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

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   7 WSUtil\r
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   9 \r
  10 <META NAME="date" CONTENT="2010-02-17">\r
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  16 {\r
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  18         parent.document.title="WSUtil";\r
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  58 &nbsp;<A HREF="../../../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server"><B>PREV CLASS</B></A>&nbsp;\r
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  79   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
  80 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
  81 DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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  85 <!-- ========= END OF TOP NAVBAR ========= -->\r
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  88 <!-- ======== START OF CLASS DATA ======== -->\r
  89 <H2>\r
  90 <FONT SIZE="-1">\r
  91 compbio.ws.server</FONT>\r
  92 <BR>\r
  93 Class WSUtil</H2>\r
  94 <PRE>\r
  95 java.lang.Object\r
  96   <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.server.WSUtil</B>\r
  97 </PRE>\r
  98 <HR>\r
  99 <DL>\r
 100 <DT><PRE>public final class <B>WSUtil</B><DT>extends java.lang.Object</DL>\r
 101 </PRE>\r
 102 \r
 103 <P>\r
 104 <HR>\r
 105 \r
 106 <P>\r
 107 \r
 108 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 109 \r
 110 <A NAME="constructor_summary"><!-- --></A>\r
 111 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 112 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 113 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 114 <B>Constructor Summary</B></FONT></TH>\r
 115 </TR>\r
 116 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 117 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#WSUtil()">WSUtil</A></B>()</CODE>\r
 118 \r
 119 <BR>\r
 120 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 121 </TR>\r
 122 </TABLE>\r
 123 &nbsp;\r
 124 <!-- ========== METHOD SUMMARY =========== -->\r
 125 \r
 126 <A NAME="method_summary"><!-- --></A>\r
 127 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 128 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 129 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 130 <B>Method Summary</B></FONT></TH>\r
 131 </TR>\r
 132 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 133 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 134 <CODE>static\r
 135 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 136 <TR ALIGN="right" VALIGN="">\r
 137 <TD NOWRAP><FONT SIZE="-1">\r
 138 <CODE>&lt;T&gt; java.lang.String</CODE></FONT></TD>\r
 139 </TR>\r
 140 </TABLE>\r
 141 </CODE></FONT></TD>\r
 142 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#align(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String, compbio.metadata.Limit)">align</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 143       <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;&nbsp;confExec,\r
 144       org.apache.log4j.Logger&nbsp;statLog,\r
 145       javax.xml.ws.WebServiceContext&nbsp;wsContext,\r
 146       java.lang.String&nbsp;callingMethod,\r
 147       <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;T&gt;&nbsp;limit)</CODE>\r
 148 \r
 149 <BR>\r
 150 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 151 </TR>\r
 152 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 153 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 154 <CODE>static&nbsp;boolean</CODE></FONT></TD>\r
 155 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#cancelJob(java.lang.String)">cancelJob</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
 156 \r
 157 <BR>\r
 158 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 159 </TR>\r
 160 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 161 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 162 <CODE>static\r
 163 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 164 <TR ALIGN="right" VALIGN="">\r
 165 <TD NOWRAP><FONT SIZE="-1">\r
 166 <CODE>&lt;T&gt; java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
 167 </TR>\r
 168 </TABLE>\r
 169 </CODE></FONT></TD>\r
 170 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#getCommands(java.util.List, java.lang.String)">getCommands</A></B>(java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;T&gt;&gt;&nbsp;options,\r
 171             java.lang.String&nbsp;keyValueSeparator)</CODE>\r
 172 \r
 173 <BR>\r
 174 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 175 </TR>\r
 176 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 177 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 178 <CODE>static&nbsp;<A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></FONT></TD>\r
 179 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#getEngine(compbio.engine.client.ConfiguredExecutable)">getEngine</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;confClustal)</CODE>\r
 180 \r
 181 <BR>\r
 182 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 183 </TR>\r
 184 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 185 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 186 <CODE>static&nbsp;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
 187 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
 188 \r
 189 <BR>\r
 190 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 191 </TR>\r
 192 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 193 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 194 <CODE>static&nbsp;byte</CODE></FONT></TD>\r
 195 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#getProgress(java.lang.String)">getProgress</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
 196 \r
 197 <BR>\r
 198 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 199 </TR>\r
 200 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 201 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 202 <CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
 203 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#getRemoteAddress(javax.xml.ws.WebServiceContext)">getRemoteAddress</A></B>(javax.xml.ws.WebServiceContext&nbsp;wsContext)</CODE>\r
 204 \r
 205 <BR>\r
 206 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 207 </TR>\r
 208 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 209 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 210 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 211 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#log(org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String)">log</A></B>(org.apache.log4j.Logger&nbsp;statLog,\r
 212     javax.xml.ws.WebServiceContext&nbsp;wsContext,\r
 213     java.lang.String&nbsp;activity)</CODE>\r
 214 \r
 215 <BR>\r
 216 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 217 </TR>\r
 218 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 219 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 220 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 221 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#log(org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String, java.lang.String)">log</A></B>(org.apache.log4j.Logger&nbsp;statLog,\r
 222     javax.xml.ws.WebServiceContext&nbsp;wsContext,\r
 223     java.lang.String&nbsp;jobId,\r
 224     java.lang.String&nbsp;activity)</CODE>\r
 225 \r
 226 <BR>\r
 227 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 228 </TR>\r
 229 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 230 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 231 <CODE>static&nbsp;<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
 232 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#pullFile(java.lang.String, long)">pullFile</A></B>(java.lang.String&nbsp;jobId,\r
 233          long&nbsp;position)</CODE>\r
 234 \r
 235 <BR>\r
 236 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 237 </TR>\r
 238 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 239 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 240 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 241 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#validateFastaInput(java.util.List)">validateFastaInput</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
 242 \r
 243 <BR>\r
 244 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 245 </TR>\r
 246 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 247 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 248 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 249 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#validateJobId(java.lang.String)">validateJobId</A></B>(java.lang.String&nbsp;jobId)</CODE>\r
 250 \r
 251 <BR>\r
 252 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 253 </TR>\r
 254 </TABLE>\r
 255 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 256 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 257 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 258 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
 259 </TR>\r
 260 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 261 <TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
 262 </TR>\r
 263 </TABLE>\r
 264 &nbsp;\r
 265 <P>\r
 266 \r
 267 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 268 \r
 269 <A NAME="constructor_detail"><!-- --></A>\r
 270 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 271 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 272 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 273 <B>Constructor Detail</B></FONT></TH>\r
 274 </TR>\r
 275 </TABLE>\r
 276 \r
 277 <A NAME="WSUtil()"><!-- --></A><H3>\r
 278 WSUtil</H3>\r
 279 <PRE>\r
 280 public <B>WSUtil</B>()</PRE>\r
 281 <DL>\r
 282 </DL>\r
 283 \r
 284 <!-- ============ METHOD DETAIL ========== -->\r
 285 \r
 286 <A NAME="method_detail"><!-- --></A>\r
 287 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 288 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 289 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 290 <B>Method Detail</B></FONT></TH>\r
 291 </TR>\r
 292 </TABLE>\r
 293 \r
 294 <A NAME="log(org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String)"><!-- --></A><H3>\r
 295 log</H3>\r
 296 <PRE>\r
 297 public static void <B>log</B>(org.apache.log4j.Logger&nbsp;statLog,\r
 298                        javax.xml.ws.WebServiceContext&nbsp;wsContext,\r
 299                        java.lang.String&nbsp;activity)</PRE>\r
 300 <DL>\r
 301 <DD><DL>\r
 302 </DL>\r
 303 </DD>\r
 304 </DL>\r
 305 <HR>\r
 306 \r
 307 <A NAME="validateJobId(java.lang.String)"><!-- --></A><H3>\r
 308 validateJobId</H3>\r
 309 <PRE>\r
 310 public static final void <B>validateJobId</B>(java.lang.String&nbsp;jobId)\r
 311                                 throws java.security.InvalidParameterException</PRE>\r
 312 <DL>\r
 313 <DD><DL>\r
 314 \r
 315 <DT><B>Throws:</B>\r
 316 <DD><CODE>java.security.InvalidParameterException</CODE></DL>\r
 317 </DD>\r
 318 </DL>\r
 319 <HR>\r
 320 \r
 321 <A NAME="validateFastaInput(java.util.List)"><!-- --></A><H3>\r
 322 validateFastaInput</H3>\r
 323 <PRE>\r
 324 public static final void <B>validateFastaInput</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)\r
 325                                      throws java.security.InvalidParameterException</PRE>\r
 326 <DL>\r
 327 <DD><DL>\r
 328 \r
 329 <DT><B>Throws:</B>\r
 330 <DD><CODE>java.security.InvalidParameterException</CODE></DL>\r
 331 </DD>\r
 332 </DL>\r
 333 <HR>\r
 334 \r
 335 <A NAME="log(org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String, java.lang.String)"><!-- --></A><H3>\r
 336 log</H3>\r
 337 <PRE>\r
 338 public static void <B>log</B>(org.apache.log4j.Logger&nbsp;statLog,\r
 339                        javax.xml.ws.WebServiceContext&nbsp;wsContext,\r
 340                        java.lang.String&nbsp;jobId,\r
 341                        java.lang.String&nbsp;activity)</PRE>\r
 342 <DL>\r
 343 <DD><DL>\r
 344 </DL>\r
 345 </DD>\r
 346 </DL>\r
 347 <HR>\r
 348 \r
 349 <A NAME="getJobStatus(java.lang.String)"><!-- --></A><H3>\r
 350 getJobStatus</H3>\r
 351 <PRE>\r
 352 public static <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>(java.lang.String&nbsp;jobId)</PRE>\r
 353 <DL>\r
 354 <DD><DL>\r
 355 </DL>\r
 356 </DD>\r
 357 </DL>\r
 358 <HR>\r
 359 \r
 360 <A NAME="pullFile(java.lang.String, long)"><!-- --></A><H3>\r
 361 pullFile</H3>\r
 362 <PRE>\r
 363 public static <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> <B>pullFile</B>(java.lang.String&nbsp;jobId,\r
 364                                    long&nbsp;position)</PRE>\r
 365 <DL>\r
 366 <DD><DL>\r
 367 </DL>\r
 368 </DD>\r
 369 </DL>\r
 370 <HR>\r
 371 \r
 372 <A NAME="getProgress(java.lang.String)"><!-- --></A><H3>\r
 373 getProgress</H3>\r
 374 <PRE>\r
 375 public static byte <B>getProgress</B>(java.lang.String&nbsp;jobId)</PRE>\r
 376 <DL>\r
 377 <DD><DL>\r
 378 </DL>\r
 379 </DD>\r
 380 </DL>\r
 381 <HR>\r
 382 \r
 383 <A NAME="getEngine(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
 384 getEngine</H3>\r
 385 <PRE>\r
 386 public static <A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A> <B>getEngine</B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;confClustal)</PRE>\r
 387 <DL>\r
 388 <DD><DL>\r
 389 </DL>\r
 390 </DD>\r
 391 </DL>\r
 392 <HR>\r
 393 \r
 394 <A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>\r
 395 cancelJob</H3>\r
 396 <PRE>\r
 397 public static boolean <B>cancelJob</B>(java.lang.String&nbsp;jobId)</PRE>\r
 398 <DL>\r
 399 <DD><DL>\r
 400 </DL>\r
 401 </DD>\r
 402 </DL>\r
 403 <HR>\r
 404 \r
 405 <A NAME="getRemoteAddress(javax.xml.ws.WebServiceContext)"><!-- --></A><H3>\r
 406 getRemoteAddress</H3>\r
 407 <PRE>\r
 408 public static java.lang.String <B>getRemoteAddress</B>(javax.xml.ws.WebServiceContext&nbsp;wsContext)</PRE>\r
 409 <DL>\r
 410 <DD><DL>\r
 411 </DL>\r
 412 </DD>\r
 413 </DL>\r
 414 <HR>\r
 415 \r
 416 <A NAME="align(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String, compbio.metadata.Limit)"><!-- --></A><H3>\r
 417 align</H3>\r
 418 <PRE>\r
 419 public static &lt;T&gt; java.lang.String <B>align</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 420                                          <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;&nbsp;confExec,\r
 421                                          org.apache.log4j.Logger&nbsp;statLog,\r
 422                                          javax.xml.ws.WebServiceContext&nbsp;wsContext,\r
 423                                          java.lang.String&nbsp;callingMethod,\r
 424                                          <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;T&gt;&nbsp;limit)\r
 425                               throws <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,\r
 426                                      <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
 427 <DL>\r
 428 <DD><DL>\r
 429 \r
 430 <DT><B>Throws:</B>\r
 431 <DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE>\r
 432 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
 433 </DD>\r
 434 </DL>\r
 435 <HR>\r
 436 \r
 437 <A NAME="getCommands(java.util.List, java.lang.String)"><!-- --></A><H3>\r
 438 getCommands</H3>\r
 439 <PRE>\r
 440 public static final &lt;T&gt; java.util.List&lt;java.lang.String&gt; <B>getCommands</B>(java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;T&gt;&gt;&nbsp;options,\r
 441                                                                      java.lang.String&nbsp;keyValueSeparator)</PRE>\r
 442 <DL>\r
 443 <DD><DL>\r
 444 </DL>\r
 445 </DD>\r
 446 </DL>\r
 447 <!-- ========= END OF CLASS DATA ========= -->\r
 448 <HR>\r
 449 \r
 450 \r
 451 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 452 <A NAME="navbar_bottom"><!-- --></A>\r
 453 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 454 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 455 <TR>\r
 456 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 457 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 458 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 459   <TR ALIGN="center" VALIGN="top">\r
 460   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 461   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 462   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 463   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/WSUtil.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 464   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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 467   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 468   </TR>\r
 469 </TABLE>\r
 470 </TD>\r
 471 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 472 </EM>\r
 473 </TD>\r
 474 </TR>\r
 475 \r
 476 <TR>\r
 477 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 478 &nbsp;<A HREF="../../../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server"><B>PREV CLASS</B></A>&nbsp;\r
 479 &nbsp;NEXT CLASS</FONT></TD>\r
 480 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 481   <A HREF="../../../index.html?compbio/ws/server/WSUtil.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 482 &nbsp;<A HREF="WSUtil.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 483 &nbsp;<SCRIPT type="text/javascript">\r
 484   <!--\r
 485   if(window==top) {\r
 486     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 487   }\r
 488   //-->\r
 489 </SCRIPT>\r
 490 <NOSCRIPT>\r
 491   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 492 </NOSCRIPT>\r
 493 \r
 494 \r
 495 </FONT></TD>\r
 496 </TR>\r
 497 <TR>\r
 498 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 499   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
 500 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 501 DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
 502 </TR>\r
 503 </TABLE>\r
 504 <A NAME="skip-navbar_bottom"></A>\r
 505 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 506 \r
 507 <HR>\r
 508 \r
 509 </BODY>\r
 510 </HTML>\r