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18 parent.document.title="RunConfiguration";
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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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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 RunConfiguration</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.RunConfiguration</B>
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100 <DT><PRE>public class <B>RunConfiguration</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></DL>
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104 Value class for persisting ConfExecutable instances
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109 <DT><B>Author:</B></DT>
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115 <!-- =========== FIELD SUMMARY =========== -->
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117 <A NAME="field_summary"><!-- --></A>
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118 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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119 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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120 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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121 <B>Field Summary</B></FONT></TH>
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123 <TR BGCOLOR="white" CLASS="TableRowColor">
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124 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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125 <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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126 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#rconfigFile">rconfigFile</A></B></CODE>
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129 </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/engine/client/RunConfiguration.html#RunConfiguration()">RunConfiguration</A></B>()</CODE>
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145 </TD>
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147 <TR BGCOLOR="white" CLASS="TableRowColor">
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148 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#RunConfiguration(compbio.engine.client.ConfExecutable)">RunConfiguration</A></B>(<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A><?> cexec)</CODE>
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151 </TD>
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155 <!-- ========== METHOD SUMMARY =========== -->
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158 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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159 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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160 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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161 <B>Method Summary</B></FONT></TH>
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163 <TR BGCOLOR="white" CLASS="TableRowColor">
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164 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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165 <CODE> boolean</CODE></FONT></TD>
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166 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.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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169 </TD>
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171 <TR BGCOLOR="white" CLASS="TableRowColor">
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172 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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173 <CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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174 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#getError()">getError</A></B>()</CODE>
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177 </TD>
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179 <TR BGCOLOR="white" CLASS="TableRowColor">
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180 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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181 <CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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182 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#getInput()">getInput</A></B>()</CODE>
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185 </TD>
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187 <TR BGCOLOR="white" CLASS="TableRowColor">
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188 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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189 <CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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190 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#getOutput()">getOutput</A></B>()</CODE>
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193 </TD>
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195 <TR BGCOLOR="white" CLASS="TableRowColor">
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196 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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197 <CODE> <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><?></CODE></FONT></TD>
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198 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#getParameters()">getParameters</A></B>()</CODE>
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201 </TD>
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203 <TR BGCOLOR="white" CLASS="TableRowColor">
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204 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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205 <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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206 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#getRunnerClassName()">getRunnerClassName</A></B>()</CODE>
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209 </TD>
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211 <TR BGCOLOR="white" CLASS="TableRowColor">
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212 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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213 <CODE> int</CODE></FONT></TD>
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214 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#hashCode()">hashCode</A></B>()</CODE>
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217 </TD>
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219 <TR BGCOLOR="white" CLASS="TableRowColor">
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220 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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221 <CODE>static <A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A></CODE></FONT></TD>
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222 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#load(java.io.InputStream)">load</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> input)</CODE>
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225 </TD>
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227 <TR BGCOLOR="white" CLASS="TableRowColor">
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228 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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229 <CODE> void</CODE></FONT></TD>
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230 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.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> error)</CODE>
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233 </TD>
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235 <TR BGCOLOR="white" CLASS="TableRowColor">
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236 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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237 <CODE> void</CODE></FONT></TD>
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238 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.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> input)</CODE>
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241 </TD>
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243 <TR BGCOLOR="white" CLASS="TableRowColor">
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244 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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245 <CODE> void</CODE></FONT></TD>
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246 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.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> output)</CODE>
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249 </TD>
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251 <TR BGCOLOR="white" CLASS="TableRowColor">
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252 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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253 <CODE> void</CODE></FONT></TD>
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254 <TD><CODE><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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257 </TD>
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259 <TR BGCOLOR="white" CLASS="TableRowColor">
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260 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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261 <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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262 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#toString()">toString</A></B>()</CODE>
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265 </TD>
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267 <TR BGCOLOR="white" CLASS="TableRowColor">
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268 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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269 <CODE>static boolean</CODE></FONT></TD>
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270 <TD><CODE><B><A HREF="../../../compbio/engine/client/RunConfiguration.html#write(compbio.engine.client.RunConfiguration)">write</A></B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> rconf)</CODE>
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273 </TD>
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276 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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277 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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278 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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279 <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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281 <TR BGCOLOR="white" CLASS="TableRowColor">
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282 <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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288 <!-- ============ FIELD DETAIL =========== -->
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290 <A NAME="field_detail"><!-- --></A>
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291 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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292 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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293 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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294 <B>Field Detail</B></FONT></TH>
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298 <A NAME="rconfigFile"><!-- --></A><H3>
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301 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>rconfigFile</B></PRE>
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304 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.engine.client.RunConfiguration.rconfigFile">Constant Field Values</A></DL>
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307 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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309 <A NAME="constructor_detail"><!-- --></A>
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310 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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311 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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312 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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313 <B>Constructor Detail</B></FONT></TH>
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317 <A NAME="RunConfiguration()"><!-- --></A><H3>
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318 RunConfiguration</H3>
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320 public <B>RunConfiguration</B>()</PRE>
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325 <A NAME="RunConfiguration(compbio.engine.client.ConfExecutable)"><!-- --></A><H3>
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326 RunConfiguration</H3>
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328 public <B>RunConfiguration</B>(<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A><?> cexec)</PRE>
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332 <!-- ============ METHOD DETAIL ========== -->
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334 <A NAME="method_detail"><!-- --></A>
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335 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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336 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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337 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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338 <B>Method Detail</B></FONT></TH>
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342 <A NAME="write(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>
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345 public static boolean <B>write</B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> rconf)
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346 throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>
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351 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>
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356 <A NAME="load(java.io.InputStream)"><!-- --></A><H3>
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359 public static <A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> <B>load</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> input)
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360 throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>
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365 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>
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370 <A NAME="setOutput(java.lang.String)"><!-- --></A><H3>
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373 public void <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> output)</PRE>
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381 <A NAME="getParameters()"><!-- --></A><H3>
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384 public <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><?> <B>getParameters</B>()</PRE>
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392 <A NAME="setParameters(compbio.engine.client.CommandBuilder)"><!-- --></A><H3>
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395 public void <B>setParameters</B>(<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><?> parameters)</PRE>
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403 <A NAME="getOutput()"><!-- --></A><H3>
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406 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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414 <A NAME="setError(java.lang.String)"><!-- --></A><H3>
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417 public void <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> error)</PRE>
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425 <A NAME="getError()"><!-- --></A><H3>
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428 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>
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436 <A NAME="getInput()"><!-- --></A><H3>
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439 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getInput</B>()</PRE>
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447 <A NAME="setInput(java.lang.String)"><!-- --></A><H3>
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450 public void <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> input)</PRE>
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458 <A NAME="getRunnerClassName()"><!-- --></A><H3>
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459 getRunnerClassName</H3>
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461 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>getRunnerClassName</B>()</PRE>
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469 <A NAME="equals(java.lang.Object)"><!-- --></A><H3>
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472 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>
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475 <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>
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483 <A NAME="hashCode()"><!-- --></A><H3>
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486 public int <B>hashCode</B>()</PRE>
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489 <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>
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497 <A NAME="toString()"><!-- --></A><H3>
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500 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>
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503 <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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509 <!-- ========= END OF CLASS DATA ========= -->
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514 <A NAME="navbar_bottom"><!-- --></A>
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