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   7 Util\r
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  79   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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  91 compbio.runner</FONT>\r
  92 <BR>\r
  93 Class Util</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.runner.Util</B>\r
  97 </PRE>\r
  98 <HR>\r
  99 <DL>\r
 100 <DT><PRE>public final class <B>Util</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 <!-- =========== FIELD SUMMARY =========== -->\r
 108 \r
 109 <A NAME="field_summary"><!-- --></A>\r
 110 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 111 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 112 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 113 <B>Field Summary</B></FONT></TH>\r
 114 </TR>\r
 115 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 116 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 117 <CODE>static&nbsp;org.apache.log4j.Logger</CODE></FONT></TD>\r
 118 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#log">log</A></B></CODE>\r
 119 \r
 120 <BR>\r
 121 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 122 </TR>\r
 123 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 124 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 125 <CODE>static&nbsp;<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
 126 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#SPACE">SPACE</A></B></CODE>\r
 127 \r
 128 <BR>\r
 129 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 130 </TR>\r
 131 </TABLE>\r
 132 &nbsp;\r
 133 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 134 \r
 135 <A NAME="constructor_summary"><!-- --></A>\r
 136 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 137 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 138 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 139 <B>Constructor Summary</B></FONT></TH>\r
 140 </TR>\r
 141 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 142 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#Util()">Util</A></B>()</CODE>\r
 143 \r
 144 <BR>\r
 145 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 146 </TR>\r
 147 </TABLE>\r
 148 &nbsp;\r
 149 <!-- ========== METHOD SUMMARY =========== -->\r
 150 \r
 151 <A NAME="method_summary"><!-- --></A>\r
 152 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 153 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 154 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 155 <B>Method Summary</B></FONT></TH>\r
 156 </TR>\r
 157 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 158 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 159 <CODE>static\r
 160 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 161 <TR ALIGN="right" VALIGN="">\r
 162 <TD NOWRAP><FONT SIZE="-1">\r
 163 <CODE>&lt;T&gt; <A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;T&gt;</CODE></FONT></TD>\r
 164 </TR>\r
 165 </TABLE>\r
 166 </CODE></FONT></TD>\r
 167 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#getPresets(java.lang.Class)">getPresets</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A>&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</CODE>\r
 168 \r
 169 <BR>\r
 170 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 171 </TR>\r
 172 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 173 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 174 <CODE>static\r
 175 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 176 <TR ALIGN="right" VALIGN="">\r
 177 <TD NOWRAP><FONT SIZE="-1">\r
 178 <CODE>&lt;T&gt; <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;T&gt;</CODE></FONT></TD>\r
 179 </TR>\r
 180 </TABLE>\r
 181 </CODE></FONT></TD>\r
 182 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#getSupportedOptions(java.lang.Class)">getSupportedOptions</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A>&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</CODE>\r
 183 \r
 184 <BR>\r
 185 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 186 </TR>\r
 187 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 188 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 189 <CODE>static&nbsp;<A HREF="../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
 190 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#readClustalFile(java.lang.String, java.lang.String)">readClustalFile</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;workDirectory,\r
 191                 <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;clustFile)</CODE>\r
 192 \r
 193 <BR>\r
 194 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 195 </TR>\r
 196 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 197 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 198 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</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>,<A HREF="../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</CODE></FONT></TD>\r
 199 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#readJronnFile(java.lang.String, java.lang.String)">readJronnFile</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;workDirectory,\r
 200               <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;clustFile)</CODE>\r
 201 \r
 202 <BR>\r
 203 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 204 </TR>\r
 205 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 206 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 207 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 208 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#writeInput(java.util.List, compbio.engine.client.ConfiguredExecutable)">writeInput</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
 209            <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;exec)</CODE>\r
 210 \r
 211 <BR>\r
 212 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 213 </TR>\r
 214 </TABLE>\r
 215 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 216 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 217 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 218 <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
 219 </TR>\r
 220 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 221 <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
 222 </TR>\r
 223 </TABLE>\r
 224 &nbsp;\r
 225 <P>\r
 226 \r
 227 <!-- ============ FIELD DETAIL =========== -->\r
 228 \r
 229 <A NAME="field_detail"><!-- --></A>\r
 230 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 231 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 232 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 233 <B>Field Detail</B></FONT></TH>\r
 234 </TR>\r
 235 </TABLE>\r
 236 \r
 237 <A NAME="log"><!-- --></A><H3>\r
 238 log</H3>\r
 239 <PRE>\r
 240 public static org.apache.log4j.Logger <B>log</B></PRE>\r
 241 <DL>\r
 242 <DL>\r
 243 </DL>\r
 244 </DL>\r
 245 <HR>\r
 246 \r
 247 <A NAME="SPACE"><!-- --></A><H3>\r
 248 SPACE</H3>\r
 249 <PRE>\r
 250 public static final <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>SPACE</B></PRE>\r
 251 <DL>\r
 252 <DL>\r
 253 <DT><B>See Also:</B><DD><A HREF="../../constant-values.html#compbio.runner.Util.SPACE">Constant Field Values</A></DL>\r
 254 </DL>\r
 255 \r
 256 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 257 \r
 258 <A NAME="constructor_detail"><!-- --></A>\r
 259 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 260 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 261 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 262 <B>Constructor Detail</B></FONT></TH>\r
 263 </TR>\r
 264 </TABLE>\r
 265 \r
 266 <A NAME="Util()"><!-- --></A><H3>\r
 267 Util</H3>\r
 268 <PRE>\r
 269 public <B>Util</B>()</PRE>\r
 270 <DL>\r
 271 </DL>\r
 272 \r
 273 <!-- ============ METHOD DETAIL ========== -->\r
 274 \r
 275 <A NAME="method_detail"><!-- --></A>\r
 276 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 277 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 278 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 279 <B>Method Detail</B></FONT></TH>\r
 280 </TR>\r
 281 </TABLE>\r
 282 \r
 283 <A NAME="getSupportedOptions(java.lang.Class)"><!-- --></A><H3>\r
 284 getSupportedOptions</H3>\r
 285 <PRE>\r
 286 public static &lt;T&gt; <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;T&gt; <B>getSupportedOptions</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A>&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</PRE>\r
 287 <DL>\r
 288 <DD><DL>\r
 289 </DL>\r
 290 </DD>\r
 291 </DL>\r
 292 <HR>\r
 293 \r
 294 <A NAME="getPresets(java.lang.Class)"><!-- --></A><H3>\r
 295 getPresets</H3>\r
 296 <PRE>\r
 297 public static &lt;T&gt; <A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;T&gt; <B>getPresets</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A>&lt;? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</PRE>\r
 298 <DL>\r
 299 <DD><DL>\r
 300 </DL>\r
 301 </DD>\r
 302 </DL>\r
 303 <HR>\r
 304 \r
 305 <A NAME="readClustalFile(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
 306 readClustalFile</H3>\r
 307 <PRE>\r
 308 public static final <A HREF="../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>readClustalFile</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;workDirectory,\r
 309                                               <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;clustFile)\r
 310                                        throws <A HREF="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>,\r
 311                                               <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A>,\r
 312                                               <A HREF="http://java.sun.com/javase/6/docs/api/java/io/FileNotFoundException.html?is-external=true" title="class or interface in java.io">FileNotFoundException</A>,\r
 313                                               <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></PRE>\r
 314 <DL>\r
 315 <DD><DL>\r
 316 \r
 317 <DT><B>Throws:</B>\r
 318 <DD><CODE><A HREF="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE>\r
 319 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE>\r
 320 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/FileNotFoundException.html?is-external=true" title="class or interface in java.io">FileNotFoundException</A></CODE>\r
 321 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></CODE></DL>\r
 322 </DD>\r
 323 </DL>\r
 324 <HR>\r
 325 \r
 326 <A NAME="readJronnFile(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
 327 readJronnFile</H3>\r
 328 <PRE>\r
 329 public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</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>,<A HREF="../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt; <B>readJronnFile</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;workDirectory,\r
 330                                                     <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;clustFile)\r
 331                                              throws <A HREF="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>,\r
 332                                                     <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A>,\r
 333                                                     <A HREF="http://java.sun.com/javase/6/docs/api/java/io/FileNotFoundException.html?is-external=true" title="class or interface in java.io">FileNotFoundException</A>,\r
 334                                                     <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></PRE>\r
 335 <DL>\r
 336 <DD><DL>\r
 337 \r
 338 <DT><B>Throws:</B>\r
 339 <DD><CODE><A HREF="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE>\r
 340 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE>\r
 341 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/FileNotFoundException.html?is-external=true" title="class or interface in java.io">FileNotFoundException</A></CODE>\r
 342 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></CODE></DL>\r
 343 </DD>\r
 344 </DL>\r
 345 <HR>\r
 346 \r
 347 <A NAME="writeInput(java.util.List, compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
 348 writeInput</H3>\r
 349 <PRE>\r
 350 public static void <B>writeInput</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
 351                               <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;exec)\r
 352                        throws <A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
 353 <DL>\r
 354 <DD><DL>\r
 355 \r
 356 <DT><B>Throws:</B>\r
 357 <DD><CODE><A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
 358 </DD>\r
 359 </DL>\r
 360 <!-- ========= END OF CLASS DATA ========= -->\r
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