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5 <!-- Generated by javadoc (build 1.6.0_24) on Wed Dec 07 12:30:43 GMT 2011 -->
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7 Uses of Class compbio.runner._SkeletalCommandBuilder
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10 <META NAME="date" CONTENT="2011-12-07">
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18 parent.document.title="Uses of Class compbio.runner._SkeletalCommandBuilder";
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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="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
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43 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
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45 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
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59 NEXT</FONT></TD>
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60 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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62 <A HREF="_SkeletalCommandBuilder.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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78 <A NAME="skip-navbar_top"></A>
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79 <!-- ========= END OF TOP NAVBAR ========= -->
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84 <B>Uses of Class<br>compbio.runner._SkeletalCommandBuilder</B></H2>
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87 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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88 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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89 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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90 Packages that use <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></FONT></TH>
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92 <TR BGCOLOR="white" CLASS="TableRowColor">
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93 <TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>
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94 <TD>Utilities commonly used by all runners. </TD>
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96 <TR BGCOLOR="white" CLASS="TableRowColor">
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97 <TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>
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98 <TD> </TD>
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103 <A NAME="compbio.runner"><!-- --></A>
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104 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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105 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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106 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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107 Uses of <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>
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113 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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114 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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115 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> that return <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></FONT></TH>
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117 <TR BGCOLOR="white" CLASS="TableRowColor">
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118 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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119 <CODE> <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>
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120 <TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)">addParameter</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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123 <B>Deprecated.</B> </TD>
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125 <TR BGCOLOR="white" CLASS="TableRowColor">
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126 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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127 <CODE> <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>
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128 <TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.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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131 <B>Deprecated.</B> </TD>
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133 <TR BGCOLOR="white" CLASS="TableRowColor">
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134 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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135 <CODE> <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>
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136 <TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])">addParameters</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>[] parameters)</CODE>
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139 <B>Deprecated.</B> </TD>
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141 <TR BGCOLOR="white" CLASS="TableRowColor">
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142 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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143 <CODE> <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>
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144 <TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setEmail(java.lang.String)">setEmail</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> email)</CODE>
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147 <B>Deprecated.</B> </TD>
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149 <TR BGCOLOR="white" CLASS="TableRowColor">
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150 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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151 <CODE> <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>
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152 <TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)">setName</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> name)</CODE>
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155 <B>Deprecated.</B> </TD>
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161 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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162 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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163 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> that return types with arguments of type <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></FONT></TH>
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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/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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168 <TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.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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171 <B>Deprecated.</B> </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/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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176 <TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimits()">getLimits</A></B>()</CODE>
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179 <B>Deprecated.</B> </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> <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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184 <TD><CODE><B>_SkeletalCommandBuilder.</B><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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187 <B>Deprecated.</B> </TD>
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192 <A NAME="compbio.runner._impl"><!-- --></A>
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193 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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194 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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195 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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196 Uses of <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> in <A HREF="../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>
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202 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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203 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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204 <TH ALIGN="left" COLSPAN="2">Subclasses of <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> in <A HREF="../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>
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206 <TR BGCOLOR="white" CLASS="TableRowColor">
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207 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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208 <CODE> class</CODE></FONT></TD>
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209 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A></B></CODE>
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212 </TD>
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214 <TR BGCOLOR="white" CLASS="TableRowColor">
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215 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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216 <CODE> class</CODE></FONT></TD>
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217 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A></B></CODE>
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220 </TD>
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222 <TR BGCOLOR="white" CLASS="TableRowColor">
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223 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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224 <CODE> class</CODE></FONT></TD>
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225 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A></B></CODE>
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228 TODO this needs fixing! Executable does not work</TD>
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230 <TR BGCOLOR="white" CLASS="TableRowColor">
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231 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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232 <CODE> class</CODE></FONT></TD>
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233 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A></B></CODE>
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236 </TD>
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238 <TR BGCOLOR="white" CLASS="TableRowColor">
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239 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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240 <CODE> class</CODE></FONT></TD>
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241 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A></B></CODE>
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244 </TD>
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246 <TR BGCOLOR="white" CLASS="TableRowColor">
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247 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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248 <CODE> class</CODE></FONT></TD>
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249 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A></B></CODE>
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252 </TD>
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260 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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261 <A NAME="navbar_bottom"><!-- --></A>
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262 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
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263 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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266 <A NAME="navbar_bottom_firstrow"><!-- --></A>
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267 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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268 <TR ALIGN="center" VALIGN="top">
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269 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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270 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
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271 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
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272 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
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273 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
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274 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
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275 <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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276 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
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280 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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286 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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288 NEXT</FONT></TD>
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289 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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290 <A HREF="../../../index.html?compbio/runner/\class-use_SkeletalCommandBuilder.html" target="_top"><B>FRAMES</B></A>
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291 <A HREF="_SkeletalCommandBuilder.html" target="_top"><B>NO FRAMES</B></A>
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292 <SCRIPT type="text/javascript">
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295 document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
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300 <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
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