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5 <!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:35 BST 2011 -->
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10 <META NAME="date" CONTENT="2011-08-12">
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15 function windowTitle()
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17 if (location.href.indexOf('is-external=true') == -1) {
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18 parent.document.title="Mcl";
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27 <BODY BGCOLOR="white" onload="windowTitle();">
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31 <!-- ========= START OF TOP NAVBAR ======= -->
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40 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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42 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
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43 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Mcl.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
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66 document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
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71 <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
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78 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
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79 SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
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81 DETAIL: FIELD | <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.runner._impl</FONT>
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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 "><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">compbio.runner._SkeletalCommandBuilder</A>
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97 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner._impl.Mcl</B>
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100 <DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></DD>
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104 <DT><PRE>public class <B>Mcl</B><DT>extends <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></DL>
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111 <!-- ======== NESTED CLASS SUMMARY ======== -->
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116 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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117 <B>Nested Class Summary</B></FONT></TH>
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120 <A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>
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121 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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122 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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123 <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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125 <TR BGCOLOR="white" CLASS="TableRowColor">
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126 <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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131 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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133 <A NAME="constructor_summary"><!-- --></A>
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134 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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135 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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136 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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137 <B>Constructor Summary</B></FONT></TH>
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139 <TR BGCOLOR="white" CLASS="TableRowColor">
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140 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Mcl.html#Mcl(java.lang.String)">Mcl</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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143 </TD>
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147 <!-- ========== METHOD SUMMARY =========== -->
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149 <A NAME="method_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>Method Summary</B></FONT></TH>
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155 <TR BGCOLOR="white" CLASS="TableRowColor">
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156 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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157 <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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158 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Mcl.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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161 </TD>
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163 <TR BGCOLOR="white" CLASS="TableRowColor">
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164 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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165 <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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166 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Mcl.html#getCommandName()">getCommandName</A></B>()</CODE>
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169 </TD>
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171 <TR BGCOLOR="white" CLASS="TableRowColor">
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172 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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173 <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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174 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Mcl.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>
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177 </TD>
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179 <TR BGCOLOR="white" CLASS="TableRowColor">
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180 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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181 <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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182 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Mcl.html#getInput()">getInput</A></B>()</CODE>
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185 </TD>
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187 <TR BGCOLOR="white" CLASS="TableRowColor">
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188 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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189 <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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190 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Mcl.html#getTestCommand()">getTestCommand</A></B>()</CODE>
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193 </TD>
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195 <TR BGCOLOR="white" CLASS="TableRowColor">
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196 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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197 <CODE>static <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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198 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Mcl.html#getTestParams()">getTestParams</A></B>()</CODE>
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201 </TD>
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204 <A NAME="methods_inherited_from_class_compbio.runner._SkeletalCommandBuilder"><!-- --></A>
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205 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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206 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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207 <TH ALIGN="left"><B>Methods inherited from class compbio.runner.<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></B></TH>
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209 <TR BGCOLOR="white" CLASS="TableRowColor">
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210 <TD><CODE><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)">addParameter</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])">addParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getClusterJobSettings()">getClusterJobSettings</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getEmail()">getEmail</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getError()">getError</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getName()">getName</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getResults(java.lang.String)">getResults</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setEmail(java.lang.String)">setEmail</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)">setName</A></CODE></TD>
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213 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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214 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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215 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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216 <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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218 <TR BGCOLOR="white" CLASS="TableRowColor">
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219 <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#toString()" title="class or interface in java.lang">toString</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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225 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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227 <A NAME="constructor_detail"><!-- --></A>
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228 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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229 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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230 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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231 <B>Constructor Detail</B></FONT></TH>
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235 <A NAME="Mcl(java.lang.String)"><!-- --></A><H3>
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238 public <B>Mcl</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>
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242 <!-- ============ METHOD DETAIL ========== -->
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244 <A NAME="method_detail"><!-- --></A>
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245 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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246 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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247 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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248 <B>Method Detail</B></FONT></TH>
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252 <A NAME="getTestParams()"><!-- --></A><H3>
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255 public static <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>getTestParams</B>()</PRE>
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263 <A NAME="getCommand(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>
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266 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)</PRE>
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274 <A NAME="getTestCommand()"><!-- --></A><H3>
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275 getTestCommand</H3>
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277 public 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> <B>getTestCommand</B>()</PRE>
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285 <A NAME="getCommandName()"><!-- --></A><H3>
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286 getCommandName</H3>
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288 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>getCommandName</B>()</PRE>
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296 <A NAME="getCreatedFiles()"><!-- --></A><H3>
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297 getCreatedFiles</H3>
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299 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>
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307 <A NAME="getInput()"><!-- --></A><H3>
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310 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>
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316 <!-- ========= END OF CLASS DATA ========= -->
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329 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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332 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Mcl.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
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335 <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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336 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
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340 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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349 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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350 <A HREF="../../../index.html?compbio/runner/_impl/Mcl.html" target="_top"><B>FRAMES</B></A>
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351 <A HREF="Mcl.html" target="_top"><B>NO FRAMES</B></A>
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352 <SCRIPT type="text/javascript">
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355 document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
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367 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
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368 SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
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369 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
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370 DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
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