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7 Uses of Package compbio.engine.client
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18 parent.document.title="Uses of Package compbio.engine.client";
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84 <B>Uses of Package<br>compbio.engine.client</B></H2>
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87 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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88 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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89 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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90 Packages that use <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>
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92 <TR BGCOLOR="white" CLASS="TableRowColor">
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93 <TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>
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94 <TD> </TD>
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96 <TR BGCOLOR="white" CLASS="TableRowColor">
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97 <TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>
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98 <TD>Classes and interfaces representing an input for engines. </TD>
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100 <TR BGCOLOR="white" CLASS="TableRowColor">
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101 <TD><A HREF="#compbio.engine.cluster.drmaa"><B>compbio.engine.cluster.drmaa</B></A></TD>
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102 <TD>An cluster engine classes responsible for execution of Executables on the clusters. </TD>
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104 <TR BGCOLOR="white" CLASS="TableRowColor">
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105 <TD><A HREF="#compbio.engine.conf"><B>compbio.engine.conf</B></A></TD>
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106 <TD>Classes commonly used by both engines. </TD>
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108 <TR BGCOLOR="white" CLASS="TableRowColor">
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109 <TD><A HREF="#compbio.engine.local"><B>compbio.engine.local</B></A></TD>
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110 <TD>An local engine classes responsible for execution of Executables on the local computer
111 (the same machine as JVM running these classes). </TD>
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113 <TR BGCOLOR="white" CLASS="TableRowColor">
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114 <TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>
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115 <TD>Utilities commonly used by all runners. </TD>
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117 <TR BGCOLOR="white" CLASS="TableRowColor">
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118 <TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>
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119 <TD> </TD>
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121 <TR BGCOLOR="white" CLASS="TableRowColor">
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122 <TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>
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123 <TD>Wrappers for native executables for multiple sequence alignment (msa) </TD>
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125 <TR BGCOLOR="white" CLASS="TableRowColor">
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126 <TD><A HREF="#compbio.runner.psiblast"><B>compbio.runner.psiblast</B></A></TD>
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127 <TD> </TD>
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129 <TR BGCOLOR="white" CLASS="TableRowColor">
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130 <TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>
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131 <TD> </TD>
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136 <A NAME="compbio.engine"><!-- --></A>
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137 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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138 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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139 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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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>
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142 <TR BGCOLOR="white" CLASS="TableRowColor">
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143 <TD><B><A HREF="../../../compbio/engine/client/class-use/ConfiguredExecutable.html#compbio.engine"><B>ConfiguredExecutable</B></A></B>
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146 </TD>
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148 <TR BGCOLOR="white" CLASS="TableRowColor">
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149 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.engine"><B>Executable</B></A></B>
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152 Interface to a native executable.</TD>
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154 <TR BGCOLOR="white" CLASS="TableRowColor">
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155 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.ExecProvider.html#compbio.engine"><B>Executable.ExecProvider</B></A></B>
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158 </TD>
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163 <A NAME="compbio.engine.client"><!-- --></A>
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164 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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165 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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166 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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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>
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169 <TR BGCOLOR="white" CLASS="TableRowColor">
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170 <TD><B><A HREF="../../../compbio/engine/client/class-use/CommandBuilder.html#compbio.engine.client"><B>CommandBuilder</B></A></B>
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173 </TD>
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175 <TR BGCOLOR="white" CLASS="TableRowColor">
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176 <TD><B><A HREF="../../../compbio/engine/client/class-use/ConfExecutable.html#compbio.engine.client"><B>ConfExecutable</B></A></B>
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179 </TD>
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181 <TR BGCOLOR="white" CLASS="TableRowColor">
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182 <TD><B><A HREF="../../../compbio/engine/client/class-use/ConfiguredExecutable.html#compbio.engine.client"><B>ConfiguredExecutable</B></A></B>
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185 </TD>
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187 <TR BGCOLOR="white" CLASS="TableRowColor">
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188 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.engine.client"><B>Executable</B></A></B>
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191 Interface to a native executable.</TD>
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193 <TR BGCOLOR="white" CLASS="TableRowColor">
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194 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.ExecProvider.html#compbio.engine.client"><B>Executable.ExecProvider</B></A></B>
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197 </TD>
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199 <TR BGCOLOR="white" CLASS="TableRowColor">
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200 <TD><B><A HREF="../../../compbio/engine/client/class-use/PipedExecutable.html#compbio.engine.client"><B>PipedExecutable</B></A></B>
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203 This is a marker interface to indicate that the output of the process must be
206 <TR BGCOLOR="white" CLASS="TableRowColor">
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207 <TD><B><A HREF="../../../compbio/engine/client/class-use/RunConfiguration.html#compbio.engine.client"><B>RunConfiguration</B></A></B>
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210 Value class for persisting ConfExecutable instances</TD>
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212 <TR BGCOLOR="white" CLASS="TableRowColor">
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213 <TD><B><A HREF="../../../compbio/engine/client/class-use/SkeletalExecutable.html#compbio.engine.client"><B>SkeletalExecutable</B></A></B>
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216 </TD>
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221 <A NAME="compbio.engine.cluster.drmaa"><!-- --></A>
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222 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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223 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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224 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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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>
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227 <TR BGCOLOR="white" CLASS="TableRowColor">
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228 <TD><B><A HREF="../../../compbio/engine/client/class-use/ConfiguredExecutable.html#compbio.engine.cluster.drmaa"><B>ConfiguredExecutable</B></A></B>
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231 </TD>
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236 <A NAME="compbio.engine.conf"><!-- --></A>
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237 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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238 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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239 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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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>
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242 <TR BGCOLOR="white" CLASS="TableRowColor">
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243 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.engine.conf"><B>Executable</B></A></B>
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246 Interface to a native executable.</TD>
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251 <A NAME="compbio.engine.local"><!-- --></A>
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252 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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253 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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254 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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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>
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257 <TR BGCOLOR="white" CLASS="TableRowColor">
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258 <TD><B><A HREF="../../../compbio/engine/client/class-use/ConfiguredExecutable.html#compbio.engine.local"><B>ConfiguredExecutable</B></A></B>
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261 </TD>
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266 <A NAME="compbio.runner"><!-- --></A>
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267 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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268 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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269 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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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>
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272 <TR BGCOLOR="white" CLASS="TableRowColor">
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273 <TD><B><A HREF="../../../compbio/engine/client/class-use/CommandBuilder.html#compbio.runner"><B>CommandBuilder</B></A></B>
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276 </TD>
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278 <TR BGCOLOR="white" CLASS="TableRowColor">
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279 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.runner"><B>Executable</B></A></B>
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282 Interface to a native executable.</TD>
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284 <TR BGCOLOR="white" CLASS="TableRowColor">
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285 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.ExecProvider.html#compbio.runner"><B>Executable.ExecProvider</B></A></B>
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288 </TD>
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290 <TR BGCOLOR="white" CLASS="TableRowColor">
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291 <TD><B><A HREF="../../../compbio/engine/client/class-use/RunConfiguration.html#compbio.runner"><B>RunConfiguration</B></A></B>
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294 Value class for persisting ConfExecutable instances</TD>
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299 <A NAME="compbio.runner._impl"><!-- --></A>
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300 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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301 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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302 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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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>
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305 <TR BGCOLOR="white" CLASS="TableRowColor">
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306 <TD><B><A HREF="../../../compbio/engine/client/class-use/CommandBuilder.html#compbio.runner._impl"><B>CommandBuilder</B></A></B>
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309 </TD>
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311 <TR BGCOLOR="white" CLASS="TableRowColor">
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312 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.runner._impl"><B>Executable</B></A></B>
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315 Interface to a native executable.</TD>
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317 <TR BGCOLOR="white" CLASS="TableRowColor">
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318 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.ExecProvider.html#compbio.runner._impl"><B>Executable.ExecProvider</B></A></B>
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321 </TD>
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323 <TR BGCOLOR="white" CLASS="TableRowColor">
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324 <TD><B><A HREF="../../../compbio/engine/client/class-use/RunConfiguration.html#compbio.runner._impl"><B>RunConfiguration</B></A></B>
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327 Value class for persisting ConfExecutable instances</TD>
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332 <A NAME="compbio.runner.msa"><!-- --></A>
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333 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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334 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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335 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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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>
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338 <TR BGCOLOR="white" CLASS="TableRowColor">
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339 <TD><B><A HREF="../../../compbio/engine/client/class-use/ClusterNativeSpecExecutable.html#compbio.runner.msa"><B>ClusterNativeSpecExecutable</B></A></B>
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342 </TD>
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344 <TR BGCOLOR="white" CLASS="TableRowColor">
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345 <TD><B><A HREF="../../../compbio/engine/client/class-use/CommandBuilder.html#compbio.runner.msa"><B>CommandBuilder</B></A></B>
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348 </TD>
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350 <TR BGCOLOR="white" CLASS="TableRowColor">
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351 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.runner.msa"><B>Executable</B></A></B>
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354 Interface to a native executable.</TD>
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356 <TR BGCOLOR="white" CLASS="TableRowColor">
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357 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.ExecProvider.html#compbio.runner.msa"><B>Executable.ExecProvider</B></A></B>
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360 </TD>
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362 <TR BGCOLOR="white" CLASS="TableRowColor">
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363 <TD><B><A HREF="../../../compbio/engine/client/class-use/PipedExecutable.html#compbio.runner.msa"><B>PipedExecutable</B></A></B>
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366 This is a marker interface to indicate that the output of the process must be
369 <TR BGCOLOR="white" CLASS="TableRowColor">
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370 <TD><B><A HREF="../../../compbio/engine/client/class-use/SkeletalExecutable.html#compbio.runner.msa"><B>SkeletalExecutable</B></A></B>
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373 </TD>
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378 <A NAME="compbio.runner.psiblast"><!-- --></A>
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379 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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380 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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381 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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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>
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384 <TR BGCOLOR="white" CLASS="TableRowColor">
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385 <TD><B><A HREF="../../../compbio/engine/client/class-use/Executable.html#compbio.runner.psiblast"><B>Executable</B></A></B>
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388 Interface to a native executable.</TD>
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390 <TR BGCOLOR="white" CLASS="TableRowColor">
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391 <TD><B><A HREF="../../../compbio/engine/client/class-use/SkeletalExecutable.html#compbio.runner.psiblast"><B>SkeletalExecutable</B></A></B>
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394 </TD>
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399 <A NAME="compbio.ws.server"><!-- --></A>
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400 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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401 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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402 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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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>
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405 <TR BGCOLOR="white" CLASS="TableRowColor">
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406 <TD><B><A HREF="../../../compbio/engine/client/class-use/ConfiguredExecutable.html#compbio.ws.server"><B>ConfiguredExecutable</B></A></B>
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409 </TD>
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423 <A NAME="navbar_bottom_firstrow"><!-- --></A>
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