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18 parent.document.title="ConfExecutable";
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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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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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95 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>
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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 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A><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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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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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 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></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 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> 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>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> 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> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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183 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getClusterJobSettings()">getClusterJobSettings</A></B>()</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> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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191 <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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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> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>></CODE></FONT></TD>
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199 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getCreatedFiles()">getCreatedFiles</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> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>,<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>></CODE></FONT></TD>
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207 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getEnvironment()">getEnvironment</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="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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215 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getError()">getError</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.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>
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223 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getExecProvider()">getExecProvider</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> <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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231 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getExecutable()">getExecutable</A></B>()</CODE>
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234 </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="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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239 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getInput()">getInput</A></B>()</CODE>
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242 Not all input paths are relative! Input path could be absolute!</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/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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247 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getLimit(java.lang.String)">getLimit</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> presetName)</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> <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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255 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getLimits()">getLimits</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="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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263 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getOutput()">getOutput</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()">getParameters</A></B>()</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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278 <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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279 <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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282 </TD>
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284 <TR BGCOLOR="white" CLASS="TableRowColor">
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285 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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287 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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288 <TR ALIGN="right" VALIGN="">
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289 <TD NOWRAP><FONT SIZE="-1">
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290 <CODE><V> V</CODE></FONT></TD>
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293 </CODE></FONT></TD>
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294 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getResults()">getResults</A></B>()</CODE>
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297 </TD>
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299 <TR BGCOLOR="white" CLASS="TableRowColor">
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300 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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302 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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303 <TR ALIGN="right" VALIGN="">
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304 <TD NOWRAP><FONT SIZE="-1">
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305 <CODE><V> V</CODE></FONT></TD>
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308 </CODE></FONT></TD>
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309 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getResults(java.lang.String)">getResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> directory)</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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316 <CODE> <A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A></CODE></FONT></TD>
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317 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunConfiguration()">getRunConfiguration</A></B>()</CODE>
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320 </TD>
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322 <TR BGCOLOR="white" CLASS="TableRowColor">
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323 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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325 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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326 <TR ALIGN="right" VALIGN="">
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327 <TD NOWRAP><FONT SIZE="-1">
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328 <CODE><V> <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><V></CODE></FONT></TD>
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331 </CODE></FONT></TD>
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332 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunnerLimits(java.lang.Class)">getRunnerLimits</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A><V> clazz)</CODE>
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335 This method should be executed once and result of its execution reused.</TD>
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337 <TR BGCOLOR="white" CLASS="TableRowColor">
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338 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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340 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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341 <TR ALIGN="right" VALIGN="">
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342 <TD NOWRAP><FONT SIZE="-1">
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343 <CODE><V> <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><V></CODE></FONT></TD>
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346 </CODE></FONT></TD>
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347 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunnerOptions(java.lang.Class)">getRunnerOptions</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A><? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><V>> clazz)</CODE>
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350 </TD>
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352 <TR BGCOLOR="white" CLASS="TableRowColor">
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353 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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355 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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356 <TR ALIGN="right" VALIGN="">
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357 <TD NOWRAP><FONT SIZE="-1">
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358 <CODE><V> <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><V></CODE></FONT></TD>
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361 </CODE></FONT></TD>
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362 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunnerPresets(java.lang.Class)">getRunnerPresets</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A><? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><V>> clazz)</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> <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>
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370 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getSupportedRuntimes()">getSupportedRuntimes</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> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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378 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getTaskId()">getTaskId</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="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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386 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getWorkDirectory()">getWorkDirectory</A></B>()</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(java.io.InputStream)">loadRunConfiguration</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> input)</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> <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#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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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>static <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?></CODE></FONT></TD>
\r
410 <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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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> boolean</CODE></FONT></TD>
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418 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#saveRunConfiguration()">saveRunConfiguration</A></B>()</CODE>
\r
421 </TD>
\r
423 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
424 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
425 <CODE> void</CODE></FONT></TD>
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426 <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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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> void</CODE></FONT></TD>
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434 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#setWorkDirectory(java.lang.String)">setWorkDirectory</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> workDirectory)</CODE>
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437 </TD>
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439 <TR BGCOLOR="white" CLASS="TableRowColor">
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440 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
441 <CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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442 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#toString()">toString</A></B>()</CODE>
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445 </TD>
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448 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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449 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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450 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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451 <TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>
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453 <TR BGCOLOR="white" CLASS="TableRowColor">
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454 <TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>
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460 <!-- ============ FIELD DETAIL =========== -->
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462 <A NAME="field_detail"><!-- --></A>
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463 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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464 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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465 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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466 <B>Field Detail</B></FONT></TH>
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470 <A NAME="CLUSTER_TASK_ID_PREFIX"><!-- --></A><H3>
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471 CLUSTER_TASK_ID_PREFIX</H3>
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473 public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>CLUSTER_TASK_ID_PREFIX</B></PRE>
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476 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.engine.client.ConfExecutable.CLUSTER_TASK_ID_PREFIX">Constant Field Values</A></DL>
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479 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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481 <A NAME="constructor_detail"><!-- --></A>
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482 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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483 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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484 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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485 <B>Constructor Detail</B></FONT></TH>
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489 <A NAME="ConfExecutable(compbio.engine.client.Executable, java.lang.String)"><!-- --></A><H3>
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490 ConfExecutable</H3>
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492 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,
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493 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> taskDirectory)</PRE>
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497 <!-- ============ METHOD DETAIL ========== -->
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499 <A NAME="method_detail"><!-- --></A>
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500 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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501 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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502 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
\r
503 <B>Method Detail</B></FONT></TH>
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507 <A NAME="getExecProvider()"><!-- --></A><H3>
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508 getExecProvider</H3>
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510 public <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> <B>getExecProvider</B>()</PRE>
\r
513 <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>
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521 <A NAME="setExecProvider(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>
\r
522 setExecProvider</H3>
\r
524 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
535 <A NAME="getCommand(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>
\r
538 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getCommand</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)
\r
539 throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></PRE>
\r
542 <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
547 <DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE></DL>
\r
552 <A NAME="getSupportedRuntimes()"><!-- --></A><H3>
\r
553 getSupportedRuntimes</H3>
\r
555 public <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> <B>getSupportedRuntimes</B>()</PRE>
\r
558 <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
566 <A NAME="getLimit(java.lang.String)"><!-- --></A><H3>
\r
569 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>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> presetName)</PRE>
\r
572 <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
580 <A NAME="getLimits()"><!-- --></A><H3>
\r
583 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
586 <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>
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594 <A NAME="getTaskId()"><!-- --></A><H3>
\r
597 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getTaskId</B>()</PRE>
\r
600 <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>
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608 <A NAME="setWorkDirectory(java.lang.String)"><!-- --></A><H3>
\r
609 setWorkDirectory</H3>
\r
611 public void <B>setWorkDirectory</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> workDirectory)</PRE>
\r
614 <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
622 <A NAME="getWorkDirectory()"><!-- --></A><H3>
\r
623 getWorkDirectory</H3>
\r
625 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getWorkDirectory</B>()</PRE>
\r
628 <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>
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636 <A NAME="addParameters(java.util.List)"><!-- --></A><H3>
\r
639 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>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> parameters)</PRE>
\r
641 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">Executable</A></CODE></B></DD>
\r
642 <DD>Adds parameter to the list of parameters for a native executable
\r
645 <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
649 <DT><B>Returns:</B><DD>this Executable</DL>
\r
654 <A NAME="getOutput()"><!-- --></A><H3>
\r
657 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getOutput</B>()</PRE>
\r
660 <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
668 <A NAME="getError()"><!-- --></A><H3>
\r
671 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getError</B>()</PRE>
\r
674 <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
682 <A NAME="getCreatedFiles()"><!-- --></A><H3>
\r
683 getCreatedFiles</H3>
\r
685 public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> <B>getCreatedFiles</B>()</PRE>
\r
688 <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
696 <A NAME="getInput()"><!-- --></A><H3>
\r
699 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getInput</B>()</PRE>
\r
701 <DD>Not all input paths are relative! Input path could be absolute!
\r
704 <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
707 <DT><B>See Also:</B><DD><CODE>compbio.engine.client.Executable#getInputFiles()</CODE></DL>
\r
712 <A NAME="getParameters()"><!-- --></A><H3>
\r
715 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
718 <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
726 <A NAME="getParameters(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>
\r
729 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
732 <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
740 <A NAME="getExecutable()"><!-- --></A><H3>
\r
743 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
746 <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
754 <A NAME="getResults()"><!-- --></A><H3>
\r
757 public <V> V <B>getResults</B>()
\r
758 throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>
\r
761 <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
766 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>
\r
771 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>
\r
774 public <V> V <B>getResults</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> directory)
\r
775 throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>
\r
778 <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
783 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>
\r
788 <A NAME="getRunnerOptions(java.lang.Class)"><!-- --></A><H3>
\r
789 getRunnerOptions</H3>
\r
791 public static <V> <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><V> <B>getRunnerOptions</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A><? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><V>> clazz)
\r
792 throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>
\r
800 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>
\r
805 <A NAME="getRunnerPresets(java.lang.Class)"><!-- --></A><H3>
\r
806 getRunnerPresets</H3>
\r
808 public static <V> <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><V> <B>getRunnerPresets</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A><? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><V>> clazz)
\r
809 throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>
\r
817 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>
\r
822 <A NAME="getRunnerLimits(java.lang.Class)"><!-- --></A><H3>
\r
823 getRunnerLimits</H3>
\r
825 public static <V> <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><V> <B>getRunnerLimits</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A><V> clazz)
\r
826 throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>
\r
828 <DD>This method should be executed once and result of its execution reused.
829 If not used carefully it could slow down the system!
\r
835 <DT><B>Type Parameters:</B><DD><CODE>V</CODE> - <DT><B>Parameters:</B><DD><CODE>clazz</CODE> -
\r
836 <DT><B>Returns:</B><DD>LimitsManager instance
\r
838 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>
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843 <A NAME="getEnvironment()"><!-- --></A><H3>
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844 getEnvironment</H3>
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846 public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>,<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> <B>getEnvironment</B>()</PRE>
\r
849 <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>
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857 <A NAME="loadRunConfiguration(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>
\r
858 loadRunConfiguration</H3>
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860 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
863 <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
871 <A NAME="newConfExecutable(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>
\r
872 newConfExecutable</H3>
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874 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
885 <A NAME="saveRunConfiguration()"><!-- --></A><H3>
\r
886 saveRunConfiguration</H3>
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888 public boolean <B>saveRunConfiguration</B>()
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889 throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>
\r
892 <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
897 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>
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902 <A NAME="getRunConfiguration()"><!-- --></A><H3>
\r
903 getRunConfiguration</H3>
\r
905 public <A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> <B>getRunConfiguration</B>()</PRE>
\r
916 <A NAME="loadRunConfiguration(java.io.InputStream)"><!-- --></A><H3>
\r
917 loadRunConfiguration</H3>
\r
919 public <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> <B>loadRunConfiguration</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> input)
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920 throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>
\r
923 <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
928 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>
\r
933 <A NAME="toString()"><!-- --></A><H3>
\r
936 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toString</B>()</PRE>
\r
939 <DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>
\r
947 <A NAME="getClusterJobSettings()"><!-- --></A><H3>
\r
948 getClusterJobSettings</H3>
\r
950 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getClusterJobSettings</B>()</PRE>
\r
953 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getClusterJobSettings()">getClusterJobSettings</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>
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959 <!-- ========= END OF CLASS DATA ========= -->
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