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5 <!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->
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7 Uses of Class compbio.engine.client.CommandBuilder
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18 parent.document.title="Uses of Class compbio.engine.client.CommandBuilder";
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42 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
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84 <B>Uses of Class<br>compbio.engine.client.CommandBuilder</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/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>
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92 <TR BGCOLOR="white" CLASS="TableRowColor">
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93 <TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>
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94 <TD>Classes and interfaces representing an input for engines. </TD>
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96 <TR BGCOLOR="white" CLASS="TableRowColor">
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97 <TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>
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98 <TD>Utilities commonly used by all runners. </TD>
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100 <TR BGCOLOR="white" CLASS="TableRowColor">
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101 <TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>
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102 <TD> </TD>
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104 <TR BGCOLOR="white" CLASS="TableRowColor">
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105 <TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>
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106 <TD>Wrappers for native executables for multiple sequence alignment (msa) </TD>
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111 <A NAME="compbio.engine.client"><!-- --></A>
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112 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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113 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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114 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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115 Uses of <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>
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121 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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122 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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123 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that return <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>
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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/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="type parameter in ConfiguredExecutable">T</A>></CODE></FONT></TD>
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128 <TD><CODE><B>ConfiguredExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html#getParameters()">getParameters</A></B>()</CODE>
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131 </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/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></FONT></TD>
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136 <TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#getParameters()">getParameters</A></B>()</CODE>
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139 </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/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><?></CODE></FONT></TD>
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144 <TD><CODE><B>RunConfiguration.</B><B><A HREF="../../../../compbio/engine/client/RunConfiguration.html#getParameters()">getParameters</A></B>()</CODE>
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147 </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/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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152 <TD><CODE><B>SkeletalExecutable.</B><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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155 </TD>
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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/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>></CODE></FONT></TD>
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160 <TD><CODE><B>Executable.</B><B><A HREF="../../../../compbio/engine/client/Executable.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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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/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>></CODE></FONT></TD>
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168 <TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</CODE>
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171 </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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176 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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177 <TR ALIGN="right" VALIGN="">
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178 <TD NOWRAP><FONT SIZE="-1">
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179 <CODE><T> <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><T></CODE></FONT></TD>
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182 </CODE></FONT></TD>
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183 <TD><CODE><B>CommandBuilder.</B><B><A HREF="../../../../compbio/engine/client/CommandBuilder.html#newCommandBuilder(java.util.List, java.lang.String)">newCommandBuilder</A></B>(java.util.List<? extends <A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><T>> arguments,
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184 java.lang.String nameValueSeparator)</CODE>
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187 This produces the same result as getCommands method.</TD>
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193 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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194 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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195 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> with parameters of type <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>
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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> void</CODE></FONT></TD>
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200 <TD><CODE><B>RunConfiguration.</B><B><A HREF="../../../../compbio/engine/client/RunConfiguration.html#setParameters(compbio.engine.client.CommandBuilder)">setParameters</A></B>(<A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><?> parameters)</CODE>
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203 </TD>
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208 <A NAME="compbio.runner"><!-- --></A>
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209 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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210 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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211 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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212 Uses of <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A> in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>
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218 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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219 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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220 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> that return <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>
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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> <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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225 <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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228 </TD>
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233 <A NAME="compbio.runner._impl"><!-- --></A>
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234 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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235 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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236 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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237 Uses of <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A> in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>
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243 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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244 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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245 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> that return <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>
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247 <TR BGCOLOR="white" CLASS="TableRowColor">
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248 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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249 <CODE> <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>></CODE></FONT></TD>
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250 <TD><CODE><B>NetNglyc.</B><B><A HREF="../../../../compbio/runner/_impl/NetNglyc.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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253 </TD>
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258 <A NAME="compbio.runner.msa"><!-- --></A>
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259 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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260 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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261 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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262 Uses of <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>
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268 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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269 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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270 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A></FONT></TH>
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272 <TR BGCOLOR="white" CLASS="TableRowColor">
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273 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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274 <CODE> <A HREF="../../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>></CODE></FONT></TD>
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275 <TD><CODE><B>Tcoffee.</B><B><A HREF="../../../../compbio/runner/msa/Tcoffee.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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278 </TD>
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