website/full_javadoc/compbio/engine/client/package-use.html

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   5 <!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:36 BST 2011 -->\r
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   7 Uses of Package compbio.engine.client\r
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   9 \r
  10 <META NAME="date" CONTENT="2011-08-12">\r
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  43   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
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  80 \r
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  83 <H2>\r
  84 <B>Uses of Package<br>compbio.engine.client</B></H2>\r
  85 </CENTER>\r
  86 \r
  87 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
  88 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
  89 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
  90 Packages that use <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
  91 </TR>\r
  92 <TR BGCOLOR="white" CLASS="TableRowColor">\r
  93 <TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>\r
  94 <TD>&nbsp;&nbsp;</TD>\r
  95 </TR>\r
  96 <TR BGCOLOR="white" CLASS="TableRowColor">\r
  97 <TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
  98 <TD>&nbsp;&nbsp;</TD>\r
  99 </TR>\r
 100 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 101 <TD><A HREF="#compbio.engine.cluster.drmaa"><B>compbio.engine.cluster.drmaa</B></A></TD>\r
 102 <TD>&nbsp;&nbsp;</TD>\r
 103 </TR>\r
 104 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 105 <TD><A HREF="#compbio.engine.conf"><B>compbio.engine.conf</B></A></TD>\r
 106 <TD>&nbsp;&nbsp;</TD>\r
 107 </TR>\r
 108 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 109 <TD><A HREF="#compbio.engine.local"><B>compbio.engine.local</B></A></TD>\r
 110 <TD>&nbsp;&nbsp;</TD>\r
 111 </TR>\r
 112 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 113 <TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
 114 <TD>Utilities commonly used by all runners.&nbsp;</TD>\r
 115 </TR>\r
 116 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 117 <TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>\r
 118 <TD>&nbsp;&nbsp;</TD>\r
 119 </TR>\r
 120 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 121 <TD><A HREF="#compbio.runner.conservation"><B>compbio.runner.conservation</B></A></TD>\r
 122 <TD>&nbsp;&nbsp;</TD>\r
 123 </TR>\r
 124 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 125 <TD><A HREF="#compbio.runner.disorder"><B>compbio.runner.disorder</B></A></TD>\r
 126 <TD>&nbsp;&nbsp;</TD>\r
 127 </TR>\r
 128 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 129 <TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
 130 <TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
 131 </TR>\r
 132 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 133 <TD><A HREF="#compbio.ws.client"><B>compbio.ws.client</B></A></TD>\r
 134 <TD>A command line client and web services testing client for
 135  JAva Bioinformatics Analysis Web Services.&nbsp;</TD>\r
 136 </TR>\r
 137 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 138 <TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
 139 <TD>&nbsp;&nbsp;</TD>\r
 140 </TR>\r
 141 </TABLE>\r
 142 &nbsp;\r
 143 <P>\r
 144 <A NAME="compbio.engine"><!-- --></A>\r
 145 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 146 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 147 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 148 Classes in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> used by <A HREF="../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>\r
 149 </TR>\r
 150 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 151 <TD><B><A HREF="../../../compbio/engine/client/class-use/ConfiguredExecutable.html#compbio.engine"><B>ConfiguredExecutable</B></A></B>\r
 152 \r
 153 <BR>\r
 154 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 155 </TR>\r
 156 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 157 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.engine"><B>Executable</B></A></B>\r
 158 \r
 159 <BR>\r
 160 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Interface to a native executable.</TD>\r
 161 </TR>\r
 162 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 163 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.ExecProvider.html#compbio.engine"><B>Executable.ExecProvider</B></A></B>\r
 164 \r
 165 <BR>\r
 166 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 167 </TR>\r
 168 </TABLE>\r
 169 &nbsp;\r
 170 <P>\r
 171 <A NAME="compbio.engine.client"><!-- --></A>\r
 172 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 173 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 174 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 175 Classes in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> used by <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
 176 </TR>\r
 177 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 178 <TD><B><A HREF="../../../compbio/engine/client/class-use/CommandBuilder.html#compbio.engine.client"><B>CommandBuilder</B></A></B>\r
 179 \r
 180 <BR>\r
 181 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 182 </TR>\r
 183 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 184 <TD><B><A HREF="../../../compbio/engine/client/class-use/ConfExecutable.html#compbio.engine.client"><B>ConfExecutable</B></A></B>\r
 185 \r
 186 <BR>\r
 187 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 188 </TR>\r
 189 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 190 <TD><B><A HREF="../../../compbio/engine/client/class-use/ConfiguredExecutable.html#compbio.engine.client"><B>ConfiguredExecutable</B></A></B>\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><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.engine.client"><B>Executable</B></A></B>\r
 197 \r
 198 <BR>\r
 199 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Interface to a native executable.</TD>\r
 200 </TR>\r
 201 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 202 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.ExecProvider.html#compbio.engine.client"><B>Executable.ExecProvider</B></A></B>\r
 203 \r
 204 <BR>\r
 205 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 206 </TR>\r
 207 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 208 <TD><B><A HREF="../../../compbio/engine/client/class-use/PipedExecutable.html#compbio.engine.client"><B>PipedExecutable</B></A></B>\r
 209 \r
 210 <BR>\r
 211 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This is a marker interface to indicate that the output of the process must be
 212  captured.</TD>\r
 213 </TR>\r
 214 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 215 <TD><B><A HREF="../../../compbio/engine/client/class-use/RunConfiguration.html#compbio.engine.client"><B>RunConfiguration</B></A></B>\r
 216 \r
 217 <BR>\r
 218 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Value class for persisting ConfExecutable instances</TD>\r
 219 </TR>\r
 220 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 221 <TD><B><A HREF="../../../compbio/engine/client/class-use/SkeletalExecutable.html#compbio.engine.client"><B>SkeletalExecutable</B></A></B>\r
 222 \r
 223 <BR>\r
 224 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 225 </TR>\r
 226 </TABLE>\r
 227 &nbsp;\r
 228 <P>\r
 229 <A NAME="compbio.engine.cluster.drmaa"><!-- --></A>\r
 230 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 231 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 232 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 233 Classes in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> used by <A HREF="../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A></FONT></TH>\r
 234 </TR>\r
 235 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 236 <TD><B><A HREF="../../../compbio/engine/client/class-use/ConfiguredExecutable.html#compbio.engine.cluster.drmaa"><B>ConfiguredExecutable</B></A></B>\r
 237 \r
 238 <BR>\r
 239 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 240 </TR>\r
 241 </TABLE>\r
 242 &nbsp;\r
 243 <P>\r
 244 <A NAME="compbio.engine.conf"><!-- --></A>\r
 245 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 246 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 247 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 248 Classes in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> used by <A HREF="../../../compbio/engine/conf/package-summary.html">compbio.engine.conf</A></FONT></TH>\r
 249 </TR>\r
 250 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 251 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.engine.conf"><B>Executable</B></A></B>\r
 252 \r
 253 <BR>\r
 254 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Interface to a native executable.</TD>\r
 255 </TR>\r
 256 </TABLE>\r
 257 &nbsp;\r
 258 <P>\r
 259 <A NAME="compbio.engine.local"><!-- --></A>\r
 260 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 261 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 262 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 263 Classes in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> used by <A HREF="../../../compbio/engine/local/package-summary.html">compbio.engine.local</A></FONT></TH>\r
 264 </TR>\r
 265 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 266 <TD><B><A HREF="../../../compbio/engine/client/class-use/ConfiguredExecutable.html#compbio.engine.local"><B>ConfiguredExecutable</B></A></B>\r
 267 \r
 268 <BR>\r
 269 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 270 </TR>\r
 271 </TABLE>\r
 272 &nbsp;\r
 273 <P>\r
 274 <A NAME="compbio.runner"><!-- --></A>\r
 275 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 276 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 277 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 278 Classes in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> used by <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
 279 </TR>\r
 280 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 281 <TD><B><A HREF="../../../compbio/engine/client/class-use/CommandBuilder.html#compbio.runner"><B>CommandBuilder</B></A></B>\r
 282 \r
 283 <BR>\r
 284 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 285 </TR>\r
 286 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 287 <TD><B><A HREF="../../../compbio/engine/client/class-use/ConfiguredExecutable.html#compbio.runner"><B>ConfiguredExecutable</B></A></B>\r
 288 \r
 289 <BR>\r
 290 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 291 </TR>\r
 292 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 293 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.runner"><B>Executable</B></A></B>\r
 294 \r
 295 <BR>\r
 296 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Interface to a native executable.</TD>\r
 297 </TR>\r
 298 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 299 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.ExecProvider.html#compbio.runner"><B>Executable.ExecProvider</B></A></B>\r
 300 \r
 301 <BR>\r
 302 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 303 </TR>\r
 304 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 305 <TD><B><A HREF="../../../compbio/engine/client/class-use/RunConfiguration.html#compbio.runner"><B>RunConfiguration</B></A></B>\r
 306 \r
 307 <BR>\r
 308 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Value class for persisting ConfExecutable instances</TD>\r
 309 </TR>\r
 310 </TABLE>\r
 311 &nbsp;\r
 312 <P>\r
 313 <A NAME="compbio.runner._impl"><!-- --></A>\r
 314 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 315 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 316 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 317 Classes in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> used by <A HREF="../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
 318 </TR>\r
 319 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 320 <TD><B><A HREF="../../../compbio/engine/client/class-use/CommandBuilder.html#compbio.runner._impl"><B>CommandBuilder</B></A></B>\r
 321 \r
 322 <BR>\r
 323 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 324 </TR>\r
 325 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 326 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.runner._impl"><B>Executable</B></A></B>\r
 327 \r
 328 <BR>\r
 329 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Interface to a native executable.</TD>\r
 330 </TR>\r
 331 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 332 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.ExecProvider.html#compbio.runner._impl"><B>Executable.ExecProvider</B></A></B>\r
 333 \r
 334 <BR>\r
 335 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 336 </TR>\r
 337 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 338 <TD><B><A HREF="../../../compbio/engine/client/class-use/RunConfiguration.html#compbio.runner._impl"><B>RunConfiguration</B></A></B>\r
 339 \r
 340 <BR>\r
 341 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Value class for persisting ConfExecutable instances</TD>\r
 342 </TR>\r
 343 </TABLE>\r
 344 &nbsp;\r
 345 <P>\r
 346 <A NAME="compbio.runner.conservation"><!-- --></A>\r
 347 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 348 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 349 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 350 Classes in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> used by <A HREF="../../../compbio/runner/conservation/package-summary.html">compbio.runner.conservation</A></FONT></TH>\r
 351 </TR>\r
 352 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 353 <TD><B><A HREF="../../../compbio/engine/client/class-use/CommandBuilder.html#compbio.runner.conservation"><B>CommandBuilder</B></A></B>\r
 354 \r
 355 <BR>\r
 356 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 357 </TR>\r
 358 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 359 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.runner.conservation"><B>Executable</B></A></B>\r
 360 \r
 361 <BR>\r
 362 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Interface to a native executable.</TD>\r
 363 </TR>\r
 364 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 365 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.ExecProvider.html#compbio.runner.conservation"><B>Executable.ExecProvider</B></A></B>\r
 366 \r
 367 <BR>\r
 368 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 369 </TR>\r
 370 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 371 <TD><B><A HREF="../../../compbio/engine/client/class-use/SkeletalExecutable.html#compbio.runner.conservation"><B>SkeletalExecutable</B></A></B>\r
 372 \r
 373 <BR>\r
 374 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 375 </TR>\r
 376 </TABLE>\r
 377 &nbsp;\r
 378 <P>\r
 379 <A NAME="compbio.runner.disorder"><!-- --></A>\r
 380 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 381 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 382 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 383 Classes in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> used by <A HREF="../../../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A></FONT></TH>\r
 384 </TR>\r
 385 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 386 <TD><B><A HREF="../../../compbio/engine/client/class-use/CommandBuilder.html#compbio.runner.disorder"><B>CommandBuilder</B></A></B>\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><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.runner.disorder"><B>Executable</B></A></B>\r
 393 \r
 394 <BR>\r
 395 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Interface to a native executable.</TD>\r
 396 </TR>\r
 397 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 398 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.ExecProvider.html#compbio.runner.disorder"><B>Executable.ExecProvider</B></A></B>\r
 399 \r
 400 <BR>\r
 401 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 402 </TR>\r
 403 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 404 <TD><B><A HREF="../../../compbio/engine/client/class-use/PipedExecutable.html#compbio.runner.disorder"><B>PipedExecutable</B></A></B>\r
 405 \r
 406 <BR>\r
 407 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This is a marker interface to indicate that the output of the process must be
 408  captured.</TD>\r
 409 </TR>\r
 410 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 411 <TD><B><A HREF="../../../compbio/engine/client/class-use/SkeletalExecutable.html#compbio.runner.disorder"><B>SkeletalExecutable</B></A></B>\r
 412 \r
 413 <BR>\r
 414 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 415 </TR>\r
 416 </TABLE>\r
 417 &nbsp;\r
 418 <P>\r
 419 <A NAME="compbio.runner.msa"><!-- --></A>\r
 420 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 421 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 422 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 423 Classes in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> used by <A HREF="../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
 424 </TR>\r
 425 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 426 <TD><B><A HREF="../../../compbio/engine/client/class-use/CommandBuilder.html#compbio.runner.msa"><B>CommandBuilder</B></A></B>\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><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.runner.msa"><B>Executable</B></A></B>\r
 433 \r
 434 <BR>\r
 435 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Interface to a native executable.</TD>\r
 436 </TR>\r
 437 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 438 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.ExecProvider.html#compbio.runner.msa"><B>Executable.ExecProvider</B></A></B>\r
 439 \r
 440 <BR>\r
 441 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 442 </TR>\r
 443 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 444 <TD><B><A HREF="../../../compbio/engine/client/class-use/PipedExecutable.html#compbio.runner.msa"><B>PipedExecutable</B></A></B>\r
 445 \r
 446 <BR>\r
 447 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This is a marker interface to indicate that the output of the process must be
 448  captured.</TD>\r
 449 </TR>\r
 450 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 451 <TD><B><A HREF="../../../compbio/engine/client/class-use/SkeletalExecutable.html#compbio.runner.msa"><B>SkeletalExecutable</B></A></B>\r
 452 \r
 453 <BR>\r
 454 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 455 </TR>\r
 456 </TABLE>\r
 457 &nbsp;\r
 458 <P>\r
 459 <A NAME="compbio.ws.client"><!-- --></A>\r
 460 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 461 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 462 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 463 Classes in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> used by <A HREF="../../../compbio/ws/client/package-summary.html">compbio.ws.client</A></FONT></TH>\r
 464 </TR>\r
 465 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 466 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.ws.client"><B>Executable</B></A></B>\r
 467 \r
 468 <BR>\r
 469 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Interface to a native executable.</TD>\r
 470 </TR>\r
 471 </TABLE>\r
 472 &nbsp;\r
 473 <P>\r
 474 <A NAME="compbio.ws.server"><!-- --></A>\r
 475 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 476 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 477 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 478 Classes in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> used by <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
 479 </TR>\r
 480 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 481 <TD><B><A HREF="../../../compbio/engine/client/class-use/ConfiguredExecutable.html#compbio.ws.server"><B>ConfiguredExecutable</B></A></B>\r
 482 \r
 483 <BR>\r
 484 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 485 </TR>\r
 486 </TABLE>\r
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