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18 parent.document.title="ConfExecutable";
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58 <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>
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78 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
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79 SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
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80 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
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81 DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
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84 <A NAME="skip-navbar_top"></A>
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85 <!-- ========= END OF TOP NAVBAR ========= -->
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88 <!-- ======== START OF CLASS DATA ======== -->
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91 compbio.engine.client</FONT>
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93 Class ConfExecutable<T></H2>
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96 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.client.ConfExecutable<T></B>
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99 <DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><T>, <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T>, <A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A><T></DD>
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103 <DT><PRE>public class <B>ConfExecutable<T></B><DT>extends java.lang.Object<DT>implements <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><T></DL>
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110 <!-- ======== NESTED CLASS SUMMARY ======== -->
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112 <A NAME="nested_class_summary"><!-- --></A>
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113 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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114 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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115 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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116 <B>Nested Class Summary</B></FONT></TH>
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119 <A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>
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120 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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121 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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122 <TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>
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124 <TR BGCOLOR="white" CLASS="TableRowColor">
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125 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>
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129 <!-- =========== FIELD SUMMARY =========== -->
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131 <A NAME="field_summary"><!-- --></A>
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132 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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133 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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134 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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135 <B>Field Summary</B></FONT></TH>
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137 <TR BGCOLOR="white" CLASS="TableRowColor">
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138 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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139 <CODE>static java.lang.String</CODE></FONT></TD>
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140 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#CLUSTER_TASK_ID_PREFIX">CLUSTER_TASK_ID_PREFIX</A></B></CODE>
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143 </TD>
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147 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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149 <A NAME="constructor_summary"><!-- --></A>
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150 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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151 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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152 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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153 <B>Constructor Summary</B></FONT></TH>
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155 <TR BGCOLOR="white" CLASS="TableRowColor">
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156 <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><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>> executable,
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157 java.lang.String taskDirectory)</CODE>
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160 </TD>
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164 <!-- ========== METHOD SUMMARY =========== -->
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166 <A NAME="method_summary"><!-- --></A>
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167 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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168 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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169 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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170 <B>Method Summary</B></FONT></TH>
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172 <TR BGCOLOR="white" CLASS="TableRowColor">
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173 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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174 <CODE> <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></FONT></TD>
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175 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List<java.lang.String> parameters)</CODE>
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178 Adds parameter to the list of parameters for a native executable</TD>
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180 <TR BGCOLOR="white" CLASS="TableRowColor">
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181 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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182 <CODE> java.lang.String</CODE></FONT></TD>
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183 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</CODE>
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186 </TD>
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188 <TR BGCOLOR="white" CLASS="TableRowColor">
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189 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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190 <CODE> java.util.List<java.lang.String></CODE></FONT></TD>
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191 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>
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194 </TD>
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196 <TR BGCOLOR="white" CLASS="TableRowColor">
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197 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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198 <CODE> java.util.Map<java.lang.String,java.lang.String></CODE></FONT></TD>
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199 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getEnvironment()">getEnvironment</A></B>()</CODE>
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202 </TD>
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204 <TR BGCOLOR="white" CLASS="TableRowColor">
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205 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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206 <CODE> java.lang.String</CODE></FONT></TD>
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207 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getError()">getError</A></B>()</CODE>
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210 </TD>
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212 <TR BGCOLOR="white" CLASS="TableRowColor">
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213 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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214 <CODE> <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>
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215 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getExecProvider()">getExecProvider</A></B>()</CODE>
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218 </TD>
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220 <TR BGCOLOR="white" CLASS="TableRowColor">
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221 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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222 <CODE> <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></FONT></TD>
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223 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getExecutable()">getExecutable</A></B>()</CODE>
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226 </TD>
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228 <TR BGCOLOR="white" CLASS="TableRowColor">
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229 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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230 <CODE> java.lang.String</CODE></FONT></TD>
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231 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getInput()">getInput</A></B>()</CODE>
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234 Not all input paths are relative! Input path could be absolute!</TD>
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236 <TR BGCOLOR="white" CLASS="TableRowColor">
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237 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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238 <CODE> <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></FONT></TD>
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239 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String presetName)</CODE>
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242 </TD>
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244 <TR BGCOLOR="white" CLASS="TableRowColor">
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245 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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246 <CODE> <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></FONT></TD>
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247 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getLimits()">getLimits</A></B>()</CODE>
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250 </TD>
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252 <TR BGCOLOR="white" CLASS="TableRowColor">
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253 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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254 <CODE> java.lang.String</CODE></FONT></TD>
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255 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getOutput()">getOutput</A></B>()</CODE>
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258 </TD>
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260 <TR BGCOLOR="white" CLASS="TableRowColor">
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261 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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262 <CODE> <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></FONT></TD>
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263 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getParameters()">getParameters</A></B>()</CODE>
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266 </TD>
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268 <TR BGCOLOR="white" CLASS="TableRowColor">
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269 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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270 <CODE> <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></FONT></TD>
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271 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</CODE>
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274 </TD>
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276 <TR BGCOLOR="white" CLASS="TableRowColor">
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277 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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279 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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280 <TR ALIGN="right" VALIGN="">
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281 <TD NOWRAP><FONT SIZE="-1">
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282 <CODE><V> V</CODE></FONT></TD>
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285 </CODE></FONT></TD>
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286 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getResults()">getResults</A></B>()</CODE>
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289 </TD>
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291 <TR BGCOLOR="white" CLASS="TableRowColor">
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292 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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294 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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295 <TR ALIGN="right" VALIGN="">
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296 <TD NOWRAP><FONT SIZE="-1">
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297 <CODE><V> V</CODE></FONT></TD>
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300 </CODE></FONT></TD>
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301 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String directory)</CODE>
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304 </TD>
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306 <TR BGCOLOR="white" CLASS="TableRowColor">
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307 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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308 <CODE> <A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A></CODE></FONT></TD>
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309 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunConfiguration()">getRunConfiguration</A></B>()</CODE>
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312 </TD>
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314 <TR BGCOLOR="white" CLASS="TableRowColor">
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315 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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317 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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318 <TR ALIGN="right" VALIGN="">
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319 <TD NOWRAP><FONT SIZE="-1">
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320 <CODE><V> <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><V></CODE></FONT></TD>
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323 </CODE></FONT></TD>
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324 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunnerLimits(java.lang.Class)">getRunnerLimits</A></B>(java.lang.Class<? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><V>> clazz)</CODE>
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327 This method should be executed once and result of its execution reused.</TD>
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329 <TR BGCOLOR="white" CLASS="TableRowColor">
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330 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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332 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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333 <TR ALIGN="right" VALIGN="">
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334 <TD NOWRAP><FONT SIZE="-1">
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335 <CODE><V> <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><V></CODE></FONT></TD>
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338 </CODE></FONT></TD>
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339 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunnerOptions(java.lang.Class)">getRunnerOptions</A></B>(java.lang.Class<? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><V>> clazz)</CODE>
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342 </TD>
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344 <TR BGCOLOR="white" CLASS="TableRowColor">
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345 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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347 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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348 <TR ALIGN="right" VALIGN="">
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349 <TD NOWRAP><FONT SIZE="-1">
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350 <CODE><V> <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><V></CODE></FONT></TD>
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353 </CODE></FONT></TD>
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354 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunnerPresets(java.lang.Class)">getRunnerPresets</A></B>(java.lang.Class<? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><V>> clazz)</CODE>
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357 </TD>
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359 <TR BGCOLOR="white" CLASS="TableRowColor">
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360 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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361 <CODE> <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>
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362 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getSupportedRuntimes()">getSupportedRuntimes</A></B>()</CODE>
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365 </TD>
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367 <TR BGCOLOR="white" CLASS="TableRowColor">
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368 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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369 <CODE> java.lang.String</CODE></FONT></TD>
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370 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getTaskId()">getTaskId</A></B>()</CODE>
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373 </TD>
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375 <TR BGCOLOR="white" CLASS="TableRowColor">
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376 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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377 <CODE> java.lang.String</CODE></FONT></TD>
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378 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getWorkDirectory()">getWorkDirectory</A></B>()</CODE>
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381 </TD>
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383 <TR BGCOLOR="white" CLASS="TableRowColor">
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384 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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385 <CODE> <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?></CODE></FONT></TD>
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386 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#loadRunConfiguration(java.io.InputStream)">loadRunConfiguration</A></B>(java.io.InputStream input)</CODE>
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389 </TD>
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391 <TR BGCOLOR="white" CLASS="TableRowColor">
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392 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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393 <CODE> <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?></CODE></FONT></TD>
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394 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> rconf)</CODE>
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397 </TD>
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399 <TR BGCOLOR="white" CLASS="TableRowColor">
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400 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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401 <CODE>static <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?></CODE></FONT></TD>
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402 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#newConfExecutable(compbio.engine.client.RunConfiguration)">newConfExecutable</A></B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> rconf)</CODE>
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405 </TD>
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407 <TR BGCOLOR="white" CLASS="TableRowColor">
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408 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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409 <CODE> boolean</CODE></FONT></TD>
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410 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#saveRunConfiguration()">saveRunConfiguration</A></B>()</CODE>
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413 </TD>
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415 <TR BGCOLOR="white" CLASS="TableRowColor">
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416 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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417 <CODE> void</CODE></FONT></TD>
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418 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#setExecProvider(compbio.engine.client.Executable.ExecProvider)">setExecProvider</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</CODE>
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421 </TD>
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423 <TR BGCOLOR="white" CLASS="TableRowColor">
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424 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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425 <CODE> void</CODE></FONT></TD>
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426 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#setWorkDirectory(java.lang.String)">setWorkDirectory</A></B>(java.lang.String workDirectory)</CODE>
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429 </TD>
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431 <TR BGCOLOR="white" CLASS="TableRowColor">
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432 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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433 <CODE> java.lang.String</CODE></FONT></TD>
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434 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#toString()">toString</A></B>()</CODE>
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437 </TD>
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440 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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441 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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442 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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443 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>
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445 <TR BGCOLOR="white" CLASS="TableRowColor">
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446 <TD><CODE>equals, getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>
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452 <!-- ============ FIELD DETAIL =========== -->
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454 <A NAME="field_detail"><!-- --></A>
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455 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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456 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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457 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
\r
458 <B>Field Detail</B></FONT></TH>
\r
462 <A NAME="CLUSTER_TASK_ID_PREFIX"><!-- --></A><H3>
\r
463 CLUSTER_TASK_ID_PREFIX</H3>
\r
465 public static final java.lang.String <B>CLUSTER_TASK_ID_PREFIX</B></PRE>
\r
468 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.engine.client.ConfExecutable.CLUSTER_TASK_ID_PREFIX">Constant Field Values</A></DL>
\r
471 <!-- ========= CONSTRUCTOR DETAIL ======== -->
\r
473 <A NAME="constructor_detail"><!-- --></A>
\r
474 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
475 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
476 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
\r
477 <B>Constructor Detail</B></FONT></TH>
\r
481 <A NAME="ConfExecutable(compbio.engine.client.Executable, java.lang.String)"><!-- --></A><H3>
\r
482 ConfExecutable</H3>
\r
484 public <B>ConfExecutable</B>(<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>> executable,
\r
485 java.lang.String taskDirectory)</PRE>
\r
489 <!-- ============ METHOD DETAIL ========== -->
\r
491 <A NAME="method_detail"><!-- --></A>
\r
492 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
493 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
494 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
\r
495 <B>Method Detail</B></FONT></TH>
\r
499 <A NAME="getExecProvider()"><!-- --></A><H3>
\r
500 getExecProvider</H3>
\r
502 public <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> <B>getExecProvider</B>()</PRE>
\r
505 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getExecProvider()">getExecProvider</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></DL>
\r
513 <A NAME="setExecProvider(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>
\r
514 setExecProvider</H3>
\r
516 public void <B>setExecProvider</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</PRE>
\r
527 <A NAME="getCommand(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>
\r
530 public java.lang.String <B>getCommand</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)
\r
531 throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></PRE>
\r
534 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></DL>
\r
539 <DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE></DL>
\r
544 <A NAME="getSupportedRuntimes()"><!-- --></A><H3>
\r
545 getSupportedRuntimes</H3>
\r
547 public <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> <B>getSupportedRuntimes</B>()</PRE>
\r
550 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getSupportedRuntimes()">getSupportedRuntimes</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></DL>
\r
558 <A NAME="getLimit(java.lang.String)"><!-- --></A><H3>
\r
561 public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>> <B>getLimit</B>(java.lang.String presetName)</PRE>
\r
564 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></DL>
\r
572 <A NAME="getLimits()"><!-- --></A><H3>
\r
575 public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>> <B>getLimits</B>()</PRE>
\r
578 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></DL>
\r
586 <A NAME="getTaskId()"><!-- --></A><H3>
\r
589 public java.lang.String <B>getTaskId</B>()</PRE>
\r
592 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getTaskId()">getTaskId</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></DL>
\r
600 <A NAME="setWorkDirectory(java.lang.String)"><!-- --></A><H3>
\r
601 setWorkDirectory</H3>
\r
603 public void <B>setWorkDirectory</B>(java.lang.String workDirectory)</PRE>
\r
606 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#setWorkDirectory(java.lang.String)">setWorkDirectory</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></DL>
\r
614 <A NAME="getWorkDirectory()"><!-- --></A><H3>
\r
615 getWorkDirectory</H3>
\r
617 public java.lang.String <B>getWorkDirectory</B>()</PRE>
\r
620 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getWorkDirectory()">getWorkDirectory</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></DL>
\r
628 <A NAME="addParameters(java.util.List)"><!-- --></A><H3>
\r
631 public <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>> <B>addParameters</B>(java.util.List<java.lang.String> parameters)</PRE>
\r
633 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">Executable</A></CODE></B></DD>
\r
634 <DD>Adds parameter to the list of parameters for a native executable
\r
637 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></DL>
\r
641 <DT><B>Returns:</B><DD>this Executable</DL>
\r
646 <A NAME="getOutput()"><!-- --></A><H3>
\r
649 public java.lang.String <B>getOutput</B>()</PRE>
\r
652 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getOutput()">getOutput</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></DL>
\r
660 <A NAME="getError()"><!-- --></A><H3>
\r
663 public java.lang.String <B>getError</B>()</PRE>
\r
666 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getError()">getError</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></DL>
\r
674 <A NAME="getCreatedFiles()"><!-- --></A><H3>
\r
675 getCreatedFiles</H3>
\r
677 public java.util.List<java.lang.String> <B>getCreatedFiles</B>()</PRE>
\r
680 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></DL>
\r
688 <A NAME="getInput()"><!-- --></A><H3>
\r
691 public java.lang.String <B>getInput</B>()</PRE>
\r
693 <DD>Not all input paths are relative! Input path could be absolute!
\r
696 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getInput()">getInput</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></DL>
\r
699 <DT><B>See Also:</B><DD><CODE>compbio.engine.client.Executable#getInputFiles()</CODE></DL>
\r
704 <A NAME="getParameters()"><!-- --></A><H3>
\r
707 public <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>> <B>getParameters</B>()</PRE>
\r
710 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getParameters()">getParameters</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></DL>
\r
718 <A NAME="getParameters(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>
\r
721 public <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>> <B>getParameters</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</PRE>
\r
724 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></DL>
\r
732 <A NAME="getExecutable()"><!-- --></A><H3>
\r
735 public <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>> <B>getExecutable</B>()</PRE>
\r
738 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getExecutable()">getExecutable</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></DL>
\r
746 <A NAME="getResults()"><!-- --></A><H3>
\r
749 public <V> V <B>getResults</B>()
\r
750 throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>
\r
753 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getResults()">getResults</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></DL>
\r
758 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>
\r
763 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>
\r
766 public <V> V <B>getResults</B>(java.lang.String directory)
\r
767 throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>
\r
770 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></DL>
\r
775 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>
\r
780 <A NAME="getRunnerOptions(java.lang.Class)"><!-- --></A><H3>
\r
781 getRunnerOptions</H3>
\r
783 public static <V> <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><V> <B>getRunnerOptions</B>(java.lang.Class<? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><V>> clazz)
\r
784 throws java.io.IOException</PRE>
\r
792 <DD><CODE>java.io.IOException</CODE></DL>
\r
797 <A NAME="getRunnerPresets(java.lang.Class)"><!-- --></A><H3>
\r
798 getRunnerPresets</H3>
\r
800 public static <V> <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><V> <B>getRunnerPresets</B>(java.lang.Class<? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><V>> clazz)
\r
801 throws java.io.IOException</PRE>
\r
809 <DD><CODE>java.io.IOException</CODE></DL>
\r
814 <A NAME="getRunnerLimits(java.lang.Class)"><!-- --></A><H3>
\r
815 getRunnerLimits</H3>
\r
817 public static <V> <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><V> <B>getRunnerLimits</B>(java.lang.Class<? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><V>> clazz)
\r
818 throws java.io.IOException</PRE>
\r
820 <DD>This method should be executed once and result of its execution reused.
821 If not used carefully it could slow down the system!
\r
827 <DT><B>Type Parameters:</B><DD><CODE>V</CODE> - <DT><B>Parameters:</B><DD><CODE>clazz</CODE> -
\r
828 <DT><B>Returns:</B><DD>
\r
830 <DD><CODE>java.io.IOException</CODE></DL>
\r
835 <A NAME="getEnvironment()"><!-- --></A><H3>
\r
836 getEnvironment</H3>
\r
838 public java.util.Map<java.lang.String,java.lang.String> <B>getEnvironment</B>()</PRE>
\r
841 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getEnvironment()">getEnvironment</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></DL>
\r
849 <A NAME="loadRunConfiguration(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>
\r
850 loadRunConfiguration</H3>
\r
852 public <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> <B>loadRunConfiguration</B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> rconf)</PRE>
\r
855 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></DL>
\r
863 <A NAME="newConfExecutable(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>
\r
864 newConfExecutable</H3>
\r
866 public static <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> <B>newConfExecutable</B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> rconf)</PRE>
\r
877 <A NAME="saveRunConfiguration()"><!-- --></A><H3>
\r
878 saveRunConfiguration</H3>
\r
880 public boolean <B>saveRunConfiguration</B>()
\r
881 throws java.io.IOException</PRE>
\r
884 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#saveRunConfiguration()">saveRunConfiguration</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></DL>
\r
889 <DD><CODE>java.io.IOException</CODE></DL>
\r
894 <A NAME="getRunConfiguration()"><!-- --></A><H3>
\r
895 getRunConfiguration</H3>
\r
897 public <A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> <B>getRunConfiguration</B>()</PRE>
\r
908 <A NAME="loadRunConfiguration(java.io.InputStream)"><!-- --></A><H3>
\r
909 loadRunConfiguration</H3>
\r
911 public <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> <B>loadRunConfiguration</B>(java.io.InputStream input)
\r
912 throws java.io.IOException</PRE>
\r
915 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#loadRunConfiguration(java.io.InputStream)">loadRunConfiguration</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></DL>
\r
920 <DD><CODE>java.io.IOException</CODE></DL>
\r
925 <A NAME="toString()"><!-- --></A><H3>
\r
928 public java.lang.String <B>toString</B>()</PRE>
\r
931 <DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>
\r
937 <!-- ========= END OF CLASS DATA ========= -->
\r
941 <!-- ======= START OF BOTTOM NAVBAR ====== -->
\r
942 <A NAME="navbar_bottom"><!-- --></A>
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943 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
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944 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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946 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
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947 <A NAME="navbar_bottom_firstrow"><!-- --></A>
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948 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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949 <TR ALIGN="center" VALIGN="top">
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950 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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951 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
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952 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
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953 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/ConfExecutable.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
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954 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
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955 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
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956 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
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957 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
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961 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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967 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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968 <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>
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969 <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>
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970 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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971 <A HREF="../../../index.html?compbio/engine/client/ConfExecutable.html" target="_top"><B>FRAMES</B></A>
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972 <A HREF="ConfExecutable.html" target="_top"><B>NO FRAMES</B></A>
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973 <SCRIPT type="text/javascript">
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976 document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
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981 <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
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988 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
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989 SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
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990 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
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991 DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
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994 <A NAME="skip-navbar_bottom"></A>
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995 <!-- ======== END OF BOTTOM NAVBAR ======= -->
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