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5 <!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->
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7 _SkeletalCommandBuilder
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10 <META NAME="date" CONTENT="2010-02-17">
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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="_SkeletalCommandBuilder";
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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/_SkeletalCommandBuilder.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
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58 <A HREF="../../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner"><B>PREV CLASS</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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80 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
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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</FONT>
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93 Class _SkeletalCommandBuilder</H2>
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96 <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.runner._SkeletalCommandBuilder</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><<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></DD>
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102 <DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>, <A HREF="../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A>, <A HREF="../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>, <A HREF="../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>, <A HREF="../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>, <A HREF="../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>, <A HREF="../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A></DD>
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106 <DT><PRE>public abstract class <B>_SkeletalCommandBuilder</B><DT>extends java.lang.Object<DT>implements <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>></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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133 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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135 <A NAME="constructor_summary"><!-- --></A>
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136 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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137 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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138 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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139 <B>Constructor Summary</B></FONT></TH>
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141 <TR BGCOLOR="white" CLASS="TableRowColor">
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142 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#_SkeletalCommandBuilder()">_SkeletalCommandBuilder</A></B>()</CODE>
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145 </TD>
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149 <!-- ========== METHOD SUMMARY =========== -->
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151 <A NAME="method_summary"><!-- --></A>
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152 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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153 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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154 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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155 <B>Method Summary</B></FONT></TH>
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157 <TR BGCOLOR="white" CLASS="TableRowColor">
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158 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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159 <CODE> <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>
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160 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)">addParameter</A></B>(java.lang.String parameter)</CODE>
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163 </TD>
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165 <TR BGCOLOR="white" CLASS="TableRowColor">
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166 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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167 <CODE> <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>
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168 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List<java.lang.String> parameters)</CODE>
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171 Adds parameter to the list of parameters for a native executable</TD>
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173 <TR BGCOLOR="white" CLASS="TableRowColor">
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174 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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175 <CODE> <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>
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176 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])">addParameters</A></B>(java.lang.String[] parameters)</CODE>
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179 </TD>
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181 <TR BGCOLOR="white" CLASS="TableRowColor">
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182 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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183 <CODE> java.lang.String</CODE></FONT></TD>
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184 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getEmail()">getEmail</A></B>()</CODE>
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187 </TD>
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189 <TR BGCOLOR="white" CLASS="TableRowColor">
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190 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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191 <CODE> java.lang.String</CODE></FONT></TD>
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192 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getError()">getError</A></B>()</CODE>
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195 </TD>
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197 <TR BGCOLOR="white" CLASS="TableRowColor">
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198 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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199 <CODE> <A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></CODE></FONT></TD>
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200 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String presetName)</CODE>
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203 </TD>
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205 <TR BGCOLOR="white" CLASS="TableRowColor">
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206 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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207 <CODE> <A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></CODE></FONT></TD>
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208 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getLimits()">getLimits</A></B>()</CODE>
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211 </TD>
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213 <TR BGCOLOR="white" CLASS="TableRowColor">
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214 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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215 <CODE> java.lang.String</CODE></FONT></TD>
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216 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getName()">getName</A></B>()</CODE>
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219 </TD>
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221 <TR BGCOLOR="white" CLASS="TableRowColor">
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222 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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223 <CODE> java.lang.String</CODE></FONT></TD>
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224 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getOutput()">getOutput</A></B>()</CODE>
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227 </TD>
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229 <TR BGCOLOR="white" CLASS="TableRowColor">
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230 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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231 <CODE> <A HREF="../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></CODE></FONT></TD>
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232 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.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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235 </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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240 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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241 <TR ALIGN="right" VALIGN="">
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242 <TD NOWRAP><FONT SIZE="-1">
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243 <CODE><V> V</CODE></FONT></TD>
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246 </CODE></FONT></TD>
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247 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String directory)</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/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?></CODE></FONT></TD>
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255 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.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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258 </TD>
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260 <TR BGCOLOR="white" CLASS="TableRowColor">
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261 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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262 <CODE> <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>
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263 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#setEmail(java.lang.String)">setEmail</A></B>(java.lang.String email)</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/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>
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271 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)">setName</A></B>(java.lang.String name)</CODE>
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274 </TD>
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277 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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278 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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279 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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280 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>
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282 <TR BGCOLOR="white" CLASS="TableRowColor">
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283 <TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
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286 <A NAME="methods_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>
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287 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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288 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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289 <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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291 <TR BGCOLOR="white" CLASS="TableRowColor">
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292 <TD><CODE><A HREF="../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A>, <A HREF="../../compbio/engine/client/Executable.html#getInput()">getInput</A></CODE></TD>
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298 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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300 <A NAME="constructor_detail"><!-- --></A>
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301 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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302 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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303 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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304 <B>Constructor Detail</B></FONT></TH>
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308 <A NAME="_SkeletalCommandBuilder()"><!-- --></A><H3>
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309 _SkeletalCommandBuilder</H3>
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311 public <B>_SkeletalCommandBuilder</B>()</PRE>
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315 <!-- ============ METHOD DETAIL ========== -->
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317 <A NAME="method_detail"><!-- --></A>
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318 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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319 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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320 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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321 <B>Method Detail</B></FONT></TH>
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325 <A NAME="setEmail(java.lang.String)"><!-- --></A><H3>
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328 public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>setEmail</B>(java.lang.String email)</PRE>
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339 <A NAME="setName(java.lang.String)"><!-- --></A><H3>
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342 public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>setName</B>(java.lang.String name)</PRE>
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353 <A NAME="getName()"><!-- --></A><H3>
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356 public java.lang.String <B>getName</B>()</PRE>
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367 <A NAME="getEmail()"><!-- --></A><H3>
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370 public java.lang.String <B>getEmail</B>()</PRE>
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381 <A NAME="addParameters(java.lang.String[])"><!-- --></A><H3>
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384 public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>addParameters</B>(java.lang.String[] parameters)</PRE>
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395 <A NAME="addParameters(java.util.List)"><!-- --></A><H3>
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398 public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>addParameters</B>(java.util.List<java.lang.String> parameters)</PRE>
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400 <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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401 <DD>Adds parameter to the list of parameters for a native executable
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404 <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/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></CODE></DL>
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408 <DT><B>Returns:</B><DD>this Executable</DL>
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413 <A NAME="getParameters(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>
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416 public <A HREF="../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</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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419 <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/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></CODE></DL>
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427 <A NAME="addParameter(java.lang.String)"><!-- --></A><H3>
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430 public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>addParameter</B>(java.lang.String parameter)</PRE>
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441 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>
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444 public <V> V <B>getResults</B>(java.lang.String directory)</PRE>
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447 <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/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></CODE></DL>
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455 <A NAME="loadRunConfiguration(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>
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456 loadRunConfiguration</H3>
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458 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>
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461 <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/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></CODE></DL>
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469 <A NAME="getOutput()"><!-- --></A><H3>
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472 public java.lang.String <B>getOutput</B>()</PRE>
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475 <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/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></CODE></DL>
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483 <A NAME="getError()"><!-- --></A><H3>
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486 public java.lang.String <B>getError</B>()</PRE>
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489 <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/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></CODE></DL>
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497 <A NAME="getLimit(java.lang.String)"><!-- --></A><H3>
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500 public <A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>> <B>getLimit</B>(java.lang.String presetName)</PRE>
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503 <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/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></CODE></DL>
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511 <A NAME="getLimits()"><!-- --></A><H3>
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514 public <A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>> <B>getLimits</B>()</PRE>
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517 <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/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></CODE></DL>
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523 <!-- ========= END OF CLASS DATA ========= -->
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527 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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528 <A NAME="navbar_bottom"><!-- --></A>
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529 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
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530 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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532 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
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