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

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   7 RunConfiguration\r
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   9 \r
  10 <META NAME="date" CONTENT="2011-08-12">\r
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  16 {\r
  17     if (location.href.indexOf('is-external=true') == -1) {\r
  18         parent.document.title="RunConfiguration";\r
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  43   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/RunConfiguration.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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  77 <TR>\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 RunConfiguration</H2>\r
  94 <PRE>\r
  95 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
  96   <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.client.RunConfiguration</B>\r
  97 </PRE>\r
  98 <HR>\r
  99 <DL>\r
 100 <DT><PRE>public class <B>RunConfiguration</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
 101 </PRE>\r
 102 \r
 103 <P>\r
 104 Value class for persisting ConfExecutable instances\r
 105 <P>\r
 106 \r
 107 <P>\r
 108 <DL>\r
 109 <DT><B>Author:</B></DT>\r
 110   <DD>pvtroshin</DD>\r
 111 </DL>\r
 112 <HR>\r
 113 \r
 114 <P>\r
 115 <!-- =========== FIELD SUMMARY =========== -->\r
 116 \r
 117 <A NAME="field_summary"><!-- --></A>\r
 118 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 119 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 120 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 121 <B>Field Summary</B></FONT></TH>\r
 122 </TR>\r
 123 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 124 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 125 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
 126 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#rconfigFile">rconfigFile</A></B></CODE>\r
 127 \r
 128 <BR>\r
 129 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 130 </TR>\r
 131 </TABLE>\r
 132 &nbsp;\r
 133 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 134 \r
 135 <A NAME="constructor_summary"><!-- --></A>\r
 136 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 137 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 138 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 139 <B>Constructor Summary</B></FONT></TH>\r
 140 </TR>\r
 141 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 142 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#RunConfiguration()">RunConfiguration</A></B>()</CODE>\r
 143 \r
 144 <BR>\r
 145 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 146 </TR>\r
 147 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 148 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#RunConfiguration(compbio.engine.client.ConfExecutable)">RunConfiguration</A></B>(<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>&lt;?&gt;&nbsp;cexec)</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 </TABLE>\r
 154 &nbsp;\r
 155 <!-- ========== METHOD SUMMARY =========== -->\r
 156 \r
 157 <A NAME="method_summary"><!-- --></A>\r
 158 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 159 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 160 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 161 <B>Method Summary</B></FONT></TH>\r
 162 </TR>\r
 163 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 164 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 165 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 166 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A>&nbsp;obj)</CODE>\r
 167 \r
 168 <BR>\r
 169 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 170 </TR>\r
 171 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 172 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 173 <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
 174 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#getError()">getError</A></B>()</CODE>\r
 175 \r
 176 <BR>\r
 177 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 178 </TR>\r
 179 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 180 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 181 <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
 182 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#getInput()">getInput</A></B>()</CODE>\r
 183 \r
 184 <BR>\r
 185 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 186 </TR>\r
 187 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 188 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 189 <CODE>&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
 190 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#getOutput()">getOutput</A></B>()</CODE>\r
 191 \r
 192 <BR>\r
 193 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 194 </TR>\r
 195 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 196 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 197 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;?&gt;</CODE></FONT></TD>\r
 198 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#getParameters()">getParameters</A></B>()</CODE>\r
 199 \r
 200 <BR>\r
 201 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 202 </TR>\r
 203 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 204 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 205 <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
 206 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#getRunnerClassName()">getRunnerClassName</A></B>()</CODE>\r
 207 \r
 208 <BR>\r
 209 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 210 </TR>\r
 211 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 212 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 213 <CODE>&nbsp;int</CODE></FONT></TD>\r
 214 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#hashCode()">hashCode</A></B>()</CODE>\r
 215 \r
 216 <BR>\r
 217 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 218 </TR>\r
 219 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 220 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 221 <CODE>static&nbsp;<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A></CODE></FONT></TD>\r
 222 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#load(java.io.InputStream)">load</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
 223 \r
 224 <BR>\r
 225 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 226 </TR>\r
 227 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 228 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 229 <CODE>&nbsp;void</CODE></FONT></TD>\r
 230 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#setError(java.lang.String)">setError</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;error)</CODE>\r
 231 \r
 232 <BR>\r
 233 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 234 </TR>\r
 235 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 236 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 237 <CODE>&nbsp;void</CODE></FONT></TD>\r
 238 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#setInput(java.lang.String)">setInput</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;input)</CODE>\r
 239 \r
 240 <BR>\r
 241 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 242 </TR>\r
 243 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 244 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 245 <CODE>&nbsp;void</CODE></FONT></TD>\r
 246 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#setOutput(java.lang.String)">setOutput</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;output)</CODE>\r
 247 \r
 248 <BR>\r
 249 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 250 </TR>\r
 251 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 252 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 253 <CODE>&nbsp;void</CODE></FONT></TD>\r
 254 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#setParameters(compbio.engine.client.CommandBuilder)">setParameters</A></B>(<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;?&gt;&nbsp;parameters)</CODE>\r
 255 \r
 256 <BR>\r
 257 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 258 </TR>\r
 259 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 260 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 261 <CODE>&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
 262 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#toString()">toString</A></B>()</CODE>\r
 263 \r
 264 <BR>\r
 265 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 266 </TR>\r
 267 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 268 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 269 <CODE>static&nbsp;boolean</CODE></FONT></TD>\r
 270 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#write(compbio.engine.client.RunConfiguration)">write</A></B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconf)</CODE>\r
 271 \r
 272 <BR>\r
 273 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 274 </TR>\r
 275 </TABLE>\r
 276 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 277 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 278 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 279 <TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
 280 </TR>\r
 281 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 282 <TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
 283 </TR>\r
 284 </TABLE>\r
 285 &nbsp;\r
 286 <P>\r
 287 \r
 288 <!-- ============ FIELD DETAIL =========== -->\r
 289 \r
 290 <A NAME="field_detail"><!-- --></A>\r
 291 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 292 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 293 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 294 <B>Field Detail</B></FONT></TH>\r
 295 </TR>\r
 296 </TABLE>\r
 297 \r
 298 <A NAME="rconfigFile"><!-- --></A><H3>\r
 299 rconfigFile</H3>\r
 300 <PRE>\r
 301 public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>rconfigFile</B></PRE>\r
 302 <DL>\r
 303 <DL>\r
 304 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.engine.client.RunConfiguration.rconfigFile">Constant Field Values</A></DL>\r
 305 </DL>\r
 306 \r
 307 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 308 \r
 309 <A NAME="constructor_detail"><!-- --></A>\r
 310 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 311 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 312 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 313 <B>Constructor Detail</B></FONT></TH>\r
 314 </TR>\r
 315 </TABLE>\r
 316 \r
 317 <A NAME="RunConfiguration()"><!-- --></A><H3>\r
 318 RunConfiguration</H3>\r
 319 <PRE>\r
 320 public <B>RunConfiguration</B>()</PRE>\r
 321 <DL>\r
 322 </DL>\r
 323 <HR>\r
 324 \r
 325 <A NAME="RunConfiguration(compbio.engine.client.ConfExecutable)"><!-- --></A><H3>\r
 326 RunConfiguration</H3>\r
 327 <PRE>\r
 328 public <B>RunConfiguration</B>(<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>&lt;?&gt;&nbsp;cexec)</PRE>\r
 329 <DL>\r
 330 </DL>\r
 331 \r
 332 <!-- ============ METHOD DETAIL ========== -->\r
 333 \r
 334 <A NAME="method_detail"><!-- --></A>\r
 335 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 336 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 337 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 338 <B>Method Detail</B></FONT></TH>\r
 339 </TR>\r
 340 </TABLE>\r
 341 \r
 342 <A NAME="write(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>\r
 343 write</H3>\r
 344 <PRE>\r
 345 public static boolean <B>write</B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconf)\r
 346                      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
 347 <DL>\r
 348 <DD><DL>\r
 349 \r
 350 <DT><B>Throws:</B>\r
 351 <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
 352 </DD>\r
 353 </DL>\r
 354 <HR>\r
 355 \r
 356 <A NAME="load(java.io.InputStream)"><!-- --></A><H3>\r
 357 load</H3>\r
 358 <PRE>\r
 359 public static <A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> <B>load</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
 360                              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
 361 <DL>\r
 362 <DD><DL>\r
 363 \r
 364 <DT><B>Throws:</B>\r
 365 <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
 366 </DD>\r
 367 </DL>\r
 368 <HR>\r
 369 \r
 370 <A NAME="setOutput(java.lang.String)"><!-- --></A><H3>\r
 371 setOutput</H3>\r
 372 <PRE>\r
 373 public void <B>setOutput</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;output)</PRE>\r
 374 <DL>\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 public <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;?&gt; <B>getParameters</B>()</PRE>\r
 385 <DL>\r
 386 <DD><DL>\r
 387 </DL>\r
 388 </DD>\r
 389 </DL>\r
 390 <HR>\r
 391 \r
 392 <A NAME="setParameters(compbio.engine.client.CommandBuilder)"><!-- --></A><H3>\r
 393 setParameters</H3>\r
 394 <PRE>\r
 395 public void <B>setParameters</B>(<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;?&gt;&nbsp;parameters)</PRE>\r
 396 <DL>\r
 397 <DD><DL>\r
 398 </DL>\r
 399 </DD>\r
 400 </DL>\r
 401 <HR>\r
 402 \r
 403 <A NAME="getOutput()"><!-- --></A><H3>\r
 404 getOutput</H3>\r
 405 <PRE>\r
 406 public <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
 407 <DL>\r
 408 <DD><DL>\r
 409 </DL>\r
 410 </DD>\r
 411 </DL>\r
 412 <HR>\r
 413 \r
 414 <A NAME="setError(java.lang.String)"><!-- --></A><H3>\r
 415 setError</H3>\r
 416 <PRE>\r
 417 public void <B>setError</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;error)</PRE>\r
 418 <DL>\r
 419 <DD><DL>\r
 420 </DL>\r
 421 </DD>\r
 422 </DL>\r
 423 <HR>\r
 424 \r
 425 <A NAME="getError()"><!-- --></A><H3>\r
 426 getError</H3>\r
 427 <PRE>\r
 428 public <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
 429 <DL>\r
 430 <DD><DL>\r
 431 </DL>\r
 432 </DD>\r
 433 </DL>\r
 434 <HR>\r
 435 \r
 436 <A NAME="getInput()"><!-- --></A><H3>\r
 437 getInput</H3>\r
 438 <PRE>\r
 439 public <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
 440 <DL>\r
 441 <DD><DL>\r
 442 </DL>\r
 443 </DD>\r
 444 </DL>\r
 445 <HR>\r
 446 \r
 447 <A NAME="setInput(java.lang.String)"><!-- --></A><H3>\r
 448 setInput</H3>\r
 449 <PRE>\r
 450 public void <B>setInput</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;input)</PRE>\r
 451 <DL>\r
 452 <DD><DL>\r
 453 </DL>\r
 454 </DD>\r
 455 </DL>\r
 456 <HR>\r
 457 \r
 458 <A NAME="getRunnerClassName()"><!-- --></A><H3>\r
 459 getRunnerClassName</H3>\r
 460 <PRE>\r
 461 public <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>getRunnerClassName</B>()</PRE>\r
 462 <DL>\r
 463 <DD><DL>\r
 464 </DL>\r
 465 </DD>\r
 466 </DL>\r
 467 <HR>\r
 468 \r
 469 <A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
 470 equals</H3>\r
 471 <PRE>\r
 472 public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A>&nbsp;obj)</PRE>\r
 473 <DL>\r
 474 <DD><DL>\r
 475 <DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
 476 </DD>\r
 477 <DD><DL>\r
 478 </DL>\r
 479 </DD>\r
 480 </DL>\r
 481 <HR>\r
 482 \r
 483 <A NAME="hashCode()"><!-- --></A><H3>\r
 484 hashCode</H3>\r
 485 <PRE>\r
 486 public int <B>hashCode</B>()</PRE>\r
 487 <DL>\r
 488 <DD><DL>\r
 489 <DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
 490 </DD>\r
 491 <DD><DL>\r
 492 </DL>\r
 493 </DD>\r
 494 </DL>\r
 495 <HR>\r
 496 \r
 497 <A NAME="toString()"><!-- --></A><H3>\r
 498 toString</H3>\r
 499 <PRE>\r
 500 public <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>toString</B>()</PRE>\r
 501 <DL>\r
 502 <DD><DL>\r
 503 <DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
 504 </DD>\r
 505 <DD><DL>\r
 506 </DL>\r
 507 </DD>\r
 508 </DL>\r
 509 <!-- ========= END OF CLASS DATA ========= -->\r
 510 <HR>\r
 511 \r
 512 \r
 513 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 514 <A NAME="navbar_bottom"><!-- --></A>\r
 515 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 516 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 517 <TR>\r
 518 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 519 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 520 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 521   <TR ALIGN="center" VALIGN="top">\r
 522   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 523   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 524   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 525   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/RunConfiguration.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 526   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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 529   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 530   </TR>\r
 531 </TABLE>\r
 532 </TD>\r
 533 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 534 </EM>\r
 535 </TD>\r
 536 </TR>\r
 537 \r
 538 <TR>\r
 539 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 540 &nbsp;<A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
 541 &nbsp;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
 542 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 543   <A HREF="../../../index.html?compbio/engine/client/RunConfiguration.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 544 &nbsp;<A HREF="RunConfiguration.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 545 &nbsp;<SCRIPT type="text/javascript">\r
 546   <!--\r
 547   if(window==top) {\r
 548     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 549   }\r
 550   //-->\r
 551 </SCRIPT>\r
 552 <NOSCRIPT>\r
 553   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 554 </NOSCRIPT>\r
 555 \r
 556 \r
 557 </FONT></TD>\r
 558 </TR>\r
 559 <TR>\r
 560 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 561   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
 562 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 563 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
 564 </TR>\r
 565 </TABLE>\r
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 570 \r
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 572 </HTML>\r