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5 <!-- Generated by javadoc (build 1.6.0_24) on Wed Dec 07 12:30:41 GMT 2011 -->
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10 <META NAME="date" CONTENT="2011-12-07">
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12 <LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">
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14 <SCRIPT type="text/javascript">
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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="SkeletalExecutable";
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27 <BODY BGCOLOR="white" onload="windowTitle();">
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31 <!-- ========= START OF TOP NAVBAR ======= -->
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32 <A NAME="navbar_top"><!-- --></A>
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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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41 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</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/SkeletalExecutable.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
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51 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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57 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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58 <A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>
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59 <A HREF="../../../compbio/engine/client/Util.html" title="class in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>
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60 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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61 <A HREF="../../../index.html?compbio/engine/client/SkeletalExecutable.html" target="_top"><B>FRAMES</B></A>
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62 <A HREF="SkeletalExecutable.html" target="_top"><B>NO FRAMES</B></A>
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63 <SCRIPT type="text/javascript">
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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 | <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 SkeletalExecutable<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.SkeletalExecutable<T></B>
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99 <DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T></DD>
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102 <DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>, <A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>, <A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>, <A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>, <A HREF="../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>, <A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>, <A HREF="../../../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>, <A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>, <A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>, <A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>, <A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></DD>
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106 <DT><PRE>public abstract class <B>SkeletalExecutable<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/Executable.html" title="interface in compbio.engine.client">Executable</A><T></DL>
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113 <!-- ======== NESTED CLASS SUMMARY ======== -->
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115 <A NAME="nested_class_summary"><!-- --></A>
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116 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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117 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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118 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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119 <B>Nested Class Summary</B></FONT></TH>
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122 <A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>
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123 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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124 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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125 <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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127 <TR BGCOLOR="white" CLASS="TableRowColor">
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128 <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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132 <!-- =========== FIELD SUMMARY =========== -->
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134 <A NAME="field_summary"><!-- --></A>
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135 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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136 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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137 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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138 <B>Field Summary</B></FONT></TH>
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140 <TR BGCOLOR="white" CLASS="TableRowColor">
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141 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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142 <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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143 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#ERROR">ERROR</A></B></CODE>
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146 </TD>
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148 <TR BGCOLOR="white" CLASS="TableRowColor">
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149 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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150 <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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151 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#INPUT">INPUT</A></B></CODE>
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154 </TD>
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156 <TR BGCOLOR="white" CLASS="TableRowColor">
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157 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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158 <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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159 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#OUTPUT">OUTPUT</A></B></CODE>
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162 </TD>
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166 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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168 <A NAME="constructor_summary"><!-- --></A>
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169 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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170 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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171 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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172 <B>Constructor Summary</B></FONT></TH>
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174 <TR BGCOLOR="white" CLASS="TableRowColor">
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175 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#SkeletalExecutable()">SkeletalExecutable</A></B>()</CODE>
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178 </TD>
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180 <TR BGCOLOR="white" CLASS="TableRowColor">
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181 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#SkeletalExecutable(java.lang.String)">SkeletalExecutable</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> parameterKeyValueDelimiter)</CODE>
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184 </TD>
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188 <!-- ========== METHOD SUMMARY =========== -->
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190 <A NAME="method_summary"><!-- --></A>
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191 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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192 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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193 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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194 <B>Method Summary</B></FONT></TH>
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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="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></FONT></TD>
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199 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.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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202 Adds parameter to the list of parameters for a native executable</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> boolean</CODE></FONT></TD>
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207 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#equals(java.lang.Object)">equals</A></B>(<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> obj)</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>static int</CODE></FONT></TD>
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215 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterCpuNum(java.lang.Class)">getClusterCpuNum</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><?>> type)</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="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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223 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterJobSettings()">getClusterJobSettings</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="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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231 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>
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234 This method cannot really tell whether the files has actually been
235 created or not.</TD>
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237 <TR BGCOLOR="white" CLASS="TableRowColor">
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238 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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239 <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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240 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getError()">getError</A></B>()</CODE>
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243 </TD>
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245 <TR BGCOLOR="white" CLASS="TableRowColor">
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246 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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247 <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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248 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getInput()">getInput</A></B>()</CODE>
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251 </TD>
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253 <TR BGCOLOR="white" CLASS="TableRowColor">
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254 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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255 <CODE> <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></FONT></TD>
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256 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.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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259 </TD>
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261 <TR BGCOLOR="white" CLASS="TableRowColor">
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262 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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263 <CODE> <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></FONT></TD>
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264 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getLimits()">getLimits</A></B>()</CODE>
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267 </TD>
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269 <TR BGCOLOR="white" CLASS="TableRowColor">
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270 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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271 <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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272 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getOutput()">getOutput</A></B>()</CODE>
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275 </TD>
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277 <TR BGCOLOR="white" CLASS="TableRowColor">
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278 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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279 <CODE> <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></FONT></TD>
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280 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.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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283 </TD>
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285 <TR BGCOLOR="white" CLASS="TableRowColor">
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286 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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287 <CODE>abstract <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><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></FONT></TD>
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288 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getType()">getType</A></B>()</CODE>
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291 </TD>
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293 <TR BGCOLOR="white" CLASS="TableRowColor">
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294 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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295 <CODE> int</CODE></FONT></TD>
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296 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#hashCode()">hashCode</A></B>()</CODE>
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299 </TD>
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301 <TR BGCOLOR="white" CLASS="TableRowColor">
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302 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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303 <CODE> <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?></CODE></FONT></TD>
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304 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> rconfig)</CODE>
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307 </TD>
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309 <TR BGCOLOR="white" CLASS="TableRowColor">
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310 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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311 <CODE> <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></FONT></TD>
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312 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setError(java.lang.String)">setError</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> errFile)</CODE>
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315 </TD>
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317 <TR BGCOLOR="white" CLASS="TableRowColor">
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318 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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319 <CODE> <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></FONT></TD>
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320 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setInput(java.lang.String)">setInput</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> inFile)</CODE>
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323 </TD>
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325 <TR BGCOLOR="white" CLASS="TableRowColor">
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326 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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327 <CODE> <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></FONT></TD>
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328 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setOutput(java.lang.String)">setOutput</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> outFile)</CODE>
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331 </TD>
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333 <TR BGCOLOR="white" CLASS="TableRowColor">
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334 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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335 <CODE> <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></FONT></TD>
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336 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)">setParameter</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> parameter)</CODE>
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339 </TD>
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341 <TR BGCOLOR="white" CLASS="TableRowColor">
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342 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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343 <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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344 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#toString()">toString</A></B>()</CODE>
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347 </TD>
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350 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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351 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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352 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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353 <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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355 <TR BGCOLOR="white" CLASS="TableRowColor">
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356 <TD><CODE><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#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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359 <A NAME="methods_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>
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360 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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361 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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362 <TH ALIGN="left"><B>Methods 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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364 <TR BGCOLOR="white" CLASS="TableRowColor">
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365 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</A></CODE></TD>
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371 <!-- ============ FIELD DETAIL =========== -->
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373 <A NAME="field_detail"><!-- --></A>
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374 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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375 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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376 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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377 <B>Field Detail</B></FONT></TH>
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381 <A NAME="INPUT"><!-- --></A><H3>
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384 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>INPUT</B></PRE>
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387 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.engine.client.SkeletalExecutable.INPUT">Constant Field Values</A></DL>
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391 <A NAME="OUTPUT"><!-- --></A><H3>
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394 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>OUTPUT</B></PRE>
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397 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.engine.client.SkeletalExecutable.OUTPUT">Constant Field Values</A></DL>
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401 <A NAME="ERROR"><!-- --></A><H3>
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404 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>ERROR</B></PRE>
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407 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.engine.client.SkeletalExecutable.ERROR">Constant Field Values</A></DL>
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410 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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412 <A NAME="constructor_detail"><!-- --></A>
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413 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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414 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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415 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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416 <B>Constructor Detail</B></FONT></TH>
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420 <A NAME="SkeletalExecutable()"><!-- --></A><H3>
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421 SkeletalExecutable</H3>
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423 public <B>SkeletalExecutable</B>()</PRE>
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428 <A NAME="SkeletalExecutable(java.lang.String)"><!-- --></A><H3>
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429 SkeletalExecutable</H3>
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431 public <B>SkeletalExecutable</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> parameterKeyValueDelimiter)</PRE>
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435 <!-- ============ METHOD DETAIL ========== -->
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437 <A NAME="method_detail"><!-- --></A>
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438 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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439 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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440 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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441 <B>Method Detail</B></FONT></TH>
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445 <A NAME="setInput(java.lang.String)"><!-- --></A><H3>
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448 public <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>> <B>setInput</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> inFile)</PRE>
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459 <A NAME="setOutput(java.lang.String)"><!-- --></A><H3>
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462 public <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>> <B>setOutput</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> outFile)</PRE>
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473 <A NAME="setError(java.lang.String)"><!-- --></A><H3>
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476 public <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>> <B>setError</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> errFile)</PRE>
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487 <A NAME="getParameters(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>
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490 public <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>> <B>getParameters</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</PRE>
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493 <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/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></DL>
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501 <A NAME="addParameters(java.util.List)"><!-- --></A><H3>
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504 public <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">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>
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506 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">Executable</A></CODE></B></DD>
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507 <DD>Adds parameter to the list of parameters for a native executable
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510 <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/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></DL>
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514 <DT><B>Returns:</B><DD>this Executable</DL>
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519 <A NAME="setParameter(java.lang.String)"><!-- --></A><H3>
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522 public <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>> <B>setParameter</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> parameter)</PRE>
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533 <A NAME="getCreatedFiles()"><!-- --></A><H3>
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534 getCreatedFiles</H3>
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536 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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538 <DD>This method cannot really tell whether the files has actually been
539 created or not. It must be overridden as required.
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542 <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/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></DL>
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545 <DT><B>See Also:</B><DD><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()"><CODE>Executable.getCreatedFiles()</CODE></A></DL>
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550 <A NAME="getInput()"><!-- --></A><H3>
\r
553 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
556 <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/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></DL>
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564 <A NAME="getOutput()"><!-- --></A><H3>
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567 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>
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570 <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/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></DL>
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578 <A NAME="getError()"><!-- --></A><H3>
\r
581 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
584 <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/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></DL>
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592 <A NAME="toString()"><!-- --></A><H3>
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595 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
598 <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>
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606 <A NAME="loadRunConfiguration(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>
\r
607 loadRunConfiguration</H3>
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609 public <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?> <B>loadRunConfiguration</B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> rconfig)</PRE>
\r
612 <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/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></DL>
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620 <A NAME="equals(java.lang.Object)"><!-- --></A><H3>
\r
623 public boolean <B>equals</B>(<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> obj)</PRE>
\r
626 <DT><B>Overrides:</B><DD><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></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
634 <A NAME="hashCode()"><!-- --></A><H3>
\r
637 public int <B>hashCode</B>()</PRE>
\r
640 <DT><B>Overrides:</B><DD><CODE><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></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
648 <A NAME="getClusterJobSettings()"><!-- --></A><H3>
\r
649 getClusterJobSettings</H3>
\r
651 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
654 <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/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></DL>
\r
662 <A NAME="getClusterCpuNum(java.lang.Class)"><!-- --></A><H3>
\r
663 getClusterCpuNum</H3>
\r
665 public static int <B>getClusterCpuNum</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><?>> type)</PRE>
\r
672 <DT><B>Returns:</B><DD>number of cpus to use on the cluster or 0 if the value is
678 <A NAME="getLimit(java.lang.String)"><!-- --></A><H3>
\r
681 public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">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
684 <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/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></DL>
\r
692 <A NAME="getLimits()"><!-- --></A><H3>
\r
695 public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>> <B>getLimits</B>()</PRE>
\r
698 <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/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></DL>
\r
706 <A NAME="getType()"><!-- --></A><H3>
\r
709 public abstract <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><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>> <B>getType</B>()</PRE>
\r
716 <DT><B>Returns:</B><DD>subclasses must return their type</DL>
\r
719 <!-- ========= END OF CLASS DATA ========= -->
\r
723 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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724 <A NAME="navbar_bottom"><!-- --></A>
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725 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
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726 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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728 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
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729 <A NAME="navbar_bottom_firstrow"><!-- --></A>
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730 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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731 <TR ALIGN="center" VALIGN="top">
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732 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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733 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
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734 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
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735 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/SkeletalExecutable.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
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736 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
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737 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
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738 <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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739 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
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743 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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749 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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750 <A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>
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751 <A HREF="../../../compbio/engine/client/Util.html" title="class in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>
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752 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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753 <A HREF="../../../index.html?compbio/engine/client/SkeletalExecutable.html" target="_top"><B>FRAMES</B></A>
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754 <A HREF="SkeletalExecutable.html" target="_top"><B>NO FRAMES</B></A>
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755 <SCRIPT type="text/javascript">
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758 document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
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763 <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
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770 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
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771 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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772 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
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773 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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776 <A NAME="skip-navbar_bottom"></A>
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777 <!-- ======== END OF BOTTOM NAVBAR ======= -->
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