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="2011-08-12">\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
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  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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  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 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\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 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></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; <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></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, java.lang.String, compbio.metadata.Limit)">align</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&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;logger,\r
 145       <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;callingMethod,\r
 146       <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;T&gt;&nbsp;limit)</CODE>\r
 147 \r
 148 <BR>\r
 149 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 150 </TR>\r
 151 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 152 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 153 <CODE>static\r
 154 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 155 <TR ALIGN="right" VALIGN="">\r
 156 <TD NOWRAP><FONT SIZE="-1">\r
 157 <CODE>&lt;T&gt; <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
 158 </TR>\r
 159 </TABLE>\r
 160 </CODE></FONT></TD>\r
 161 <TD><CODE><B><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></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 162         <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;&nbsp;confExec,\r
 163         org.apache.log4j.Logger&nbsp;log,\r
 164         <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;method,\r
 165         <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;T&gt;&nbsp;limit)</CODE>\r
 166 \r
 167 <BR>\r
 168 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 169 </TR>\r
 170 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 171 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 172 <CODE>static&nbsp;boolean</CODE></FONT></TD>\r
 173 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#cancelJob(java.lang.String)">cancelJob</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;jobId)</CODE>\r
 174 \r
 175 <BR>\r
 176 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 177 </TR>\r
 178 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 179 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 180 <CODE>static\r
 181 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 182 <TR ALIGN="right" VALIGN="">\r
 183 <TD NOWRAP><FONT SIZE="-1">\r
 184 <CODE>&lt;T&gt; <A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>\r
 185 </TR>\r
 186 </TABLE>\r
 187 </CODE></FONT></TD>\r
 188 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#getAnnotation(java.lang.String, org.apache.log4j.Logger)">getAnnotation</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;jobId,\r
 189               org.apache.log4j.Logger&nbsp;log)</CODE>\r
 190 \r
 191 <BR>\r
 192 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 193 </TR>\r
 194 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 195 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 196 <CODE>static\r
 197 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 198 <TR ALIGN="right" VALIGN="">\r
 199 <TD NOWRAP><FONT SIZE="-1">\r
 200 <CODE>&lt;T&gt; <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&gt;</CODE></FONT></TD>\r
 201 </TR>\r
 202 </TABLE>\r
 203 </CODE></FONT></TD>\r
 204 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#getCommands(java.util.List, java.lang.String)">getCommands</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;T&gt;&gt;&nbsp;options,\r
 205             <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;keyValueSeparator)</CODE>\r
 206 \r
 207 <BR>\r
 208 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 209 </TR>\r
 210 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 211 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 212 <CODE>static&nbsp;<A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></FONT></TD>\r
 213 <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
 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;<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
 221 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;jobId)</CODE>\r
 222 \r
 223 <BR>\r
 224 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 225 </TR>\r
 226 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 227 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 228 <CODE>static&nbsp;byte</CODE></FONT></TD>\r
 229 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#getProgress(java.lang.String)">getProgress</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;jobId)</CODE>\r
 230 \r
 231 <BR>\r
 232 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 233 </TR>\r
 234 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 235 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 236 <CODE>static&nbsp;<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
 237 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#pullFile(java.lang.String, long)">pullFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;file,\r
 238          long&nbsp;position)</CODE>\r
 239 \r
 240 <BR>\r
 241 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 242 </TR>\r
 243 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 244 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 245 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 246 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#validateAAConInput(java.util.List)">validateAAConInput</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
 247 \r
 248 <BR>\r
 249 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 250 </TR>\r
 251 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 252 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 253 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 254 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#validateFastaInput(java.util.List)">validateFastaInput</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
 255 \r
 256 <BR>\r
 257 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 258 </TR>\r
 259 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 260 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 261 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 262 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#validateJobId(java.lang.String)">validateJobId</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;jobId)</CODE>\r
 263 \r
 264 <BR>\r
 265 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 266 </TR>\r
 267 </TABLE>\r
 268 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 269 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 270 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 271 <TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
 272 </TR>\r
 273 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 274 <TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
 275 </TR>\r
 276 </TABLE>\r
 277 &nbsp;\r
 278 <P>\r
 279 \r
 280 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 281 \r
 282 <A NAME="constructor_detail"><!-- --></A>\r
 283 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 284 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 285 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 286 <B>Constructor Detail</B></FONT></TH>\r
 287 </TR>\r
 288 </TABLE>\r
 289 \r
 290 <A NAME="WSUtil()"><!-- --></A><H3>\r
 291 WSUtil</H3>\r
 292 <PRE>\r
 293 public <B>WSUtil</B>()</PRE>\r
 294 <DL>\r
 295 </DL>\r
 296 \r
 297 <!-- ============ METHOD DETAIL ========== -->\r
 298 \r
 299 <A NAME="method_detail"><!-- --></A>\r
 300 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 301 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 302 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 303 <B>Method Detail</B></FONT></TH>\r
 304 </TR>\r
 305 </TABLE>\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>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;jobId)\r
 311                                 throws <A HREF="http://java.sun.com/javase/6/docs/api/java/security/InvalidParameterException.html?is-external=true" title="class or interface in java.security">InvalidParameterException</A></PRE>\r
 312 <DL>\r
 313 <DD><DL>\r
 314 \r
 315 <DT><B>Throws:</B>\r
 316 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/security/InvalidParameterException.html?is-external=true" title="class or interface in java.security">InvalidParameterException</A></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>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)\r
 325                                      throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
 326 <DL>\r
 327 <DD><DL>\r
 328 \r
 329 <DT><B>Throws:</B>\r
 330 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
 331 </DD>\r
 332 </DL>\r
 333 <HR>\r
 334 \r
 335 <A NAME="getJobStatus(java.lang.String)"><!-- --></A><H3>\r
 336 getJobStatus</H3>\r
 337 <PRE>\r
 338 public static <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;jobId)</PRE>\r
 339 <DL>\r
 340 <DD><DL>\r
 341 </DL>\r
 342 </DD>\r
 343 </DL>\r
 344 <HR>\r
 345 \r
 346 <A NAME="pullFile(java.lang.String, long)"><!-- --></A><H3>\r
 347 pullFile</H3>\r
 348 <PRE>\r
 349 public static <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> <B>pullFile</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;file,\r
 350                                    long&nbsp;position)</PRE>\r
 351 <DL>\r
 352 <DD><DL>\r
 353 </DL>\r
 354 </DD>\r
 355 </DL>\r
 356 <HR>\r
 357 \r
 358 <A NAME="getProgress(java.lang.String)"><!-- --></A><H3>\r
 359 getProgress</H3>\r
 360 <PRE>\r
 361 public static byte <B>getProgress</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;jobId)</PRE>\r
 362 <DL>\r
 363 <DD><DL>\r
 364 </DL>\r
 365 </DD>\r
 366 </DL>\r
 367 <HR>\r
 368 \r
 369 <A NAME="getEngine(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
 370 getEngine</H3>\r
 371 <PRE>\r
 372 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
 373 <DL>\r
 374 <DD><DL>\r
 375 </DL>\r
 376 </DD>\r
 377 </DL>\r
 378 <HR>\r
 379 \r
 380 <A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>\r
 381 cancelJob</H3>\r
 382 <PRE>\r
 383 public static boolean <B>cancelJob</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;jobId)</PRE>\r
 384 <DL>\r
 385 <DD><DL>\r
 386 </DL>\r
 387 </DD>\r
 388 </DL>\r
 389 <HR>\r
 390 \r
 391 <A NAME="align(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, java.lang.String, compbio.metadata.Limit)"><!-- --></A><H3>\r
 392 align</H3>\r
 393 <PRE>\r
 394 public static &lt;T&gt; <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>align</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 395                                <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;&nbsp;confExec,\r
 396                                org.apache.log4j.Logger&nbsp;logger,\r
 397                                <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;callingMethod,\r
 398                                <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;T&gt;&nbsp;limit)\r
 399                     throws <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,\r
 400                            <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
 401 <DL>\r
 402 <DD><DL>\r
 403 \r
 404 <DT><B>Throws:</B>\r
 405 <DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE>\r
 406 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
 407 </DD>\r
 408 </DL>\r
 409 <HR>\r
 410 \r
 411 <A NAME="analize(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, java.lang.String, compbio.metadata.Limit)"><!-- --></A><H3>\r
 412 analize</H3>\r
 413 <PRE>\r
 414 public static &lt;T&gt; <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>analize</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
 415                                  <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;&nbsp;confExec,\r
 416                                  org.apache.log4j.Logger&nbsp;log,\r
 417                                  <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;method,\r
 418                                  <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;T&gt;&nbsp;limit)\r
 419                       throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
 420 <DL>\r
 421 <DD><DL>\r
 422 \r
 423 <DT><B>Throws:</B>\r
 424 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
 425 </DD>\r
 426 </DL>\r
 427 <HR>\r
 428 \r
 429 <A NAME="getCommands(java.util.List, java.lang.String)"><!-- --></A><H3>\r
 430 getCommands</H3>\r
 431 <PRE>\r
 432 public static final &lt;T&gt; <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&gt; <B>getCommands</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;T&gt;&gt;&nbsp;options,\r
 433                                                  <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;keyValueSeparator)</PRE>\r
 434 <DL>\r
 435 <DD><DL>\r
 436 </DL>\r
 437 </DD>\r
 438 </DL>\r
 439 <HR>\r
 440 \r
 441 <A NAME="validateAAConInput(java.util.List)"><!-- --></A><H3>\r
 442 validateAAConInput</H3>\r
 443 <PRE>\r
 444 public static void <B>validateAAConInput</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)\r
 445                                throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
 446 <DL>\r
 447 <DD><DL>\r
 448 \r
 449 <DT><B>Throws:</B>\r
 450 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
 451 </DD>\r
 452 </DL>\r
 453 <HR>\r
 454 \r
 455 <A NAME="getAnnotation(java.lang.String, org.apache.log4j.Logger)"><!-- --></A><H3>\r
 456 getAnnotation</H3>\r
 457 <PRE>\r
 458 public static &lt;T&gt; <A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A> <B>getAnnotation</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;jobId,\r
 459                                              org.apache.log4j.Logger&nbsp;log)\r
 460                                   throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 461 <DL>\r
 462 <DD><DL>\r
 463 \r
 464 <DT><B>Throws:</B>\r
 465 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
 466 </DD>\r
 467 </DL>\r
 468 <!-- ========= END OF CLASS DATA ========= -->\r
 469 <HR>\r
 470 \r
 471 \r
 472 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 473 <A NAME="navbar_bottom"><!-- --></A>\r
 474 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 475 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 476 <TR>\r
 477 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 478 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 479 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 480   <TR ALIGN="center" VALIGN="top">\r
 481   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 482   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 483   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 484   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/WSUtil.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 485   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 486   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 487   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 488   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 489   </TR>\r
 490 </TABLE>\r
 491 </TD>\r
 492 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 493 </EM>\r
 494 </TD>\r
 495 </TR>\r
 496 \r
 497 <TR>\r
 498 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 499 &nbsp;<A HREF="../../../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server"><B>PREV CLASS</B></A>&nbsp;\r
 500 &nbsp;NEXT CLASS</FONT></TD>\r
 501 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 502   <A HREF="../../../index.html?compbio/ws/server/WSUtil.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 503 &nbsp;<A HREF="WSUtil.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 504 &nbsp;<SCRIPT type="text/javascript">\r
 505   <!--\r
 506   if(window==top) {\r
 507     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 508   }\r
 509   //-->\r
 510 </SCRIPT>\r
 511 <NOSCRIPT>\r
 512   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 513 </NOSCRIPT>\r
 514 \r
 515 \r
 516 </FONT></TD>\r
 517 </TR>\r
 518 <TR>\r
 519 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 520   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
 521 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 522 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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 524 </TABLE>\r
 525 <A NAME="skip-navbar_bottom"></A>\r
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 527 \r
 528 <HR>\r
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 530 </BODY>\r
 531 </HTML>\r