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

   1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
   2 <!--NewPage-->\r
   3 <HTML>\r
   4 <HEAD>\r
   5 <!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
   6 <TITLE>\r
   7 Uses of Package compbio.engine.client\r
   8 </TITLE>\r
   9 \r
  10 <META NAME="date" CONTENT="2010-02-17">\r
  11 \r
  12 <LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
  13 \r
  14 <SCRIPT type="text/javascript">\r
  15 function windowTitle()\r
  16 {\r
  17     if (location.href.indexOf('is-external=true') == -1) {\r
  18         parent.document.title="Uses of Package compbio.engine.client";\r
  19     }\r
  20 }\r
  21 </SCRIPT>\r
  22 <NOSCRIPT>\r
  23 </NOSCRIPT>\r
  24 \r
  25 </HEAD>\r
  26 \r
  27 <BODY BGCOLOR="white" onload="windowTitle();">\r
  28 <HR>\r
  29 \r
  30 \r
  31 <!-- ========= START OF TOP NAVBAR ======= -->\r
  32 <A NAME="navbar_top"><!-- --></A>\r
  33 <A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
  34 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
  35 <TR>\r
  36 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
  37 <A NAME="navbar_top_firstrow"><!-- --></A>\r
  38 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
  39   <TR ALIGN="center" VALIGN="top">\r
  40   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
  41   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
  42   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
  43   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
  44   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
  45   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
  46   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
  47   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
  48   </TR>\r
  49 </TABLE>\r
  50 </TD>\r
  51 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
  52 </EM>\r
  53 </TD>\r
  54 </TR>\r
  55 \r
  56 <TR>\r
  57 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
  58 &nbsp;PREV&nbsp;\r
  59 &nbsp;NEXT</FONT></TD>\r
  60 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
  61   <A HREF="../../../index.html?compbio/engine/client/package-use.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
  62 &nbsp;<A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
  63 &nbsp;<SCRIPT type="text/javascript">\r
  64   <!--\r
  65   if(window==top) {\r
  66     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
  67   }\r
  68   //-->\r
  69 </SCRIPT>\r
  70 <NOSCRIPT>\r
  71   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
  72 </NOSCRIPT>\r
  73 \r
  74 \r
  75 </FONT></TD>\r
  76 </TR>\r
  77 </TABLE>\r
  78 <A NAME="skip-navbar_top"></A>\r
  79 <!-- ========= END OF TOP NAVBAR ========= -->\r
  80 \r
  81 <HR>\r
  82 <CENTER>\r
  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>Classes and interfaces representing an input for engines.&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>An cluster engine classes responsible for execution of Executables on the clusters.&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>Classes commonly used by both engines.&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>An local engine classes responsible for execution of Executables on the local computer
 111  (the same machine as JVM running these classes).&nbsp;</TD>\r
 112 </TR>\r
 113 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 114 <TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
 115 <TD>Utilities commonly used by all runners.&nbsp;</TD>\r
 116 </TR>\r
 117 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 118 <TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>\r
 119 <TD>&nbsp;&nbsp;</TD>\r
 120 </TR>\r
 121 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 122 <TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
 123 <TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
 124 </TR>\r
 125 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 126 <TD><A HREF="#compbio.runner.psiblast"><B>compbio.runner.psiblast</B></A></TD>\r
 127 <TD>&nbsp;&nbsp;</TD>\r
 128 </TR>\r
 129 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 130 <TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
 131 <TD>&nbsp;&nbsp;</TD>\r
 132 </TR>\r
 133 </TABLE>\r
 134 &nbsp;\r
 135 <P>\r
 136 <A NAME="compbio.engine"><!-- --></A>\r
 137 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 138 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 139 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 140 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
 141 </TR>\r
 142 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 143 <TD><B><A HREF="../../../compbio/engine/client/class-use/ConfiguredExecutable.html#compbio.engine"><B>ConfiguredExecutable</B></A></B>\r
 144 \r
 145 <BR>\r
 146 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 147 </TR>\r
 148 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 149 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.engine"><B>Executable</B></A></B>\r
 150 \r
 151 <BR>\r
 152 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Interface to a native executable.</TD>\r
 153 </TR>\r
 154 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 155 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.ExecProvider.html#compbio.engine"><B>Executable.ExecProvider</B></A></B>\r
 156 \r
 157 <BR>\r
 158 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 159 </TR>\r
 160 </TABLE>\r
 161 &nbsp;\r
 162 <P>\r
 163 <A NAME="compbio.engine.client"><!-- --></A>\r
 164 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 165 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 166 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 167 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
 168 </TR>\r
 169 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 170 <TD><B><A HREF="../../../compbio/engine/client/class-use/CommandBuilder.html#compbio.engine.client"><B>CommandBuilder</B></A></B>\r
 171 \r
 172 <BR>\r
 173 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 174 </TR>\r
 175 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 176 <TD><B><A HREF="../../../compbio/engine/client/class-use/ConfExecutable.html#compbio.engine.client"><B>ConfExecutable</B></A></B>\r
 177 \r
 178 <BR>\r
 179 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 180 </TR>\r
 181 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 182 <TD><B><A HREF="../../../compbio/engine/client/class-use/ConfiguredExecutable.html#compbio.engine.client"><B>ConfiguredExecutable</B></A></B>\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><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.engine.client"><B>Executable</B></A></B>\r
 189 \r
 190 <BR>\r
 191 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Interface to a native executable.</TD>\r
 192 </TR>\r
 193 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 194 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.ExecProvider.html#compbio.engine.client"><B>Executable.ExecProvider</B></A></B>\r
 195 \r
 196 <BR>\r
 197 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 198 </TR>\r
 199 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 200 <TD><B><A HREF="../../../compbio/engine/client/class-use/PipedExecutable.html#compbio.engine.client"><B>PipedExecutable</B></A></B>\r
 201 \r
 202 <BR>\r
 203 &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
 204  captured.</TD>\r
 205 </TR>\r
 206 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 207 <TD><B><A HREF="../../../compbio/engine/client/class-use/RunConfiguration.html#compbio.engine.client"><B>RunConfiguration</B></A></B>\r
 208 \r
 209 <BR>\r
 210 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Value class for persisting ConfExecutable instances</TD>\r
 211 </TR>\r
 212 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 213 <TD><B><A HREF="../../../compbio/engine/client/class-use/SkeletalExecutable.html#compbio.engine.client"><B>SkeletalExecutable</B></A></B>\r
 214 \r
 215 <BR>\r
 216 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 217 </TR>\r
 218 </TABLE>\r
 219 &nbsp;\r
 220 <P>\r
 221 <A NAME="compbio.engine.cluster.drmaa"><!-- --></A>\r
 222 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 223 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 224 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 225 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
 226 </TR>\r
 227 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 228 <TD><B><A HREF="../../../compbio/engine/client/class-use/ConfiguredExecutable.html#compbio.engine.cluster.drmaa"><B>ConfiguredExecutable</B></A></B>\r
 229 \r
 230 <BR>\r
 231 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 232 </TR>\r
 233 </TABLE>\r
 234 &nbsp;\r
 235 <P>\r
 236 <A NAME="compbio.engine.conf"><!-- --></A>\r
 237 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 238 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 239 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 240 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
 241 </TR>\r
 242 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 243 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.engine.conf"><B>Executable</B></A></B>\r
 244 \r
 245 <BR>\r
 246 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Interface to a native executable.</TD>\r
 247 </TR>\r
 248 </TABLE>\r
 249 &nbsp;\r
 250 <P>\r
 251 <A NAME="compbio.engine.local"><!-- --></A>\r
 252 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 253 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 254 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 255 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
 256 </TR>\r
 257 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 258 <TD><B><A HREF="../../../compbio/engine/client/class-use/ConfiguredExecutable.html#compbio.engine.local"><B>ConfiguredExecutable</B></A></B>\r
 259 \r
 260 <BR>\r
 261 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 262 </TR>\r
 263 </TABLE>\r
 264 &nbsp;\r
 265 <P>\r
 266 <A NAME="compbio.runner"><!-- --></A>\r
 267 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 268 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 269 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 270 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
 271 </TR>\r
 272 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 273 <TD><B><A HREF="../../../compbio/engine/client/class-use/CommandBuilder.html#compbio.runner"><B>CommandBuilder</B></A></B>\r
 274 \r
 275 <BR>\r
 276 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 277 </TR>\r
 278 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 279 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.runner"><B>Executable</B></A></B>\r
 280 \r
 281 <BR>\r
 282 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Interface to a native executable.</TD>\r
 283 </TR>\r
 284 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 285 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.ExecProvider.html#compbio.runner"><B>Executable.ExecProvider</B></A></B>\r
 286 \r
 287 <BR>\r
 288 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 289 </TR>\r
 290 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 291 <TD><B><A HREF="../../../compbio/engine/client/class-use/RunConfiguration.html#compbio.runner"><B>RunConfiguration</B></A></B>\r
 292 \r
 293 <BR>\r
 294 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Value class for persisting ConfExecutable instances</TD>\r
 295 </TR>\r
 296 </TABLE>\r
 297 &nbsp;\r
 298 <P>\r
 299 <A NAME="compbio.runner._impl"><!-- --></A>\r
 300 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 301 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 302 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 303 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
 304 </TR>\r
 305 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 306 <TD><B><A HREF="../../../compbio/engine/client/class-use/CommandBuilder.html#compbio.runner._impl"><B>CommandBuilder</B></A></B>\r
 307 \r
 308 <BR>\r
 309 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 310 </TR>\r
 311 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 312 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.runner._impl"><B>Executable</B></A></B>\r
 313 \r
 314 <BR>\r
 315 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Interface to a native executable.</TD>\r
 316 </TR>\r
 317 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 318 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.ExecProvider.html#compbio.runner._impl"><B>Executable.ExecProvider</B></A></B>\r
 319 \r
 320 <BR>\r
 321 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 322 </TR>\r
 323 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 324 <TD><B><A HREF="../../../compbio/engine/client/class-use/RunConfiguration.html#compbio.runner._impl"><B>RunConfiguration</B></A></B>\r
 325 \r
 326 <BR>\r
 327 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Value class for persisting ConfExecutable instances</TD>\r
 328 </TR>\r
 329 </TABLE>\r
 330 &nbsp;\r
 331 <P>\r
 332 <A NAME="compbio.runner.msa"><!-- --></A>\r
 333 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 334 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 335 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 336 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
 337 </TR>\r
 338 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 339 <TD><B><A HREF="../../../compbio/engine/client/class-use/ClusterNativeSpecExecutable.html#compbio.runner.msa"><B>ClusterNativeSpecExecutable</B></A></B>\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><B><A HREF="../../../compbio/engine/client/class-use/CommandBuilder.html#compbio.runner.msa"><B>CommandBuilder</B></A></B>\r
 346 \r
 347 <BR>\r
 348 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 349 </TR>\r
 350 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 351 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.runner.msa"><B>Executable</B></A></B>\r
 352 \r
 353 <BR>\r
 354 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Interface to a native executable.</TD>\r
 355 </TR>\r
 356 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 357 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.ExecProvider.html#compbio.runner.msa"><B>Executable.ExecProvider</B></A></B>\r
 358 \r
 359 <BR>\r
 360 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 361 </TR>\r
 362 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 363 <TD><B><A HREF="../../../compbio/engine/client/class-use/PipedExecutable.html#compbio.runner.msa"><B>PipedExecutable</B></A></B>\r
 364 \r
 365 <BR>\r
 366 &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
 367  captured.</TD>\r
 368 </TR>\r
 369 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 370 <TD><B><A HREF="../../../compbio/engine/client/class-use/SkeletalExecutable.html#compbio.runner.msa"><B>SkeletalExecutable</B></A></B>\r
 371 \r
 372 <BR>\r
 373 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 374 </TR>\r
 375 </TABLE>\r
 376 &nbsp;\r
 377 <P>\r
 378 <A NAME="compbio.runner.psiblast"><!-- --></A>\r
 379 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 380 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 381 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 382 Classes in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> used by <A HREF="../../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A></FONT></TH>\r
 383 </TR>\r
 384 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 385 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.runner.psiblast"><B>Executable</B></A></B>\r
 386 \r
 387 <BR>\r
 388 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Interface to a native executable.</TD>\r
 389 </TR>\r
 390 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 391 <TD><B><A HREF="../../../compbio/engine/client/class-use/SkeletalExecutable.html#compbio.runner.psiblast"><B>SkeletalExecutable</B></A></B>\r
 392 \r
 393 <BR>\r
 394 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 395 </TR>\r
 396 </TABLE>\r
 397 &nbsp;\r
 398 <P>\r
 399 <A NAME="compbio.ws.server"><!-- --></A>\r
 400 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 401 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 402 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 403 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
 404 </TR>\r
 405 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 406 <TD><B><A HREF="../../../compbio/engine/client/class-use/ConfiguredExecutable.html#compbio.ws.server"><B>ConfiguredExecutable</B></A></B>\r
 407 \r
 408 <BR>\r
 409 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 410 </TR>\r
 411 </TABLE>\r
 412 &nbsp;\r
 413 <P>\r
 414 <HR>\r
 415 \r
 416 \r
 417 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 418 <A NAME="navbar_bottom"><!-- --></A>\r
 419 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 420 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 421 <TR>\r
 422 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 423 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 424 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 425   <TR ALIGN="center" VALIGN="top">\r
 426   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 427   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 428   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
 429   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
 430   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 431   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 432   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 433   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 434   </TR>\r
 435 </TABLE>\r
 436 </TD>\r
 437 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 438 </EM>\r
 439 </TD>\r
 440 </TR>\r
 441 \r
 442 <TR>\r
 443 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 444 &nbsp;PREV&nbsp;\r
 445 &nbsp;NEXT</FONT></TD>\r
 446 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 447   <A HREF="../../../index.html?compbio/engine/client/package-use.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 448 &nbsp;<A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 449 &nbsp;<SCRIPT type="text/javascript">\r
 450   <!--\r
 451   if(window==top) {\r
 452     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 453   }\r
 454   //-->\r
 455 </SCRIPT>\r
 456 <NOSCRIPT>\r
 457   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 458 </NOSCRIPT>\r
 459 \r
 460 \r
 461 </FONT></TD>\r
 462 </TR>\r
 463 </TABLE>\r
 464 <A NAME="skip-navbar_bottom"></A>\r
 465 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 466 \r
 467 <HR>\r
 468 \r
 469 </BODY>\r
 470 </HTML>\r