 <dt><span class="throwsLabel">Throws:</span></dt>
 387 <dd><code><a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></code></dd>
 388 </dl>
 389 </li>
 390 </ul>
 391 <a name="customAlign-java.util.List-java.util.List-">
 392 <!--   -->
 393 </a>
 394 <ul class="blockList">
 395 <li class="blockList">
 396 <h4>customAlign</h4>
 397 <pre>public&nbsp;java.lang.String&nbsp;customAlign(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 398                                     java.util.List&lt;<a href="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;&gt;&nbsp;options)
 399                              throws <a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a>,
 400                                     <a href="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</a></pre>
 401 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../compbio/data/msa/MsaWS.html#customAlign-java.util.List-java.util.List-">MsaWS</a></code></span></div>
 402 <div class="block">Align a list of sequences with options.</div>
 403 <dl>
 404 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 405 <dd><code><a href="../../../compbio/data/msa/MsaWS.html#customAlign-java.util.List-java.util.List-">customAlign</a></code>&nbsp;in interface&nbsp;<code><a href="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;</code></dd>
 406 <dt><span class="paramLabel">Parameters:</span></dt>
 407 <dd><code>sequences</code> - List of FastaSequence objects. The programme does not perform
 408             any sequence validity checks. Nor does it checks whether the
 409             sequences names are unique. It is responsibility of the caller
 410             to validate this information</dd>
 411 <dd><code>options</code> - A list of Options</dd>
 412 <dt><span class="returnLabel">Returns:</span></dt>
 413 <dd>jobId - unique identifier for the job</dd>
 414 <dt><span class="throwsLabel">Throws:</span></dt>
 415 <dd><code><a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></code> - is thrown when the job could not be submitted due to the
 416              following reasons: 1) The number of sequences in the
 417              submission or their average length is greater then defined by
 418              the default Limit. 2) Any problems on the server side e.g. it
 419              is misconfigured or malfunction, is reported via this
 420              exception. In the first case the information on the limit
 421              could be obtained from an exception.</dd>
 422 <dd><code><a href="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</a></code> - thrown if server OS does not support native executables for a
 423              given web service, e.g. JABAWS is deployed on Windows and
 424              Mafft service is called</dd>
 425 <dd><code><a href="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a></code> - is throw if the input sequences number or their average
 426              length exceeds what is defined by the limit</dd>
 427 <dd><code><a href="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</a></code> - is throws when 1) One of the Options provided is not
 428              supported, 2) The value of the option is defined outside the
 429              boundaries. In both cases exception object contain the
 430              information on the violating Option.</dd>
 431 <dt><span class="seeLabel">See Also:</span></dt>
 432 <dd><a href="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><code>Default Limit is used to decide whether the calculation will be
 433       permitted or denied</code></a></dd>
 434 </dl>
 435 </li>
 436 </ul>
 437 <a name="presetAlign-java.util.List-compbio.metadata.Preset-">
 438 <!--   -->
 439 </a>
 440 <ul class="blockList">
 441 <li class="blockList">
 442 <h4>presetAlign</h4>
 443 <pre>public&nbsp;java.lang.String&nbsp;presetAlign(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 444                                     <a href="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;&nbsp;preset)
 445                              throws <a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a>,
 446                                     <a href="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</a></pre>
 447 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../compbio/data/msa/MsaWS.html#presetAlign-java.util.List-compbio.metadata.Preset-">MsaWS</a></code></span></div>
 448 <div class="block">Align a list of sequences with preset.
 449
 450  Limit for a presetName is used whether the calculation will be permitted
 451  or denied. If no Limit was defined for a presetName, than default limit
 452  is used.</div>
 453 <dl>
 454 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 455 <dd><code><a href="../../../compbio/data/msa/MsaWS.html#presetAlign-java.util.List-compbio.metadata.Preset-">presetAlign</a></code>&nbsp;in interface&nbsp;<code><a href="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;</code></dd>
 456 <dt><span class="paramLabel">Parameters:</span></dt>
 457 <dd><code>sequences</code> - List of FastaSequence objects. The programme does not perform
 458             any sequence validity checks. Nor does it checks whether the
 459             sequences names are unique. It is responsibility of the caller
 460             to validate this information</dd>
 461 <dd><code>preset</code> - A list of Options</dd>
 462 <dt><span class="returnLabel">Returns:</span></dt>
 463 <dd>String - jobId - unique identifier for the job</dd>
 464 <dt><span class="throwsLabel">Throws:</span></dt>
 465 <dd><code><a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></code> - is thrown when the job could not be submitted due to the
 466              following reasons: 1) The number of sequences in the
 467              submission or their average length is greater then defined by
 468              the default Limit. 2) Any problems on the server side e.g. it
 469              is misconfigured or malfunction, is reported via this
 470              exception. In the first case the information on the limit
 471              could be obtained from an exception.</dd>
 472 <dd><code><a href="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</a></code> - thrown if server OS does not support native executables for a
 473              given web service, e.g. JABAWS is deployed on Windows and
 474              Mafft service is called</dd>
 475 <dd><code><a href="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a></code> - is throw if the input sequences number or average length
 476              exceeds what is defined by the limit</dd>
 477 <dd><code><a href="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</a></code> - is throws when 1) One of the Options provided is not
 478              supported, 2) The value of the option is defined outside the
 479              boundaries. In both cases exception object contain the
 480              information on the violating Option.</dd>
 481 <dt><span class="seeLabel">See Also:</span></dt>
 482 <dd><a href="../../../compbio/metadata/Preset.html" title="class in compbio.metadata"><code>Preset</code></a></dd>
 483 </dl>
 484 </li>
 485 </ul>
 486 <a name="getResult-java.lang.String-">
 487 <!--   -->
 488 </a>
 489 <ul class="blockList">
 490 <li class="blockList">
 491 <h4>getResult</h4>
 492 <pre>public&nbsp;<a href="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a>&nbsp;getResult(java.lang.String&nbsp;jobId)
 493                     throws <a href="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</a></pre>
 494 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../compbio/data/msa/MsaWS.html#getResult-java.lang.String-">MsaWS</a></code></span></div>
 495 <div class="block">Return the result of the job. This method waits for the job
 496  <code>jobId</code> to complete before return.</div>
 497 <dl>
 498 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 499 <dd><code><a href="../../../compbio/data/msa/MsaWS.html#getResult-java.lang.String-">getResult</a></code>&nbsp;in interface&nbsp;<code><a href="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;</code></dd>
 500 <dt><span class="paramLabel">Parameters:</span></dt>
 501 <dd><code>jobId</code> - a unique job identifier</dd>
 502 <dt><span class="returnLabel">Returns:</span></dt>
 503 <dd>Alignment</dd>
 504 <dt><span class="throwsLabel">Throws:</span></dt>
 505 <dd><code><a href="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</a></code> - this exception is throw if the job execution was not
 506              successful or the result of the execution could not be found.
 507              (e.g. removed). Exception could also be thrown due to the
 508              lower level problems on the server i.e. IOException,
 509              FileNotFoundException problems as well as
 510              UnknownFileFormatException.</dd>
 511 </dl>
 512 </li>
 513 </ul>
 514 <a name="getLimit-java.lang.String-">
 515 <!--   -->
 516 </a>
 517 <ul class="blockList">
 518 <li class="blockList">
 519 <h4>getLimit</h4>
 520 <pre>public&nbsp;<a href="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;&nbsp;getLimit(java.lang.String&nbsp;presetName)</pre>
 521 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../compbio/data/msa/Metadata.html#getLimit-java.lang.String-">Metadata</a></code></span></div>
 522 <div class="block">Get a Limit for a preset.</div>
 523 <dl>
 524 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 525 <dd><code><a href="../../../compbio/data/msa/Metadata.html#getLimit-java.lang.String-">getLimit</a></code>&nbsp;in interface&nbsp;<code><a href="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;</code></dd>
 526 <dt><span class="paramLabel">Parameters:</span></dt>
 527 <dd><code>presetName</code> - the name of the preset. if no name is provided, then the
 528             default preset is returned. If no limit for a particular
 529             preset is defined then the default preset is returned</dd>
 530 <dt><span class="returnLabel">Returns:</span></dt>
 531 <dd>Limit</dd>
 532 </dl>
 533 </li>
 534 </ul>
 535 <a name="getLimits--">
 536 <!--   -->
 537 </a>
 538 <ul class="blockList">
 539 <li class="blockList">
 540 <h4>getLimits</h4>
 541 <pre>public&nbsp;<a href="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;&nbsp;getLimits()</pre>
 542 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../compbio/data/msa/Metadata.html#getLimits--">Metadata</a></code></span></div>
 543 <div class="block">List Limits supported by a web service.</div>
 544 <dl>
 545 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 546 <dd><code><a href="../../../compbio/data/msa/Metadata.html#getLimits--">getLimits</a></code>&nbsp;in interface&nbsp;<code><a href="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;</code></dd>
 547 <dt><span class="returnLabel">Returns:</span></dt>
 548 <dd>LimitManager</dd>
 549 </dl>
 550 </li>
 551 </ul>
 552 <a name="pullExecStatistics-java.lang.String-long-">
 553 <!--   -->
 554 </a>
 555 <ul class="blockList">
 556 <li class="blockList">
 557 <h4>pullExecStatistics</h4>
 558 <pre>public&nbsp;<a href="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</a>&nbsp;pullExecStatistics(java.lang.String&nbsp;jobId,
 559                                       long&nbsp;position)</pre>
 560 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../compbio/data/msa/JManagement.html#pullExecStatistics-java.lang.String-long-">JManagement</a></code></span></div>
 561 <div class="block">Reads 1kb chunk from the statistics file which is specific to a given web
 562  service from the <code>position</code>. If in time of a request less then
 563  1kb data is available from the position to the end of the file, then it
 564  returns all the data available from the position to the end of the file.</div>
 565 <dl>
 566 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 567 <dd><code><a href="../../../compbio/data/msa/JManagement.html#pullExecStatistics-java.lang.String-long-">pullExecStatistics</a></code>&nbsp;in interface&nbsp;<code><a href="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</a></code></dd>
 568 <dt><span class="paramLabel">Parameters:</span></dt>
 569 <dd><code>jobId</code> - - unique job identifier</dd>
 570 <dd><code>position</code> - - next position within the file to read</dd>
 571 <dt><span class="returnLabel">Returns:</span></dt>
 572 <dd>ChunkHolder - which contains a chunk of data and a next position
 573          within the file from which no data has been read</dd>
 574 <dt><span class="seeLabel">See Also:</span></dt>
 575 <dd><a href="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><code>ChunkHolder</code></a></dd>
 576 </dl>
 577 </li>
 578 </ul>
 579 <a name="cancelJob-java.lang.String-">
 580 <!--   -->
 581 </a>
 582 <ul class="blockList">
 583 <li class="blockList">
 584 <h4>cancelJob</h4>
 585 <pre>public&nbsp;boolean&nbsp;cancelJob(java.lang.String&nbsp;jobId)</pre>
 586 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../compbio/data/msa/JManagement.html#cancelJob-java.lang.String-">JManagement</a></code></span></div>
 587 <div class="block">Stop running the job <code>jobId</code> but leave its output untouched</div>
 588 <dl>
 589 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 590 <dd><code><a href="../../../compbio/data/msa/JManagement.html#cancelJob-java.lang.String-">cancelJob</a></code>&nbsp;in interface&nbsp;<code><a href="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</a></code></dd>
 591 <dt><span class="returnLabel">Returns:</span></dt>
 592 <dd>true if job was cancelled successfully, false otherwise</dd>
 593 </dl>
 594 </li>
 595 </ul>
 596 <a name="getJobStatus-java.lang.String-">
 597 <!--   -->
 598 </a>
 599 <ul class="blockList">
 600 <li class="blockList">
 601 <h4>getJobStatus</h4>
 602 <pre>public&nbsp;<a href="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</a>&nbsp;getJobStatus(java.lang.String&nbsp;jobId)</pre>
 603 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../compbio/data/msa/JManagement.html#getJobStatus-java.lang.String-">JManagement</a></code></span></div>
 604 <div class="block">Return the status of the job.</div>
 605 <dl>
 606 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 607 <dd><code><a href="../../../compbio/data/msa/JManagement.html#getJobStatus-java.lang.String-">getJobStatus</a></code>&nbsp;in interface&nbsp;<code><a href="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</a></code></dd>
 608 <dt><span class="paramLabel">Parameters:</span></dt>
 609 <dd><code>jobId</code> - - unique job identifier</dd>
 610 <dt><span class="returnLabel">Returns:</span></dt>
 611 <dd>JobStatus - status of the job</dd>
 612 <dt><span class="seeLabel">See Also:</span></dt>
 613 <dd><a href="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><code>JobStatus</code></a></dd>
 614 </dl>
 615 </li>
 616 </ul>
 617 <a name="getPresets--">
 618 <!--   -->
 619 </a>
 620 <ul class="blockList">
 621 <li class="blockList">
 622 <h4>getPresets</h4>
 623 <pre>public&nbsp;<a href="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;&nbsp;getPresets()</pre>
 624 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../compbio/data/msa/Metadata.html#getPresets--">Metadata</a></code></span></div>
 625 <div class="block">Get presets supported by a web service</div>
 626 <dl>
 627 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 628 <dd><code><a href="../../../compbio/data/msa/Metadata.html#getPresets--">getPresets</a></code>&nbsp;in interface&nbsp;<code><a href="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;</code></dd>
 629 <dt><span class="returnLabel">Returns:</span></dt>
 630 <dd>PresetManager the object contains information about presets
 631          supported by a web service</dd>
 632 </dl>
 633 </li>
 634 </ul>
 635 <a name="getRunnerOptions--">
 636 <!--   -->
 637 </a>
 638 <ul class="blockListLast">
 639 <li class="blockList">
 640 <h4>getRunnerOptions</h4>
 641 <pre>public&nbsp;<a href="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;&nbsp;getRunnerOptions()</pre>
 642 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../compbio/data/msa/Metadata.html#getRunnerOptions--">Metadata</a></code></span></div>
 643 <div class="block">Get options supported by a web service</div>
 644 <dl>
 645 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 646 <dd><code><a href="../../../compbio/data/msa/Metadata.html#getRunnerOptions--">getRunnerOptions</a></code>&nbsp;in interface&nbsp;<code><a href="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</a>&lt;<a href="../../../compbio/runner/msa/MSAprobs.html" title="class in compbio.runner.msa">MSAprobs</a>&gt;</code></dd>
 647 <dt><span class="returnLabel">Returns:</span></dt>
 648 <dd>RunnerConfig the list of options and parameters supported by a
 649          web service.</dd>
 650 </dl>
 651 </li>
 652 </ul>
 653 </li>
 654 </ul>
 655 </li>
 656 </ul>
 657 </div>
 658 </div>
 659 <!-- ========= END OF CLASS DATA ========= -->
 660 <!-- ======= START OF BOTTOM NAVBAR ====== -->
 661 <div class="bottomNav"><a name="navbar.bottom">
 662 <!--   -->
 663 </a>
 664 <div class="skipNav"><a href="#skip.navbar.bottom" title="Skip navigation links">Skip navigation links</a></div>
 665 <a name="navbar.bottom.firstrow">
 666 <!--   -->
 667 </a>
 668 <ul class="navList" title="Navigation">
 669 <li><a href="../../../overview-summary.html">Overview</a></li>
 670 <li><a href="package-summary.html">Package</a></li>
 671 <li class="navBarCell1Rev">Class</li>
 672 <li><a href="class-use/MSAprobsWS.html">Use</a></li>
 673 <li><a href="package-tree.html">Tree</a></li>
 674 <li><a href="../../../deprecated-list.html">Deprecated</a></li>
 675 <li><a href="../../../index-files/index-1.html">Index</a></li>
 676 <li><a href="../../../help-doc.html">Help</a></li>
 677 </ul>
 678 </div>
 679 <div class="subNav">
 680 <ul class="navList">
 681 <li><a href="../../../compbio/ws/server/MainManager.html" title="class in compbio.ws.server"><span class="typeNameLink">Prev&nbsp;Class</span></a></li>
 682 <li><a href="../../../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server"><span class="typeNameLink">Next&nbsp;Class</span></a></li>
 683 </ul>
 684 <ul class="navList">
 685 <li><a href="../../../index.html?compbio/ws/server/MSAprobsWS.html" target="_top">Frames</a></li>
 686 <li><a href="MSAprobsWS.html" target="_top">No&nbsp;Frames</a></li>
 687 </ul>
 688 <ul class="navList" id="allclasses_navbar_bottom">
 689 <li><a href="../../../allclasses-noframe.html">All&nbsp;Classes</a></li>
 690 </ul>
 691 <div>
 692 <script type="text/javascript"><!--
 693   allClassesLink = document.getElementById("allclasses_navbar_bottom");
 694   if(window==top) {
 695     allClassesLink.style.display = "block";
 696   }
 697   else {
 698     allClassesLink.style.display = "none";
 699   }
 700   //-->
 701 </script>
 702 </div>
 703 <div>
 704 <ul class="subNavList">
 705 <li>Summary:&nbsp;</li>
 706 <li>Nested&nbsp;|&nbsp;</li>
 707 <li><a href="#field.summary">Field</a>&nbsp;|&nbsp;</li>
 708 <li><a href="#constructor.summary">Constr</a>&nbsp;|&nbsp;</li>
 709 <li><a href="#method.summary">Method</a></li>
 710 </ul>
 711 <ul class="subNavList">
 712 <li>Detail:&nbsp;</li>
 713 <li><a href="#field.detail">Field</a>&nbsp;|&nbsp;</li>
 714 <li><a href="#constructor.detail">Constr</a>&nbsp;|&nbsp;</li>
 715 <li><a href="#method.detail">Method</a></li>
 716 </ul>
 717 </div>
 718 <a name="skip.navbar.bottom">
 719 <!--   -->
 720 </a></div>
 721 <!-- ======== END OF BOTTOM NAVBAR ======= -->
 722 </body>
 723 </html>