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

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   7 ConfExecutable\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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  81 DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&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.engine.client</FONT>\r
  92 <BR>\r
  93 Class ConfExecutable&lt;T&gt;</H2>\r
  94 <PRE>\r
  95 java.lang.Object\r
  96   <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.client.ConfExecutable&lt;T&gt;</B>\r
  97 </PRE>\r
  98 <DL>\r
  99 <DT><B>All Implemented Interfaces:</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/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;, <A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A>&lt;T&gt;</DD>\r
 100 </DL>\r
 101 <HR>\r
 102 <DL>\r
 103 <DT><PRE>public class <B>ConfExecutable&lt;T&gt;</B><DT>extends java.lang.Object<DT>implements <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</DL>\r
 104 </PRE>\r
 105 \r
 106 <P>\r
 107 <HR>\r
 108 \r
 109 <P>\r
 110 <!-- ======== NESTED CLASS SUMMARY ======== -->\r
 111 \r
 112 <A NAME="nested_class_summary"><!-- --></A>\r
 113 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 114 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 115 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 116 <B>Nested Class Summary</B></FONT></TH>\r
 117 </TR>\r
 118 </TABLE>\r
 119 &nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
 120 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 121 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 122 <TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
 123 </TR>\r
 124 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 125 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
 126 </TR>\r
 127 </TABLE>\r
 128 &nbsp;\r
 129 <!-- =========== FIELD SUMMARY =========== -->\r
 130 \r
 131 <A NAME="field_summary"><!-- --></A>\r
 132 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 133 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 134 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 135 <B>Field Summary</B></FONT></TH>\r
 136 </TR>\r
 137 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 138 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 139 <CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
 140 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#CLUSTER_TASK_ID_PREFIX">CLUSTER_TASK_ID_PREFIX</A></B></CODE>\r
 141 \r
 142 <BR>\r
 143 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 144 </TR>\r
 145 </TABLE>\r
 146 &nbsp;\r
 147 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 148 \r
 149 <A NAME="constructor_summary"><!-- --></A>\r
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 151 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 152 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 153 <B>Constructor Summary</B></FONT></TH>\r
 154 </TR>\r
 155 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 156 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#ConfExecutable(compbio.engine.client.Executable, java.lang.String)">ConfExecutable</A></B>(<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;&nbsp;executable,\r
 157                java.lang.String&nbsp;taskDirectory)</CODE>\r
 158 \r
 159 <BR>\r
 160 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 161 </TR>\r
 162 </TABLE>\r
 163 &nbsp;\r
 164 <!-- ========== METHOD SUMMARY =========== -->\r
 165 \r
 166 <A NAME="method_summary"><!-- --></A>\r
 167 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 168 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 169 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 170 <B>Method Summary</B></FONT></TH>\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>&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
 175 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</CODE>\r
 176 \r
 177 <BR>\r
 178 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adds parameter to the list of parameters for a native executable</TD>\r
 179 </TR>\r
 180 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 181 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 182 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 183 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
 184 \r
 185 <BR>\r
 186 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 187 </TR>\r
 188 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 189 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 190 <CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
 191 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getCreatedFiles()">getCreatedFiles</A></B>()</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>&nbsp;java.util.Map&lt;java.lang.String,java.lang.String&gt;</CODE></FONT></TD>\r
 199 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getEnvironment()">getEnvironment</A></B>()</CODE>\r
 200 \r
 201 <BR>\r
 202 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 203 </TR>\r
 204 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 205 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 206 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 207 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getError()">getError</A></B>()</CODE>\r
 208 \r
 209 <BR>\r
 210 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 211 </TR>\r
 212 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 213 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 214 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
 215 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getExecProvider()">getExecProvider</A></B>()</CODE>\r
 216 \r
 217 <BR>\r
 218 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 219 </TR>\r
 220 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 221 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 222 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
 223 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getExecutable()">getExecutable</A></B>()</CODE>\r
 224 \r
 225 <BR>\r
 226 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 227 </TR>\r
 228 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 229 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 230 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 231 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getInput()">getInput</A></B>()</CODE>\r
 232 \r
 233 <BR>\r
 234 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Not all input paths are relative! Input path could be absolute!</TD>\r
 235 </TR>\r
 236 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 237 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 238 <CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
 239 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
 240 \r
 241 <BR>\r
 242 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 243 </TR>\r
 244 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 245 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 246 <CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
 247 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getLimits()">getLimits</A></B>()</CODE>\r
 248 \r
 249 <BR>\r
 250 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 251 </TR>\r
 252 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 253 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 254 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 255 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getOutput()">getOutput</A></B>()</CODE>\r
 256 \r
 257 <BR>\r
 258 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 259 </TR>\r
 260 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 261 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 262 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
 263 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getParameters()">getParameters</A></B>()</CODE>\r
 264 \r
 265 <BR>\r
 266 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 267 </TR>\r
 268 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 269 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 270 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
 271 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.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
 272 \r
 273 <BR>\r
 274 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 275 </TR>\r
 276 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 277 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 278 <CODE>\r
 279 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 280 <TR ALIGN="right" VALIGN="">\r
 281 <TD NOWRAP><FONT SIZE="-1">\r
 282 <CODE>&lt;V&gt; V</CODE></FONT></TD>\r
 283 </TR>\r
 284 </TABLE>\r
 285 </CODE></FONT></TD>\r
 286 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getResults()">getResults</A></B>()</CODE>\r
 287 \r
 288 <BR>\r
 289 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 290 </TR>\r
 291 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 292 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 293 <CODE>\r
 294 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 295 <TR ALIGN="right" VALIGN="">\r
 296 <TD NOWRAP><FONT SIZE="-1">\r
 297 <CODE>&lt;V&gt; V</CODE></FONT></TD>\r
 298 </TR>\r
 299 </TABLE>\r
 300 </CODE></FONT></TD>\r
 301 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;directory)</CODE>\r
 302 \r
 303 <BR>\r
 304 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 305 </TR>\r
 306 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 307 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 308 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A></CODE></FONT></TD>\r
 309 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunConfiguration()">getRunConfiguration</A></B>()</CODE>\r
 310 \r
 311 <BR>\r
 312 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 313 </TR>\r
 314 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 315 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 316 <CODE>static\r
 317 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 318 <TR ALIGN="right" VALIGN="">\r
 319 <TD NOWRAP><FONT SIZE="-1">\r
 320 <CODE>&lt;V&gt; <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;V&gt;</CODE></FONT></TD>\r
 321 </TR>\r
 322 </TABLE>\r
 323 </CODE></FONT></TD>\r
 324 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunnerLimits(java.lang.Class)">getRunnerLimits</A></B>(java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)</CODE>\r
 325 \r
 326 <BR>\r
 327 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method should be executed once and result of its execution reused.</TD>\r
 328 </TR>\r
 329 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 330 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 331 <CODE>static\r
 332 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 333 <TR ALIGN="right" VALIGN="">\r
 334 <TD NOWRAP><FONT SIZE="-1">\r
 335 <CODE>&lt;V&gt; <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;V&gt;</CODE></FONT></TD>\r
 336 </TR>\r
 337 </TABLE>\r
 338 </CODE></FONT></TD>\r
 339 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunnerOptions(java.lang.Class)">getRunnerOptions</A></B>(java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)</CODE>\r
 340 \r
 341 <BR>\r
 342 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 343 </TR>\r
 344 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 345 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 346 <CODE>static\r
 347 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 348 <TR ALIGN="right" VALIGN="">\r
 349 <TD NOWRAP><FONT SIZE="-1">\r
 350 <CODE>&lt;V&gt; <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;V&gt;</CODE></FONT></TD>\r
 351 </TR>\r
 352 </TABLE>\r
 353 </CODE></FONT></TD>\r
 354 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunnerPresets(java.lang.Class)">getRunnerPresets</A></B>(java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)</CODE>\r
 355 \r
 356 <BR>\r
 357 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 358 </TR>\r
 359 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 360 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 361 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
 362 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getSupportedRuntimes()">getSupportedRuntimes</A></B>()</CODE>\r
 363 \r
 364 <BR>\r
 365 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 366 </TR>\r
 367 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 368 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 369 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 370 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getTaskId()">getTaskId</A></B>()</CODE>\r
 371 \r
 372 <BR>\r
 373 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 374 </TR>\r
 375 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 376 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 377 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 378 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getWorkDirectory()">getWorkDirectory</A></B>()</CODE>\r
 379 \r
 380 <BR>\r
 381 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 382 </TR>\r
 383 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 384 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 385 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
 386 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#loadRunConfiguration(java.io.InputStream)">loadRunConfiguration</A></B>(java.io.InputStream&nbsp;input)</CODE>\r
 387 \r
 388 <BR>\r
 389 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 390 </TR>\r
 391 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 392 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 393 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
 394 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.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;rconf)</CODE>\r
 395 \r
 396 <BR>\r
 397 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 398 </TR>\r
 399 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 400 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 401 <CODE>static&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
 402 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#newConfExecutable(compbio.engine.client.RunConfiguration)">newConfExecutable</A></B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconf)</CODE>\r
 403 \r
 404 <BR>\r
 405 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 406 </TR>\r
 407 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 408 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 409 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 410 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#saveRunConfiguration()">saveRunConfiguration</A></B>()</CODE>\r
 411 \r
 412 <BR>\r
 413 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 414 </TR>\r
 415 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 416 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 417 <CODE>&nbsp;void</CODE></FONT></TD>\r
 418 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#setExecProvider(compbio.engine.client.Executable.ExecProvider)">setExecProvider</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
 419 \r
 420 <BR>\r
 421 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 422 </TR>\r
 423 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 424 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 425 <CODE>&nbsp;void</CODE></FONT></TD>\r
 426 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#setWorkDirectory(java.lang.String)">setWorkDirectory</A></B>(java.lang.String&nbsp;workDirectory)</CODE>\r
 427 \r
 428 <BR>\r
 429 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 430 </TR>\r
 431 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 432 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 433 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 434 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#toString()">toString</A></B>()</CODE>\r
 435 \r
 436 <BR>\r
 437 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 438 </TR>\r
 439 </TABLE>\r
 440 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 441 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 442 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 443 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
 444 </TR>\r
 445 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 446 <TD><CODE>equals, getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>\r
 447 </TR>\r
 448 </TABLE>\r
 449 &nbsp;\r
 450 <P>\r
 451 \r
 452 <!-- ============ FIELD DETAIL =========== -->\r
 453 \r
 454 <A NAME="field_detail"><!-- --></A>\r
 455 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 456 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 457 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 458 <B>Field Detail</B></FONT></TH>\r
 459 </TR>\r
 460 </TABLE>\r
 461 \r
 462 <A NAME="CLUSTER_TASK_ID_PREFIX"><!-- --></A><H3>\r
 463 CLUSTER_TASK_ID_PREFIX</H3>\r
 464 <PRE>\r
 465 public static final java.lang.String <B>CLUSTER_TASK_ID_PREFIX</B></PRE>\r
 466 <DL>\r
 467 <DL>\r
 468 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.engine.client.ConfExecutable.CLUSTER_TASK_ID_PREFIX">Constant Field Values</A></DL>\r
 469 </DL>\r
 470 \r
 471 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 472 \r
 473 <A NAME="constructor_detail"><!-- --></A>\r
 474 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 475 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 476 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 477 <B>Constructor Detail</B></FONT></TH>\r
 478 </TR>\r
 479 </TABLE>\r
 480 \r
 481 <A NAME="ConfExecutable(compbio.engine.client.Executable, java.lang.String)"><!-- --></A><H3>\r
 482 ConfExecutable</H3>\r
 483 <PRE>\r
 484 public <B>ConfExecutable</B>(<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;&nbsp;executable,\r
 485                       java.lang.String&nbsp;taskDirectory)</PRE>\r
 486 <DL>\r
 487 </DL>\r
 488 \r
 489 <!-- ============ METHOD DETAIL ========== -->\r
 490 \r
 491 <A NAME="method_detail"><!-- --></A>\r
 492 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 493 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 494 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 495 <B>Method Detail</B></FONT></TH>\r
 496 </TR>\r
 497 </TABLE>\r
 498 \r
 499 <A NAME="getExecProvider()"><!-- --></A><H3>\r
 500 getExecProvider</H3>\r
 501 <PRE>\r
 502 public <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> <B>getExecProvider</B>()</PRE>\r
 503 <DL>\r
 504 <DD><DL>\r
 505 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getExecProvider()">getExecProvider</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
 506 </DD>\r
 507 <DD><DL>\r
 508 </DL>\r
 509 </DD>\r
 510 </DL>\r
 511 <HR>\r
 512 \r
 513 <A NAME="setExecProvider(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
 514 setExecProvider</H3>\r
 515 <PRE>\r
 516 public void <B>setExecProvider</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</PRE>\r
 517 <DL>\r
 518 <DD><DL>\r
 519 </DL>\r
 520 </DD>\r
 521 <DD><DL>\r
 522 </DL>\r
 523 </DD>\r
 524 </DL>\r
 525 <HR>\r
 526 \r
 527 <A NAME="getCommand(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
 528 getCommand</H3>\r
 529 <PRE>\r
 530 public java.lang.String <B>getCommand</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)\r
 531                             throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></PRE>\r
 532 <DL>\r
 533 <DD><DL>\r
 534 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
 535 </DD>\r
 536 <DD><DL>\r
 537 \r
 538 <DT><B>Throws:</B>\r
 539 <DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE></DL>\r
 540 </DD>\r
 541 </DL>\r
 542 <HR>\r
 543 \r
 544 <A NAME="getSupportedRuntimes()"><!-- --></A><H3>\r
 545 getSupportedRuntimes</H3>\r
 546 <PRE>\r
 547 public <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> <B>getSupportedRuntimes</B>()</PRE>\r
 548 <DL>\r
 549 <DD><DL>\r
 550 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getSupportedRuntimes()">getSupportedRuntimes</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
 551 </DD>\r
 552 <DD><DL>\r
 553 </DL>\r
 554 </DD>\r
 555 </DL>\r
 556 <HR>\r
 557 \r
 558 <A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
 559 getLimit</H3>\r
 560 <PRE>\r
 561 public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt; <B>getLimit</B>(java.lang.String&nbsp;presetName)</PRE>\r
 562 <DL>\r
 563 <DD><DL>\r
 564 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
 565 </DD>\r
 566 <DD><DL>\r
 567 </DL>\r
 568 </DD>\r
 569 </DL>\r
 570 <HR>\r
 571 \r
 572 <A NAME="getLimits()"><!-- --></A><H3>\r
 573 getLimits</H3>\r
 574 <PRE>\r
 575 public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt; <B>getLimits</B>()</PRE>\r
 576 <DL>\r
 577 <DD><DL>\r
 578 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
 579 </DD>\r
 580 <DD><DL>\r
 581 </DL>\r
 582 </DD>\r
 583 </DL>\r
 584 <HR>\r
 585 \r
 586 <A NAME="getTaskId()"><!-- --></A><H3>\r
 587 getTaskId</H3>\r
 588 <PRE>\r
 589 public java.lang.String <B>getTaskId</B>()</PRE>\r
 590 <DL>\r
 591 <DD><DL>\r
 592 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getTaskId()">getTaskId</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
 593 </DD>\r
 594 <DD><DL>\r
 595 </DL>\r
 596 </DD>\r
 597 </DL>\r
 598 <HR>\r
 599 \r
 600 <A NAME="setWorkDirectory(java.lang.String)"><!-- --></A><H3>\r
 601 setWorkDirectory</H3>\r
 602 <PRE>\r
 603 public void <B>setWorkDirectory</B>(java.lang.String&nbsp;workDirectory)</PRE>\r
 604 <DL>\r
 605 <DD><DL>\r
 606 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#setWorkDirectory(java.lang.String)">setWorkDirectory</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
 607 </DD>\r
 608 <DD><DL>\r
 609 </DL>\r
 610 </DD>\r
 611 </DL>\r
 612 <HR>\r
 613 \r
 614 <A NAME="getWorkDirectory()"><!-- --></A><H3>\r
 615 getWorkDirectory</H3>\r
 616 <PRE>\r
 617 public java.lang.String <B>getWorkDirectory</B>()</PRE>\r
 618 <DL>\r
 619 <DD><DL>\r
 620 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getWorkDirectory()">getWorkDirectory</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
 621 </DD>\r
 622 <DD><DL>\r
 623 </DL>\r
 624 </DD>\r
 625 </DL>\r
 626 <HR>\r
 627 \r
 628 <A NAME="addParameters(java.util.List)"><!-- --></A><H3>\r
 629 addParameters</H3>\r
 630 <PRE>\r
 631 public <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt; <B>addParameters</B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</PRE>\r
 632 <DL>\r
 633 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">Executable</A></CODE></B></DD>\r
 634 <DD>Adds parameter to the list of parameters for a native executable\r
 635 <P>\r
 636 <DD><DL>\r
 637 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
 638 </DD>\r
 639 <DD><DL>\r
 640 \r
 641 <DT><B>Returns:</B><DD>this Executable</DL>\r
 642 </DD>\r
 643 </DL>\r
 644 <HR>\r
 645 \r
 646 <A NAME="getOutput()"><!-- --></A><H3>\r
 647 getOutput</H3>\r
 648 <PRE>\r
 649 public java.lang.String <B>getOutput</B>()</PRE>\r
 650 <DL>\r
 651 <DD><DL>\r
 652 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getOutput()">getOutput</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
 653 </DD>\r
 654 <DD><DL>\r
 655 </DL>\r
 656 </DD>\r
 657 </DL>\r
 658 <HR>\r
 659 \r
 660 <A NAME="getError()"><!-- --></A><H3>\r
 661 getError</H3>\r
 662 <PRE>\r
 663 public java.lang.String <B>getError</B>()</PRE>\r
 664 <DL>\r
 665 <DD><DL>\r
 666 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getError()">getError</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
 667 </DD>\r
 668 <DD><DL>\r
 669 </DL>\r
 670 </DD>\r
 671 </DL>\r
 672 <HR>\r
 673 \r
 674 <A NAME="getCreatedFiles()"><!-- --></A><H3>\r
 675 getCreatedFiles</H3>\r
 676 <PRE>\r
 677 public java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>\r
 678 <DL>\r
 679 <DD><DL>\r
 680 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
 681 </DD>\r
 682 <DD><DL>\r
 683 </DL>\r
 684 </DD>\r
 685 </DL>\r
 686 <HR>\r
 687 \r
 688 <A NAME="getInput()"><!-- --></A><H3>\r
 689 getInput</H3>\r
 690 <PRE>\r
 691 public java.lang.String <B>getInput</B>()</PRE>\r
 692 <DL>\r
 693 <DD>Not all input paths are relative! Input path could be absolute!\r
 694 <P>\r
 695 <DD><DL>\r
 696 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getInput()">getInput</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
 697 </DD>\r
 698 <DD><DL>\r
 699 <DT><B>See Also:</B><DD><CODE>compbio.engine.client.Executable#getInputFiles()</CODE></DL>\r
 700 </DD>\r
 701 </DL>\r
 702 <HR>\r
 703 \r
 704 <A NAME="getParameters()"><!-- --></A><H3>\r
 705 getParameters</H3>\r
 706 <PRE>\r
 707 public <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt; <B>getParameters</B>()</PRE>\r
 708 <DL>\r
 709 <DD><DL>\r
 710 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getParameters()">getParameters</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
 711 </DD>\r
 712 <DD><DL>\r
 713 </DL>\r
 714 </DD>\r
 715 </DL>\r
 716 <HR>\r
 717 \r
 718 <A NAME="getParameters(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
 719 getParameters</H3>\r
 720 <PRE>\r
 721 public <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">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
 722 <DL>\r
 723 <DD><DL>\r
 724 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
 725 </DD>\r
 726 <DD><DL>\r
 727 </DL>\r
 728 </DD>\r
 729 </DL>\r
 730 <HR>\r
 731 \r
 732 <A NAME="getExecutable()"><!-- --></A><H3>\r
 733 getExecutable</H3>\r
 734 <PRE>\r
 735 public <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt; <B>getExecutable</B>()</PRE>\r
 736 <DL>\r
 737 <DD><DL>\r
 738 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getExecutable()">getExecutable</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
 739 </DD>\r
 740 <DD><DL>\r
 741 </DL>\r
 742 </DD>\r
 743 </DL>\r
 744 <HR>\r
 745 \r
 746 <A NAME="getResults()"><!-- --></A><H3>\r
 747 getResults</H3>\r
 748 <PRE>\r
 749 public &lt;V&gt; V <B>getResults</B>()\r
 750              throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 751 <DL>\r
 752 <DD><DL>\r
 753 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getResults()">getResults</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
 754 </DD>\r
 755 <DD><DL>\r
 756 \r
 757 <DT><B>Throws:</B>\r
 758 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
 759 </DD>\r
 760 </DL>\r
 761 <HR>\r
 762 \r
 763 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
 764 getResults</H3>\r
 765 <PRE>\r
 766 public &lt;V&gt; V <B>getResults</B>(java.lang.String&nbsp;directory)\r
 767              throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 768 <DL>\r
 769 <DD><DL>\r
 770 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
 771 </DD>\r
 772 <DD><DL>\r
 773 \r
 774 <DT><B>Throws:</B>\r
 775 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
 776 </DD>\r
 777 </DL>\r
 778 <HR>\r
 779 \r
 780 <A NAME="getRunnerOptions(java.lang.Class)"><!-- --></A><H3>\r
 781 getRunnerOptions</H3>\r
 782 <PRE>\r
 783 public static &lt;V&gt; <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;V&gt; <B>getRunnerOptions</B>(java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)\r
 784                                         throws java.io.IOException</PRE>\r
 785 <DL>\r
 786 <DD><DL>\r
 787 </DL>\r
 788 </DD>\r
 789 <DD><DL>\r
 790 \r
 791 <DT><B>Throws:</B>\r
 792 <DD><CODE>java.io.IOException</CODE></DL>\r
 793 </DD>\r
 794 </DL>\r
 795 <HR>\r
 796 \r
 797 <A NAME="getRunnerPresets(java.lang.Class)"><!-- --></A><H3>\r
 798 getRunnerPresets</H3>\r
 799 <PRE>\r
 800 public static &lt;V&gt; <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;V&gt; <B>getRunnerPresets</B>(java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)\r
 801                                          throws java.io.IOException</PRE>\r
 802 <DL>\r
 803 <DD><DL>\r
 804 </DL>\r
 805 </DD>\r
 806 <DD><DL>\r
 807 \r
 808 <DT><B>Throws:</B>\r
 809 <DD><CODE>java.io.IOException</CODE></DL>\r
 810 </DD>\r
 811 </DL>\r
 812 <HR>\r
 813 \r
 814 <A NAME="getRunnerLimits(java.lang.Class)"><!-- --></A><H3>\r
 815 getRunnerLimits</H3>\r
 816 <PRE>\r
 817 public static &lt;V&gt; <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;V&gt; <B>getRunnerLimits</B>(java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)\r
 818                                         throws java.io.IOException</PRE>\r
 819 <DL>\r
 820 <DD>This method should be executed once and result of its execution reused.
 821  If not used carefully it could slow down the system!\r
 822 <P>\r
 823 <DD><DL>\r
 824 </DL>\r
 825 </DD>\r
 826 <DD><DL>\r
 827 <DT><B>Type Parameters:</B><DD><CODE>V</CODE> - <DT><B>Parameters:</B><DD><CODE>clazz</CODE> - \r
 828 <DT><B>Returns:</B><DD>\r
 829 <DT><B>Throws:</B>\r
 830 <DD><CODE>java.io.IOException</CODE></DL>\r
 831 </DD>\r
 832 </DL>\r
 833 <HR>\r
 834 \r
 835 <A NAME="getEnvironment()"><!-- --></A><H3>\r
 836 getEnvironment</H3>\r
 837 <PRE>\r
 838 public java.util.Map&lt;java.lang.String,java.lang.String&gt; <B>getEnvironment</B>()</PRE>\r
 839 <DL>\r
 840 <DD><DL>\r
 841 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getEnvironment()">getEnvironment</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
 842 </DD>\r
 843 <DD><DL>\r
 844 </DL>\r
 845 </DD>\r
 846 </DL>\r
 847 <HR>\r
 848 \r
 849 <A NAME="loadRunConfiguration(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>\r
 850 loadRunConfiguration</H3>\r
 851 <PRE>\r
 852 public <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>loadRunConfiguration</B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconf)</PRE>\r
 853 <DL>\r
 854 <DD><DL>\r
 855 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
 856 </DD>\r
 857 <DD><DL>\r
 858 </DL>\r
 859 </DD>\r
 860 </DL>\r
 861 <HR>\r
 862 \r
 863 <A NAME="newConfExecutable(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>\r
 864 newConfExecutable</H3>\r
 865 <PRE>\r
 866 public static <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>newConfExecutable</B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconf)</PRE>\r
 867 <DL>\r
 868 <DD><DL>\r
 869 </DL>\r
 870 </DD>\r
 871 <DD><DL>\r
 872 </DL>\r
 873 </DD>\r
 874 </DL>\r
 875 <HR>\r
 876 \r
 877 <A NAME="saveRunConfiguration()"><!-- --></A><H3>\r
 878 saveRunConfiguration</H3>\r
 879 <PRE>\r
 880 public boolean <B>saveRunConfiguration</B>()\r
 881                              throws java.io.IOException</PRE>\r
 882 <DL>\r
 883 <DD><DL>\r
 884 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#saveRunConfiguration()">saveRunConfiguration</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
 885 </DD>\r
 886 <DD><DL>\r
 887 \r
 888 <DT><B>Throws:</B>\r
 889 <DD><CODE>java.io.IOException</CODE></DL>\r
 890 </DD>\r
 891 </DL>\r
 892 <HR>\r
 893 \r
 894 <A NAME="getRunConfiguration()"><!-- --></A><H3>\r
 895 getRunConfiguration</H3>\r
 896 <PRE>\r
 897 public <A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> <B>getRunConfiguration</B>()</PRE>\r
 898 <DL>\r
 899 <DD><DL>\r
 900 </DL>\r
 901 </DD>\r
 902 <DD><DL>\r
 903 </DL>\r
 904 </DD>\r
 905 </DL>\r
 906 <HR>\r
 907 \r
 908 <A NAME="loadRunConfiguration(java.io.InputStream)"><!-- --></A><H3>\r
 909 loadRunConfiguration</H3>\r
 910 <PRE>\r
 911 public <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>loadRunConfiguration</B>(java.io.InputStream&nbsp;input)\r
 912                                              throws java.io.IOException</PRE>\r
 913 <DL>\r
 914 <DD><DL>\r
 915 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#loadRunConfiguration(java.io.InputStream)">loadRunConfiguration</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
 916 </DD>\r
 917 <DD><DL>\r
 918 \r
 919 <DT><B>Throws:</B>\r
 920 <DD><CODE>java.io.IOException</CODE></DL>\r
 921 </DD>\r
 922 </DL>\r
 923 <HR>\r
 924 \r
 925 <A NAME="toString()"><!-- --></A><H3>\r
 926 toString</H3>\r
 927 <PRE>\r
 928 public java.lang.String <B>toString</B>()</PRE>\r
 929 <DL>\r
 930 <DD><DL>\r
 931 <DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
 932 </DD>\r
 933 <DD><DL>\r
 934 </DL>\r
 935 </DD>\r
 936 </DL>\r
 937 <!-- ========= END OF CLASS DATA ========= -->\r
 938 <HR>\r
 939 \r
 940 \r
 941 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 942 <A NAME="navbar_bottom"><!-- --></A>\r
 943 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 944 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 945 <TR>\r
 946 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 947 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 948 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 949   <TR ALIGN="center" VALIGN="top">\r
 950   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 951   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 952   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 953   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ConfExecutable.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 954   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 955   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 956   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 957   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 958   </TR>\r
 959 </TABLE>\r
 960 </TD>\r
 961 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 962 </EM>\r
 963 </TD>\r
 964 </TR>\r
 965 \r
 966 <TR>\r
 967 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 968 &nbsp;<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
 969 &nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
 970 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 971   <A HREF="../../../index.html?compbio/engine/client/ConfExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 972 &nbsp;<A HREF="ConfExecutable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 973 &nbsp;<SCRIPT type="text/javascript">\r
 974   <!--\r
 975   if(window==top) {\r
 976     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 977   }\r
 978   //-->\r
 979 </SCRIPT>\r
 980 <NOSCRIPT>\r
 981   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 982 </NOSCRIPT>\r
 983 \r
 984 \r
 985 </FONT></TD>\r
 986 </TR>\r
 987 <TR>\r
 988 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 989   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
 990 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 991 DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
 992 </TR>\r
 993 </TABLE>\r
 994 <A NAME="skip-navbar_bottom"></A>\r
 995 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 996 \r
 997 <HR>\r
 998 \r
 999 </BODY>\r
1000 </HTML>\r