website/full_javadoc/compbio/engine/client/class-use/Executable.html

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   7 Uses of Interface compbio.engine.client.Executable\r
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  83 <H2>\r
  84 <B>Uses of Interface<br>compbio.engine.client.Executable</B></H2>\r
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  86 \r
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  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/Executable.html" title="interface in compbio.engine.client">Executable</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.conf"><B>compbio.engine.conf</B></A></TD>\r
 102 <TD>Classes commonly used by both engines.&nbsp;</TD>\r
 103 </TR>\r
 104 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 105 <TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
 106 <TD>Utilities commonly used by all runners.&nbsp;</TD>\r
 107 </TR>\r
 108 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 109 <TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</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.msa"><B>compbio.runner.msa</B></A></TD>\r
 114 <TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
 115 </TR>\r
 116 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 117 <TD><A HREF="#compbio.runner.psiblast"><B>compbio.runner.psiblast</B></A></TD>\r
 118 <TD>&nbsp;&nbsp;</TD>\r
 119 </TR>\r
 120 </TABLE>\r
 121 &nbsp;\r
 122 <P>\r
 123 <A NAME="compbio.engine"><!-- --></A>\r
 124 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 125 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 126 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 127 Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>\r
 128 </TR>\r
 129 </TABLE>\r
 130 &nbsp;\r
 131 <P>\r
 132 \r
 133 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 134 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 135 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A> with parameters of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
 136 </TR>\r
 137 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 138 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 139 <CODE>static\r
 140 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 141 <TR ALIGN="right" VALIGN="">\r
 142 <TD NOWRAP><FONT SIZE="-1">\r
 143 <CODE>&lt;T&gt; <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
 144 </TR>\r
 145 </TABLE>\r
 146 </CODE></FONT></TD>\r
 147 <TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable)">configureExecutable</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable)</CODE>\r
 148 \r
 149 <BR>\r
 150 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 151 </TR>\r
 152 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 153 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 154 <CODE>static\r
 155 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 156 <TR ALIGN="right" VALIGN="">\r
 157 <TD NOWRAP><FONT SIZE="-1">\r
 158 <CODE>&lt;T&gt; <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
 159 </TR>\r
 160 </TABLE>\r
 161 </CODE></FONT></TD>\r
 162 <TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, compbio.engine.client.Executable.ExecProvider)">configureExecutable</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable,\r
 163                     <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
 164 \r
 165 <BR>\r
 166 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 167 </TR>\r
 168 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 169 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 170 <CODE>static\r
 171 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 172 <TR ALIGN="right" VALIGN="">\r
 173 <TD NOWRAP><FONT SIZE="-1">\r
 174 <CODE>&lt;T&gt; <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
 175 </TR>\r
 176 </TABLE>\r
 177 </CODE></FONT></TD>\r
 178 <TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, java.util.List)">configureExecutable</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable,\r
 179                     java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;dataSet)</CODE>\r
 180 \r
 181 <BR>\r
 182 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 183 </TR>\r
 184 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 185 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 186 <CODE>static&nbsp;<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
 187 <TD><CODE><B>LoadBalancer.</B><B><A HREF="../../../../compbio/engine/LoadBalancer.html#getEngine(compbio.engine.client.Executable)">getEngine</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&nbsp;executable)</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>static\r
 195 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 196 <TR ALIGN="right" VALIGN="">\r
 197 <TD NOWRAP><FONT SIZE="-1">\r
 198 <CODE>&lt;T,V&gt; <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
 199 </TR>\r
 200 </TABLE>\r
 201 </CODE></FONT></TD>\r
 202 <TD><CODE><B>LoadBalancer.</B><B><A HREF="../../../../compbio/engine/LoadBalancer.html#getEngine(compbio.engine.client.Executable, java.util.List)">getEngine</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&nbsp;executable,\r
 203           java.util.List&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;dataSet)</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 </TABLE>\r
 209 &nbsp;\r
 210 <P>\r
 211 <A NAME="compbio.engine.client"><!-- --></A>\r
 212 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 213 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 214 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 215 Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
 216 </TR>\r
 217 </TABLE>\r
 218 &nbsp;\r
 219 <P>\r
 220 \r
 221 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 222 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 223 <TH ALIGN="left" COLSPAN="2">Subinterfaces of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
 224 </TR>\r
 225 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 226 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 227 <CODE>&nbsp;interface</CODE></FONT></TD>\r
 228 <TD><CODE><B><A HREF="../../../../compbio/engine/client/ClusterNativeSpecExecutable.html" title="interface in compbio.engine.client">ClusterNativeSpecExecutable&lt;T&gt;</A></B></CODE>\r
 229 \r
 230 <BR>\r
 231 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 232 </TR>\r
 233 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 234 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 235 <CODE>&nbsp;interface</CODE></FONT></TD>\r
 236 <TD><CODE><B><A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable&lt;T&gt;</A></B></CODE>\r
 237 \r
 238 <BR>\r
 239 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 240 </TR>\r
 241 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 242 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 243 <CODE>&nbsp;interface</CODE></FONT></TD>\r
 244 <TD><CODE><B><A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable&lt;T&gt;</A></B></CODE>\r
 245 \r
 246 <BR>\r
 247 &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
 248  captured.</TD>\r
 249 </TR>\r
 250 </TABLE>\r
 251 &nbsp;\r
 252 <P>\r
 253 \r
 254 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 255 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 256 <TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that implement <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
 257 </TR>\r
 258 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 259 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 260 <CODE>&nbsp;class</CODE></FONT></TD>\r
 261 <TD><CODE><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable&lt;T&gt;</A></B></CODE>\r
 262 \r
 263 <BR>\r
 264 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 265 </TR>\r
 266 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 267 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 268 <CODE>&nbsp;class</CODE></FONT></TD>\r
 269 <TD><CODE><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable&lt;T&gt;</A></B></CODE>\r
 270 \r
 271 <BR>\r
 272 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 273 </TR>\r
 274 </TABLE>\r
 275 &nbsp;\r
 276 <P>\r
 277 \r
 278 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 279 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 280 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that return <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
 281 </TR>\r
 282 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 283 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 284 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
 285 <TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</CODE>\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 ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 292 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt;</CODE></FONT></TD>\r
 293 <TD><CODE><B>Executable.</B><B><A HREF="../../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</CODE>\r
 294 \r
 295 <BR>\r
 296 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adds parameter to the list of parameters for a native executable</TD>\r
 297 </TR>\r
 298 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 299 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 300 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
 301 <TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</CODE>\r
 302 \r
 303 <BR>\r
 304 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 305 </TR>\r
 306 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 307 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 308 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/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
 309 <TD><CODE><B>ConfiguredExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html#getExecutable()">getExecutable</A></B>()</CODE>\r
 310 \r
 311 <BR>\r
 312 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 313 </TR>\r
 314 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 315 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 316 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
 317 <TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#getExecutable()">getExecutable</A></B>()</CODE>\r
 318 \r
 319 <BR>\r
 320 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 321 </TR>\r
 322 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 323 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 324 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
 325 <TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</CODE>\r
 326 \r
 327 <BR>\r
 328 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 329 </TR>\r
 330 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 331 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 332 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
 333 <TD><CODE><B>Executable.</B><B><A HREF="../../../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</CODE>\r
 334 \r
 335 <BR>\r
 336 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 337 </TR>\r
 338 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 339 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 340 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
 341 <TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)">setParameter</A></B>(java.lang.String&nbsp;parameter)</CODE>\r
 342 \r
 343 <BR>\r
 344 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 345 </TR>\r
 346 </TABLE>\r
 347 &nbsp;\r
 348 <P>\r
 349 \r
 350 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 351 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 352 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that return types with arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
 353 </TR>\r
 354 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 355 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 356 <CODE>abstract &nbsp;java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
 357 <TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#getType()">getType</A></B>()</CODE>\r
 358 \r
 359 <BR>\r
 360 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 361 </TR>\r
 362 </TABLE>\r
 363 &nbsp;\r
 364 <P>\r
 365 \r
 366 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 367 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 368 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> with parameters of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
 369 </TR>\r
 370 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 371 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 372 <CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
 373 <TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/engine/client/Util.html#getExecProperty(java.lang.String, compbio.engine.client.Executable)">getExecProperty</A></B>(java.lang.String&nbsp;propertySpec,\r
 374                 <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&nbsp;exec)</CODE>\r
 375 \r
 376 <BR>\r
 377 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 378 </TR>\r
 379 </TABLE>\r
 380 &nbsp;\r
 381 <P>\r
 382 \r
 383 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 384 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 385 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> with type arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
 386 </TR>\r
 387 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 388 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 389 <CODE>static\r
 390 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 391 <TR ALIGN="right" VALIGN="">\r
 392 <TD NOWRAP><FONT SIZE="-1">\r
 393 <CODE>&lt;V&gt; <A HREF="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;V&gt;</CODE></FONT></TD>\r
 394 </TR>\r
 395 </TABLE>\r
 396 </CODE></FONT></TD>\r
 397 <TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#getRunnerLimits(java.lang.Class)">getRunnerLimits</A></B>(java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)</CODE>\r
 398 \r
 399 <BR>\r
 400 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method should be executed once and result of its execution reused.</TD>\r
 401 </TR>\r
 402 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 403 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 404 <CODE>static\r
 405 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 406 <TR ALIGN="right" VALIGN="">\r
 407 <TD NOWRAP><FONT SIZE="-1">\r
 408 <CODE>&lt;V&gt; <A HREF="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;V&gt;</CODE></FONT></TD>\r
 409 </TR>\r
 410 </TABLE>\r
 411 </CODE></FONT></TD>\r
 412 <TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#getRunnerOptions(java.lang.Class)">getRunnerOptions</A></B>(java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)</CODE>\r
 413 \r
 414 <BR>\r
 415 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 416 </TR>\r
 417 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 418 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 419 <CODE>static\r
 420 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 421 <TR ALIGN="right" VALIGN="">\r
 422 <TD NOWRAP><FONT SIZE="-1">\r
 423 <CODE>&lt;V&gt; <A HREF="../../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;V&gt;</CODE></FONT></TD>\r
 424 </TR>\r
 425 </TABLE>\r
 426 </CODE></FONT></TD>\r
 427 <TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#getRunnerPresets(java.lang.Class)">getRunnerPresets</A></B>(java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)</CODE>\r
 428 \r
 429 <BR>\r
 430 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 431 </TR>\r
 432 </TABLE>\r
 433 &nbsp;\r
 434 <P>\r
 435 \r
 436 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 437 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 438 <TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> with parameters of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
 439 </TR>\r
 440 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 441 <TD><CODE><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#ConfExecutable(compbio.engine.client.Executable, java.lang.String)">ConfExecutable</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;&nbsp;executable,\r
 442                java.lang.String&nbsp;taskDirectory)</CODE>\r
 443 \r
 444 <BR>\r
 445 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 446 </TR>\r
 447 </TABLE>\r
 448 &nbsp;\r
 449 <P>\r
 450 <A NAME="compbio.engine.conf"><!-- --></A>\r
 451 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 452 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 453 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 454 Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/engine/conf/package-summary.html">compbio.engine.conf</A></FONT></TH>\r
 455 </TR>\r
 456 </TABLE>\r
 457 &nbsp;\r
 458 <P>\r
 459 \r
 460 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 461 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 462 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/conf/package-summary.html">compbio.engine.conf</A> that return types with arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
 463 </TR>\r
 464 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 465 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 466 <CODE>static&nbsp;java.lang.Class&lt;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
 467 <TD><CODE><B>DirectoryManager.</B><B><A HREF="../../../../compbio/engine/conf/DirectoryManager.html#getClass(java.lang.String)">getClass</A></B>(java.lang.String&nbsp;taskId)</CODE>\r
 468 \r
 469 <BR>\r
 470 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 471 </TR>\r
 472 </TABLE>\r
 473 &nbsp;\r
 474 <P>\r
 475 <A NAME="compbio.runner"><!-- --></A>\r
 476 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 477 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 478 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 479 Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
 480 </TR>\r
 481 </TABLE>\r
 482 &nbsp;\r
 483 <P>\r
 484 \r
 485 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 486 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 487 <TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> that implement <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
 488 </TR>\r
 489 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 490 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 491 <CODE>&nbsp;class</CODE></FONT></TD>\r
 492 <TD><CODE><B><A HREF="../../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></B></CODE>\r
 493 \r
 494 <BR>\r
 495 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 496 </TR>\r
 497 </TABLE>\r
 498 &nbsp;\r
 499 <P>\r
 500 \r
 501 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 502 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 503 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> that return <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
 504 </TR>\r
 505 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 506 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 507 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
 508 <TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../../compbio/runner/_SkeletalCommandBuilder.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</CODE>\r
 509 \r
 510 <BR>\r
 511 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 512 </TR>\r
 513 </TABLE>\r
 514 &nbsp;\r
 515 <P>\r
 516 \r
 517 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 518 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 519 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> with type arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
 520 </TR>\r
 521 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 522 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 523 <CODE>static&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
 524 <TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List, compbio.metadata.RunnerConfig)">argumentsToCommandString</A></B>(java.util.List&lt;? extends <A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&gt;&nbsp;arguments,\r
 525                          <A HREF="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;&nbsp;rconfig)</CODE>\r
 526 \r
 527 <BR>\r
 528 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 529 </TR>\r
 530 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 531 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 532 <CODE>static\r
 533 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 534 <TR ALIGN="right" VALIGN="">\r
 535 <TD NOWRAP><FONT SIZE="-1">\r
 536 <CODE>&lt;T&gt; <A HREF="../../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;T&gt;</CODE></FONT></TD>\r
 537 </TR>\r
 538 </TABLE>\r
 539 </CODE></FONT></TD>\r
 540 <TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/runner/Util.html#getLimits(java.lang.Class)">getLimits</A></B>(java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</CODE>\r
 541 \r
 542 <BR>\r
 543 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;For now just assume that all parameters which came in needs setting it
 544  will be a client responsibility to prepare RunnerConfig object then</TD>\r
 545 </TR>\r
 546 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 547 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 548 <CODE>static\r
 549 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 550 <TR ALIGN="right" VALIGN="">\r
 551 <TD NOWRAP><FONT SIZE="-1">\r
 552 <CODE>&lt;T&gt; <A HREF="../../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;T&gt;</CODE></FONT></TD>\r
 553 </TR>\r
 554 </TABLE>\r
 555 </CODE></FONT></TD>\r
 556 <TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/runner/Util.html#getPresets(java.lang.Class)">getPresets</A></B>(java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</CODE>\r
 557 \r
 558 <BR>\r
 559 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 560 </TR>\r
 561 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 562 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 563 <CODE>static\r
 564 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 565 <TR ALIGN="right" VALIGN="">\r
 566 <TD NOWRAP><FONT SIZE="-1">\r
 567 <CODE>&lt;T&gt; <A HREF="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;T&gt;</CODE></FONT></TD>\r
 568 </TR>\r
 569 </TABLE>\r
 570 </CODE></FONT></TD>\r
 571 <TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/runner/Util.html#getSupportedOptions(java.lang.Class)">getSupportedOptions</A></B>(java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&gt;&nbsp;clazz)</CODE>\r
 572 \r
 573 <BR>\r
 574 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 575 </TR>\r
 576 </TABLE>\r
 577 &nbsp;\r
 578 <P>\r
 579 \r
 580 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 581 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 582 <TH ALIGN="left" COLSPAN="2">Constructor parameters in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> with type arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
 583 </TR>\r
 584 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 585 <TD><CODE><B><A HREF="../../../../compbio/runner/OptionCombinator.html#OptionCombinator(compbio.metadata.RunnerConfig)">OptionCombinator</A></B>(<A HREF="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;&nbsp;rconfig)</CODE>\r
 586 \r
 587 <BR>\r
 588 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 589 </TR>\r
 590 </TABLE>\r
 591 &nbsp;\r
 592 <P>\r
 593 <A NAME="compbio.runner._impl"><!-- --></A>\r
 594 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 595 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 596 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 597 Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
 598 </TR>\r
 599 </TABLE>\r
 600 &nbsp;\r
 601 <P>\r
 602 \r
 603 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 604 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 605 <TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> that implement <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
 606 </TR>\r
 607 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 608 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 609 <CODE>&nbsp;class</CODE></FONT></TD>\r
 610 <TD><CODE><B><A HREF="../../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A></B></CODE>\r
 611 \r
 612 <BR>\r
 613 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 614 </TR>\r
 615 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 616 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 617 <CODE>&nbsp;class</CODE></FONT></TD>\r
 618 <TD><CODE><B><A HREF="../../../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A></B></CODE>\r
 619 \r
 620 <BR>\r
 621 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 622 </TR>\r
 623 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 624 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 625 <CODE>&nbsp;class</CODE></FONT></TD>\r
 626 <TD><CODE><B><A HREF="../../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A></B></CODE>\r
 627 \r
 628 <BR>\r
 629 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 630 </TR>\r
 631 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 632 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 633 <CODE>&nbsp;class</CODE></FONT></TD>\r
 634 <TD><CODE><B><A HREF="../../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A></B></CODE>\r
 635 \r
 636 <BR>\r
 637 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 638 </TR>\r
 639 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 640 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 641 <CODE>&nbsp;class</CODE></FONT></TD>\r
 642 <TD><CODE><B><A HREF="../../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A></B></CODE>\r
 643 \r
 644 <BR>\r
 645 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;TODO this needs fixing! Executable does not work</TD>\r
 646 </TR>\r
 647 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 648 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 649 <CODE>&nbsp;class</CODE></FONT></TD>\r
 650 <TD><CODE><B><A HREF="../../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A></B></CODE>\r
 651 \r
 652 <BR>\r
 653 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 654 </TR>\r
 655 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 656 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 657 <CODE>&nbsp;class</CODE></FONT></TD>\r
 658 <TD><CODE><B><A HREF="../../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A></B></CODE>\r
 659 \r
 660 <BR>\r
 661 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 662 </TR>\r
 663 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 664 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 665 <CODE>&nbsp;class</CODE></FONT></TD>\r
 666 <TD><CODE><B><A HREF="../../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A></B></CODE>\r
 667 \r
 668 <BR>\r
 669 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 670 </TR>\r
 671 </TABLE>\r
 672 &nbsp;\r
 673 <P>\r
 674 \r
 675 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 676 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 677 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> that return <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
 678 </TR>\r
 679 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 680 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 681 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
 682 <TD><CODE><B>NetNglyc.</B><B><A HREF="../../../../compbio/runner/_impl/NetNglyc.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</CODE>\r
 683 \r
 684 <BR>\r
 685 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 686 </TR>\r
 687 </TABLE>\r
 688 &nbsp;\r
 689 <P>\r
 690 <A NAME="compbio.runner.msa"><!-- --></A>\r
 691 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 692 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 693 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 694 Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
 695 </TR>\r
 696 </TABLE>\r
 697 &nbsp;\r
 698 <P>\r
 699 \r
 700 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 701 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 702 <TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that implement <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
 703 </TR>\r
 704 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 705 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 706 <CODE>&nbsp;class</CODE></FONT></TD>\r
 707 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A></B></CODE>\r
 708 \r
 709 <BR>\r
 710 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 711 </TR>\r
 712 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 713 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 714 <CODE>&nbsp;class</CODE></FONT></TD>\r
 715 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></B></CODE>\r
 716 \r
 717 <BR>\r
 718 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 719 </TR>\r
 720 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 721 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 722 <CODE>&nbsp;class</CODE></FONT></TD>\r
 723 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></B></CODE>\r
 724 \r
 725 <BR>\r
 726 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 727 </TR>\r
 728 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 729 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 730 <CODE>&nbsp;class</CODE></FONT></TD>\r
 731 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></B></CODE>\r
 732 \r
 733 <BR>\r
 734 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 735 </TR>\r
 736 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 737 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 738 <CODE>&nbsp;class</CODE></FONT></TD>\r
 739 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></B></CODE>\r
 740 \r
 741 <BR>\r
 742 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 743 </TR>\r
 744 </TABLE>\r
 745 &nbsp;\r
 746 <P>\r
 747 \r
 748 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 749 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 750 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return types with arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
 751 </TR>\r
 752 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 753 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 754 <CODE>&nbsp;java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
 755 <TD><CODE><B>Tcoffee.</B><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html#getType()">getType</A></B>()</CODE>\r
 756 \r
 757 <BR>\r
 758 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 759 </TR>\r
 760 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 761 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 762 <CODE>&nbsp;java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
 763 <TD><CODE><B>ClustalW.</B><B><A HREF="../../../../compbio/runner/msa/ClustalW.html#getType()">getType</A></B>()</CODE>\r
 764 \r
 765 <BR>\r
 766 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 767 </TR>\r
 768 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 769 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 770 <CODE>&nbsp;java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
 771 <TD><CODE><B>Probcons.</B><B><A HREF="../../../../compbio/runner/msa/Probcons.html#getType()">getType</A></B>()</CODE>\r
 772 \r
 773 <BR>\r
 774 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 775 </TR>\r
 776 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 777 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 778 <CODE>&nbsp;java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
 779 <TD><CODE><B>Muscle.</B><B><A HREF="../../../../compbio/runner/msa/Muscle.html#getType()">getType</A></B>()</CODE>\r
 780 \r
 781 <BR>\r
 782 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 783 </TR>\r
 784 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 785 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 786 <CODE>&nbsp;java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
 787 <TD><CODE><B>Mafft.</B><B><A HREF="../../../../compbio/runner/msa/Mafft.html#getType()">getType</A></B>()</CODE>\r
 788 \r
 789 <BR>\r
 790 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 791 </TR>\r
 792 </TABLE>\r
 793 &nbsp;\r
 794 <P>\r
 795 <A NAME="compbio.runner.psiblast"><!-- --></A>\r
 796 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 797 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 798 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 799 Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A></FONT></TH>\r
 800 </TR>\r
 801 </TABLE>\r
 802 &nbsp;\r
 803 <P>\r
 804 \r
 805 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 806 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 807 <TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A> that implement <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
 808 </TR>\r
 809 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 810 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 811 <CODE>&nbsp;class</CODE></FONT></TD>\r
 812 <TD><CODE><B><A HREF="../../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A></B></CODE>\r
 813 \r
 814 <BR>\r
 815 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 816 </TR>\r
 817 </TABLE>\r
 818 &nbsp;\r
 819 <P>\r
 820 \r
 821 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 822 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 823 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A> that return types with arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
 824 </TR>\r
 825 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 826 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 827 <CODE>&nbsp;java.lang.Class&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
 828 <TD><CODE><B>PsiBlast.</B><B><A HREF="../../../../compbio/runner/psiblast/PsiBlast.html#getType()">getType</A></B>()</CODE>\r
 829 \r
 830 <BR>\r
 831 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 832 </TR>\r
 833 </TABLE>\r
 834 &nbsp;\r
 835 <P>\r
 836 <HR>\r
 837 \r
 838 \r
 839 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 840 <A NAME="navbar_bottom"><!-- --></A>\r
 841 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 842 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 843 <TR>\r
 844 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 845 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 846 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 847   <TR ALIGN="center" VALIGN="top">\r
 848   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 849   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 850   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
 851   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
 852   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 853   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 854   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 855   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 856   </TR>\r
 857 </TABLE>\r
 858 </TD>\r
 859 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 860 </EM>\r
 861 </TD>\r
 862 </TR>\r
 863 \r
 864 <TR>\r
 865 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 866 &nbsp;PREV&nbsp;\r
 867 &nbsp;NEXT</FONT></TD>\r
 868 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 869   <A HREF="../../../../index.html?compbio/engine/client/\class-useExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 870 &nbsp;<A HREF="Executable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 871 &nbsp;<SCRIPT type="text/javascript">\r
 872   <!--\r
 873   if(window==top) {\r
 874     document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 875   }\r
 876   //-->\r
 877 </SCRIPT>\r
 878 <NOSCRIPT>\r
 879   <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 880 </NOSCRIPT>\r
 881 \r
 882 \r
 883 </FONT></TD>\r
 884 </TR>\r
 885 </TABLE>\r
 886 <A NAME="skip-navbar_bottom"></A>\r
 887 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 888 \r
 889 <HR>\r
 890 \r
 891 </BODY>\r
 892 </HTML>\r