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

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   7 ConfiguredExecutable\r
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   9 \r
  10 <META NAME="date" CONTENT="2011-08-12">\r
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  18         parent.document.title="ConfiguredExecutable";\r
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  42   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
  43   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ConfiguredExecutable.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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  55 \r
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  58 &nbsp;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
  59 &nbsp;<A HREF="../../../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
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  79   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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  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
  90 <FONT SIZE="-1">\r
  91 compbio.engine.client</FONT>\r
  92 <BR>\r
  93 Interface ConfiguredExecutable&lt;T&gt;</H2>\r
  94 <DL>\r
  95 <DT><B>All Superinterfaces:</B> <DD><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
  96 </DL>\r
  97 <DL>\r
  98 <DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A></DD>\r
  99 </DL>\r
 100 <HR>\r
 101 <DL>\r
 102 <DT><PRE>public interface <B>ConfiguredExecutable&lt;T&gt;</B><DT>extends <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;</DL>\r
 103 </PRE>\r
 104 \r
 105 <P>\r
 106 <HR>\r
 107 \r
 108 <P>\r
 109 <!-- ======== NESTED CLASS SUMMARY ======== -->\r
 110 \r
 111 <A NAME="nested_class_summary"><!-- --></A>\r
 112 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 113 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 114 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 115 <B>Nested Class Summary</B></FONT></TH>\r
 116 </TR>\r
 117 </TABLE>\r
 118 &nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
 119 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 120 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 121 <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
 122 </TR>\r
 123 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 124 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
 125 </TR>\r
 126 </TABLE>\r
 127 &nbsp;\r
 128 \r
 129 <!-- ========== METHOD SUMMARY =========== -->\r
 130 \r
 131 <A NAME="method_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>Method 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>&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
 140 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.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
 141 \r
 142 <BR>\r
 143 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\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="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="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
 148 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getEnvironment()">getEnvironment</A></B>()</CODE>\r
 149 \r
 150 <BR>\r
 151 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
 156 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getExecProvider()">getExecProvider</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="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="type parameter in ConfiguredExecutable">T</A>&gt;</CODE></FONT></TD>\r
 164 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getExecutable()">getExecutable</A></B>()</CODE>\r
 165 \r
 166 <BR>\r
 167 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&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="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="type parameter in ConfiguredExecutable">T</A>&gt;</CODE></FONT></TD>\r
 172 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getParameters()">getParameters</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>\r
 180 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 181 <TR ALIGN="right" VALIGN="">\r
 182 <TD NOWRAP><FONT SIZE="-1">\r
 183 <CODE>&lt;V&gt; V</CODE></FONT></TD>\r
 184 </TR>\r
 185 </TABLE>\r
 186 </CODE></FONT></TD>\r
 187 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getResults()">getResults</A></B>()</CODE>\r
 188 \r
 189 <BR>\r
 190 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 191 </TR>\r
 192 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 193 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 194 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
 195 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getSupportedRuntimes()">getSupportedRuntimes</A></B>()</CODE>\r
 196 \r
 197 <BR>\r
 198 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 199 </TR>\r
 200 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 201 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 202 <CODE>&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
 203 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getTaskId()">getTaskId</A></B>()</CODE>\r
 204 \r
 205 <BR>\r
 206 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 207 </TR>\r
 208 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 209 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 210 <CODE>&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
 211 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getWorkDirectory()">getWorkDirectory</A></B>()</CODE>\r
 212 \r
 213 <BR>\r
 214 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 215 </TR>\r
 216 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 217 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 218 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
 219 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#loadRunConfiguration(java.io.InputStream)">loadRunConfiguration</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A>&nbsp;input)</CODE>\r
 220 \r
 221 <BR>\r
 222 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 223 </TR>\r
 224 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 225 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 226 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 227 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#saveRunConfiguration()">saveRunConfiguration</A></B>()</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;void</CODE></FONT></TD>\r
 235 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#setWorkDirectory(java.lang.String)">setWorkDirectory</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)</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;<A NAME="methods_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
 242 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 243 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 244 <TH ALIGN="left"><B>Methods inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
 245 </TR>\r
 246 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 247 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/engine/client/Executable.html#getClusterJobSettings()">getClusterJobSettings</A>, <A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A>, <A HREF="../../../compbio/engine/client/Executable.html#getError()">getError</A>, <A HREF="../../../compbio/engine/client/Executable.html#getInput()">getInput</A>, <A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/engine/client/Executable.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</A>, <A HREF="../../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></CODE></TD>\r
 248 </TR>\r
 249 </TABLE>\r
 250 &nbsp;\r
 251 <P>\r
 252 \r
 253 <!-- ============ METHOD DETAIL ========== -->\r
 254 \r
 255 <A NAME="method_detail"><!-- --></A>\r
 256 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 257 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 258 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 259 <B>Method Detail</B></FONT></TH>\r
 260 </TR>\r
 261 </TABLE>\r
 262 \r
 263 <A NAME="getEnvironment()"><!-- --></A><H3>\r
 264 getEnvironment</H3>\r
 265 <PRE>\r
 266 <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="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>getEnvironment</B>()</PRE>\r
 267 <DL>\r
 268 <DD><DL>\r
 269 </DL>\r
 270 </DD>\r
 271 <DD><DL>\r
 272 </DL>\r
 273 </DD>\r
 274 </DL>\r
 275 <HR>\r
 276 \r
 277 <A NAME="getTaskId()"><!-- --></A><H3>\r
 278 getTaskId</H3>\r
 279 <PRE>\r
 280 <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>getTaskId</B>()</PRE>\r
 281 <DL>\r
 282 <DD><DL>\r
 283 </DL>\r
 284 </DD>\r
 285 <DD><DL>\r
 286 </DL>\r
 287 </DD>\r
 288 </DL>\r
 289 <HR>\r
 290 \r
 291 <A NAME="getCommand(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
 292 getCommand</H3>\r
 293 <PRE>\r
 294 <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>getCommand</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)\r
 295                   throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
 296 <DL>\r
 297 <DD><DL>\r
 298 </DL>\r
 299 </DD>\r
 300 <DD><DL>\r
 301 \r
 302 <DT><B>Throws:</B>\r
 303 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
 304 </DD>\r
 305 </DL>\r
 306 <HR>\r
 307 \r
 308 <A NAME="getSupportedRuntimes()"><!-- --></A><H3>\r
 309 getSupportedRuntimes</H3>\r
 310 <PRE>\r
 311 <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> <B>getSupportedRuntimes</B>()</PRE>\r
 312 <DL>\r
 313 <DD><DL>\r
 314 </DL>\r
 315 </DD>\r
 316 <DD><DL>\r
 317 </DL>\r
 318 </DD>\r
 319 </DL>\r
 320 <HR>\r
 321 \r
 322 <A NAME="getWorkDirectory()"><!-- --></A><H3>\r
 323 getWorkDirectory</H3>\r
 324 <PRE>\r
 325 <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>getWorkDirectory</B>()</PRE>\r
 326 <DL>\r
 327 <DD><DL>\r
 328 </DL>\r
 329 </DD>\r
 330 <DD><DL>\r
 331 </DL>\r
 332 </DD>\r
 333 </DL>\r
 334 <HR>\r
 335 \r
 336 <A NAME="setWorkDirectory(java.lang.String)"><!-- --></A><H3>\r
 337 setWorkDirectory</H3>\r
 338 <PRE>\r
 339 void <B>setWorkDirectory</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)</PRE>\r
 340 <DL>\r
 341 <DD><DL>\r
 342 </DL>\r
 343 </DD>\r
 344 <DD><DL>\r
 345 </DL>\r
 346 </DD>\r
 347 </DL>\r
 348 <HR>\r
 349 \r
 350 <A NAME="getResults()"><!-- --></A><H3>\r
 351 getResults</H3>\r
 352 <PRE>\r
 353 &lt;V&gt; V <B>getResults</B>()\r
 354              throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 355 <DL>\r
 356 <DD><DL>\r
 357 </DL>\r
 358 </DD>\r
 359 <DD><DL>\r
 360 \r
 361 <DT><B>Throws:</B>\r
 362 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
 363 </DD>\r
 364 </DL>\r
 365 <HR>\r
 366 \r
 367 <A NAME="getExecutable()"><!-- --></A><H3>\r
 368 getExecutable</H3>\r
 369 <PRE>\r
 370 <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="type parameter in ConfiguredExecutable">T</A>&gt; <B>getExecutable</B>()</PRE>\r
 371 <DL>\r
 372 <DD><DL>\r
 373 </DL>\r
 374 </DD>\r
 375 <DD><DL>\r
 376 </DL>\r
 377 </DD>\r
 378 </DL>\r
 379 <HR>\r
 380 \r
 381 <A NAME="getParameters()"><!-- --></A><H3>\r
 382 getParameters</H3>\r
 383 <PRE>\r
 384 <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="type parameter in ConfiguredExecutable">T</A>&gt; <B>getParameters</B>()</PRE>\r
 385 <DL>\r
 386 <DD><DL>\r
 387 </DL>\r
 388 </DD>\r
 389 <DD><DL>\r
 390 </DL>\r
 391 </DD>\r
 392 </DL>\r
 393 <HR>\r
 394 \r
 395 <A NAME="saveRunConfiguration()"><!-- --></A><H3>\r
 396 saveRunConfiguration</H3>\r
 397 <PRE>\r
 398 boolean <B>saveRunConfiguration</B>()\r
 399                              throws <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></PRE>\r
 400 <DL>\r
 401 <DD><DL>\r
 402 </DL>\r
 403 </DD>\r
 404 <DD><DL>\r
 405 \r
 406 <DT><B>Throws:</B>\r
 407 <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></DL>\r
 408 </DD>\r
 409 </DL>\r
 410 <HR>\r
 411 \r
 412 <A NAME="loadRunConfiguration(java.io.InputStream)"><!-- --></A><H3>\r
 413 loadRunConfiguration</H3>\r
 414 <PRE>\r
 415 <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>loadRunConfiguration</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A>&nbsp;input)\r
 416                                              throws <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></PRE>\r
 417 <DL>\r
 418 <DD><DL>\r
 419 </DL>\r
 420 </DD>\r
 421 <DD><DL>\r
 422 \r
 423 <DT><B>Throws:</B>\r
 424 <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></DL>\r
 425 </DD>\r
 426 </DL>\r
 427 <HR>\r
 428 \r
 429 <A NAME="getExecProvider()"><!-- --></A><H3>\r
 430 getExecProvider</H3>\r
 431 <PRE>\r
 432 <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> <B>getExecProvider</B>()</PRE>\r
 433 <DL>\r
 434 <DD><DL>\r
 435 </DL>\r
 436 </DD>\r
 437 <DD><DL>\r
 438 </DL>\r
 439 </DD>\r
 440 </DL>\r
 441 <!-- ========= END OF CLASS DATA ========= -->\r
 442 <HR>\r
 443 \r
 444 \r
 445 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 446 <A NAME="navbar_bottom"><!-- --></A>\r
 447 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 448 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 449 <TR>\r
 450 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 451 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 452 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 453   <TR ALIGN="center" VALIGN="top">\r
 454   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 455   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 456   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 457   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ConfiguredExecutable.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 458   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 459   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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 462   </TR>\r
 463 </TABLE>\r
 464 </TD>\r
 465 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 466 </EM>\r
 467 </TD>\r
 468 </TR>\r
 469 \r
 470 <TR>\r
 471 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 472 &nbsp;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
 473 &nbsp;<A HREF="../../../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
 474 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 475   <A HREF="../../../index.html?compbio/engine/client/ConfiguredExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 476 &nbsp;<A HREF="ConfiguredExecutable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 477 &nbsp;<SCRIPT type="text/javascript">\r
 478   <!--\r
 479   if(window==top) {\r
 480     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 481   }\r
 482   //-->\r
 483 </SCRIPT>\r
 484 <NOSCRIPT>\r
 485   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 486 </NOSCRIPT>\r
 487 \r
 488 \r
 489 </FONT></TD>\r
 490 </TR>\r
 491 <TR>\r
 492 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 493   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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 499 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 500 \r
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