website/full_javadoc/compbio/engine/client/Executable.html

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   7 Executable\r
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   9 \r
  10 <META NAME="date" CONTENT="2011-08-12">\r
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  18         parent.document.title="Executable";\r
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  43   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Executable.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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  58 &nbsp;<A HREF="../../../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
  59 &nbsp;<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
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  79   SUMMARY:&nbsp;<A HREF="#nested_class_summary">NESTED</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&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;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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  89 <H2>\r
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  91 compbio.engine.client</FONT>\r
  92 <BR>\r
  93 Interface Executable&lt;T&gt;</H2>\r
  94 <DL>\r
  95 <DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - </DL>\r
  96 <DL>\r
  97 <DT><B>All Known Subinterfaces:</B> <DD><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;, <A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A>&lt;T&gt;</DD>\r
  98 </DL>\r
  99 <DL>\r
 100 <DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>, <A HREF="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>, <A HREF="../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>, <A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>, <A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>, <A HREF="../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>, <A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>, <A HREF="../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>, <A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>, <A HREF="../../../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>, <A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>, <A HREF="../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>, <A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>, <A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>, <A HREF="../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>, <A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>, <A HREF="../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>, <A HREF="../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>, <A HREF="../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>, <A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></DD>\r
 101 </DL>\r
 102 <HR>\r
 103 <DL>\r
 104 <DT><PRE>public interface <B>Executable&lt;T&gt;</B></DL>\r
 105 </PRE>\r
 106 \r
 107 <P>\r
 108 Interface to a native executable.\r
 109 <P>\r
 110 \r
 111 <P>\r
 112 <DL>\r
 113 <DT><B>Author:</B></DT>\r
 114   <DD>pvtroshin</DD>\r
 115 </DL>\r
 116 <HR>\r
 117 \r
 118 <P>\r
 119 <!-- ======== NESTED CLASS SUMMARY ======== -->\r
 120 \r
 121 <A NAME="nested_class_summary"><!-- --></A>\r
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 124 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 125 <B>Nested Class Summary</B></FONT></TH>\r
 126 </TR>\r
 127 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 128 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 129 <CODE>static&nbsp;class</CODE></FONT></TD>\r
 130 <TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></B></CODE>\r
 131 \r
 132 <BR>\r
 133 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 134 </TR>\r
 135 </TABLE>\r
 136 &nbsp;\r
 137 <!-- ========== METHOD SUMMARY =========== -->\r
 138 \r
 139 <A NAME="method_summary"><!-- --></A>\r
 140 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 141 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 142 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 143 <B>Method Summary</B></FONT></TH>\r
 144 </TR>\r
 145 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 146 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 147 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt;</CODE></FONT></TD>\r
 148 <TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</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="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;&nbsp;parameters)</CODE>\r
 149 \r
 150 <BR>\r
 151 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adds parameter to the list of parameters for a native executable</TD>\r
 152 </TR>\r
 153 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 154 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 155 <CODE>&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
 156 <TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#getClusterJobSettings()">getClusterJobSettings</A></B>()</CODE>\r
 157 \r
 158 <BR>\r
 159 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 160 </TR>\r
 161 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 162 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 163 <CODE>&nbsp;<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
 164 <TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
 165 \r
 166 <BR>\r
 167 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Deprecated.</B>&nbsp;</TD>\r
 168 </TR>\r
 169 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 170 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 171 <CODE>&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
 172 <TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#getError()">getError</A></B>()</CODE>\r
 173 \r
 174 <BR>\r
 175 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 176 </TR>\r
 177 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 178 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 179 <CODE>&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
 180 <TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#getInput()">getInput</A></B>()</CODE>\r
 181 \r
 182 <BR>\r
 183 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 184 </TR>\r
 185 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 186 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 187 <CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt;</CODE></FONT></TD>\r
 188 <TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</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;presetName)</CODE>\r
 189 \r
 190 <BR>\r
 191 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 192 </TR>\r
 193 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 194 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 195 <CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt;</CODE></FONT></TD>\r
 196 <TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</A></B>()</CODE>\r
 197 \r
 198 <BR>\r
 199 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 200 </TR>\r
 201 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 202 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 203 <CODE>&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
 204 <TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#getOutput()">getOutput</A></B>()</CODE>\r
 205 \r
 206 <BR>\r
 207 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 208 </TR>\r
 209 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 210 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 211 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt;</CODE></FONT></TD>\r
 212 <TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
 213 \r
 214 <BR>\r
 215 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 216 </TR>\r
 217 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 218 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 219 <CODE>\r
 220 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 221 <TR ALIGN="right" VALIGN="">\r
 222 <TD NOWRAP><FONT SIZE="-1">\r
 223 <CODE>&lt;V&gt; V</CODE></FONT></TD>\r
 224 </TR>\r
 225 </TABLE>\r
 226 </CODE></FONT></TD>\r
 227 <TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</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;directory)</CODE>\r
 228 \r
 229 <BR>\r
 230 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 231 </TR>\r
 232 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 233 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 234 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
 235 <TD><CODE><B><A HREF="../../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</CODE>\r
 236 \r
 237 <BR>\r
 238 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 239 </TR>\r
 240 </TABLE>\r
 241 &nbsp;\r
 242 <P>\r
 243 \r
 244 <!-- ============ METHOD DETAIL ========== -->\r
 245 \r
 246 <A NAME="method_detail"><!-- --></A>\r
 247 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 248 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 249 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 250 <B>Method Detail</B></FONT></TH>\r
 251 </TR>\r
 252 </TABLE>\r
 253 \r
 254 <A NAME="addParameters(java.util.List)"><!-- --></A><H3>\r
 255 addParameters</H3>\r
 256 <PRE>\r
 257 <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt; <B>addParameters</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="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;&nbsp;parameters)</PRE>\r
 258 <DL>\r
 259 <DD>Adds parameter to the list of parameters for a native executable\r
 260 <P>\r
 261 <DD><DL>\r
 262 <DT><B>Parameters:</B><DD><CODE>parameters</CODE> - \r
 263 <DT><B>Returns:</B><DD>this Executable</DL>\r
 264 </DD>\r
 265 </DL>\r
 266 <HR>\r
 267 \r
 268 <A NAME="getCreatedFiles()"><!-- --></A><H3>\r
 269 getCreatedFiles</H3>\r
 270 <PRE>\r
 271 <FONT SIZE="-1"><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Deprecated.html?is-external=true" title="class or interface in java.lang">@Deprecated</A>\r
 272 </FONT><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>getCreatedFiles</B>()</PRE>\r
 273 <DL>\r
 274 <DD><B>Deprecated.</B>&nbsp;\r
 275 <P>\r
 276 <DD><DL>\r
 277 </DL>\r
 278 </DD>\r
 279 </DL>\r
 280 <HR>\r
 281 \r
 282 <A NAME="getInput()"><!-- --></A><H3>\r
 283 getInput</H3>\r
 284 <PRE>\r
 285 <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>getInput</B>()</PRE>\r
 286 <DL>\r
 287 <DD><DL>\r
 288 </DL>\r
 289 </DD>\r
 290 </DL>\r
 291 <HR>\r
 292 \r
 293 <A NAME="getOutput()"><!-- --></A><H3>\r
 294 getOutput</H3>\r
 295 <PRE>\r
 296 <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>getOutput</B>()</PRE>\r
 297 <DL>\r
 298 <DD><DL>\r
 299 </DL>\r
 300 </DD>\r
 301 </DL>\r
 302 <HR>\r
 303 \r
 304 <A NAME="getError()"><!-- --></A><H3>\r
 305 getError</H3>\r
 306 <PRE>\r
 307 <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>getError</B>()</PRE>\r
 308 <DL>\r
 309 <DD><DL>\r
 310 </DL>\r
 311 </DD>\r
 312 </DL>\r
 313 <HR>\r
 314 \r
 315 <A NAME="getParameters(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
 316 getParameters</H3>\r
 317 <PRE>\r
 318 <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt; <B>getParameters</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</PRE>\r
 319 <DL>\r
 320 <DD><DL>\r
 321 </DL>\r
 322 </DD>\r
 323 </DL>\r
 324 <HR>\r
 325 \r
 326 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
 327 getResults</H3>\r
 328 <PRE>\r
 329 &lt;V&gt; V <B>getResults</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;directory)\r
 330              throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 331 <DL>\r
 332 <DD><DL>\r
 333 \r
 334 <DT><B>Throws:</B>\r
 335 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
 336 </DD>\r
 337 </DL>\r
 338 <HR>\r
 339 \r
 340 <A NAME="loadRunConfiguration(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>\r
 341 loadRunConfiguration</H3>\r
 342 <PRE>\r
 343 <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt; <B>loadRunConfiguration</B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</PRE>\r
 344 <DL>\r
 345 <DD><DL>\r
 346 </DL>\r
 347 </DD>\r
 348 </DL>\r
 349 <HR>\r
 350 \r
 351 <A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
 352 getLimit</H3>\r
 353 <PRE>\r
 354 <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt; <B>getLimit</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;presetName)</PRE>\r
 355 <DL>\r
 356 <DD><DL>\r
 357 </DL>\r
 358 </DD>\r
 359 </DL>\r
 360 <HR>\r
 361 \r
 362 <A NAME="getLimits()"><!-- --></A><H3>\r
 363 getLimits</H3>\r
 364 <PRE>\r
 365 <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt; <B>getLimits</B>()</PRE>\r
 366 <DL>\r
 367 <DD><DL>\r
 368 </DL>\r
 369 </DD>\r
 370 </DL>\r
 371 <HR>\r
 372 \r
 373 <A NAME="getClusterJobSettings()"><!-- --></A><H3>\r
 374 getClusterJobSettings</H3>\r
 375 <PRE>\r
 376 <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>getClusterJobSettings</B>()</PRE>\r
 377 <DL>\r
 378 <DD><DL>\r
 379 </DL>\r
 380 </DD>\r
 381 </DL>\r
 382 <!-- ========= END OF CLASS DATA ========= -->\r
 383 <HR>\r
 384 \r
 385 \r
 386 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 387 <A NAME="navbar_bottom"><!-- --></A>\r
 388 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 389 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 390 <TR>\r
 391 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 392 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 393 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 394   <TR ALIGN="center" VALIGN="top">\r
 395   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 396   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 397   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 398   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Executable.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 399   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 400   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 401   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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 403   </TR>\r
 404 </TABLE>\r
 405 </TD>\r
 406 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 407 </EM>\r
 408 </TD>\r
 409 </TR>\r
 410 \r
 411 <TR>\r
 412 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 413 &nbsp;<A HREF="../../../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
 414 &nbsp;<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
 415 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 416   <A HREF="../../../index.html?compbio/engine/client/Executable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 417 &nbsp;<A HREF="Executable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 418 &nbsp;<SCRIPT type="text/javascript">\r
 419   <!--\r
 420   if(window==top) {\r
 421     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 422   }\r
 423   //-->\r
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 425 <NOSCRIPT>\r
 426   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 427 </NOSCRIPT>\r
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 429 \r
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 431 </TR>\r
 432 <TR>\r
 433 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 434   SUMMARY:&nbsp;<A HREF="#nested_class_summary">NESTED</A>&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
 435 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
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 439 <A NAME="skip-navbar_bottom"></A>\r
 440 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 441 \r
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