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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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85 <!-- ========= END OF TOP NAVBAR ========= -->
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88 <!-- ======== START OF CLASS DATA ======== -->
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91 compbio.metadata</FONT>
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93 Class RunnerConfig<T></H2>
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96 <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.RunnerConfig<T></B>
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99 <DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - type of an Executable</DL>
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102 <DT><PRE><FONT SIZE="-1">@NotThreadSafe
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103 </FONT>public class <B>RunnerConfig<T></B><DT>extends java.lang.Object</DL>
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107 The list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>s and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>s supported by executable.
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112 <DT><B>Author:</B></DT>
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115 Date October 2009</DD>
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121 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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123 <A NAME="constructor_summary"><!-- --></A>
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124 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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125 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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126 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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127 <B>Constructor Summary</B></FONT></TH>
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129 <TR BGCOLOR="white" CLASS="TableRowColor">
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130 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#RunnerConfig()">RunnerConfig</A></B>()</CODE>
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133 </TD>
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137 <!-- ========== METHOD SUMMARY =========== -->
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139 <A NAME="method_summary"><!-- --></A>
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140 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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141 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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142 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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143 <B>Method Summary</B></FONT></TH>
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145 <TR BGCOLOR="white" CLASS="TableRowColor">
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146 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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147 <CODE> void</CODE></FONT></TD>
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148 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#addOption(compbio.metadata.Option)">addOption</A></B>(<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> option)</CODE>
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151 </TD>
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153 <TR BGCOLOR="white" CLASS="TableRowColor">
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154 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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155 <CODE> void</CODE></FONT></TD>
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156 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#addParameter(compbio.metadata.Parameter)">addParameter</A></B>(<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> param)</CODE>
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159 </TD>
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161 <TR BGCOLOR="white" CLASS="TableRowColor">
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162 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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163 <CODE> <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>></CODE></FONT></TD>
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164 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#copyAndValidateRConfig(compbio.metadata.RunnerConfig)">copyAndValidateRConfig</A></B>(<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><?> runnerConf)</CODE>
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167 </TD>
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169 <TR BGCOLOR="white" CLASS="TableRowColor">
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170 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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171 <CODE> boolean</CODE></FONT></TD>
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172 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object obj)</CODE>
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175 </TD>
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177 <TR BGCOLOR="white" CLASS="TableRowColor">
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178 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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179 <CODE> <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>></CODE></FONT></TD>
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180 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)">getArgument</A></B>(java.lang.String name)</CODE>
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183 Returns the argument by its name if found, NULL otherwise</TD>
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185 <TR BGCOLOR="white" CLASS="TableRowColor">
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186 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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187 <CODE> <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>></CODE></FONT></TD>
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188 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)">getArgumentByOptionName</A></B>(java.lang.String optionName)</CODE>
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191 Returns the argument by option name, NULL if the argument is not found</TD>
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193 <TR BGCOLOR="white" CLASS="TableRowColor">
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194 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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195 <CODE> java.util.List<<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>></CODE></FONT></TD>
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196 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getArguments()">getArguments</A></B>()</CODE>
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199 </TD>
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201 <TR BGCOLOR="white" CLASS="TableRowColor">
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202 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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203 <CODE> java.util.List<<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>></CODE></FONT></TD>
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204 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getOptions()">getOptions</A></B>()</CODE>
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207 </TD>
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209 <TR BGCOLOR="white" CLASS="TableRowColor">
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210 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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211 <CODE> java.util.List<<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>></CODE></FONT></TD>
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212 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getParameters()">getParameters</A></B>()</CODE>
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215 </TD>
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217 <TR BGCOLOR="white" CLASS="TableRowColor">
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218 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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219 <CODE> java.lang.String</CODE></FONT></TD>
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220 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getPrmSeparator()">getPrmSeparator</A></B>()</CODE>
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223 </TD>
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225 <TR BGCOLOR="white" CLASS="TableRowColor">
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226 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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227 <CODE> java.lang.String</CODE></FONT></TD>
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228 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getRunnerClassName()">getRunnerClassName</A></B>()</CODE>
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231 </TD>
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233 <TR BGCOLOR="white" CLASS="TableRowColor">
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234 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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235 <CODE> boolean</CODE></FONT></TD>
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236 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#removeArgument(java.lang.String)">removeArgument</A></B>(java.lang.String name)</CODE>
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239 Removes the argument <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> if found.</TD>
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241 <TR BGCOLOR="white" CLASS="TableRowColor">
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242 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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243 <CODE> boolean</CODE></FONT></TD>
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244 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#removeArgumentByOptionName(java.lang.String)">removeArgumentByOptionName</A></B>(java.lang.String optionName)</CODE>
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247 Removes the argument</TD>
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249 <TR BGCOLOR="white" CLASS="TableRowColor">
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250 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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251 <CODE> void</CODE></FONT></TD>
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252 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#setOptions(java.util.List)">setOptions</A></B>(java.util.List<<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> parameters)</CODE>
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255 </TD>
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257 <TR BGCOLOR="white" CLASS="TableRowColor">
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258 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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259 <CODE> void</CODE></FONT></TD>
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260 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#setParameters(java.util.List)">setParameters</A></B>(java.util.List<<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> parameters)</CODE>
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263 </TD>
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265 <TR BGCOLOR="white" CLASS="TableRowColor">
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266 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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267 <CODE> void</CODE></FONT></TD>
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268 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#setPrmSeparator(java.lang.String)">setPrmSeparator</A></B>(java.lang.String prmSeparator)</CODE>
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271 </TD>
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273 <TR BGCOLOR="white" CLASS="TableRowColor">
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274 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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275 <CODE> void</CODE></FONT></TD>
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276 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#setRunnerClassName(java.lang.String)">setRunnerClassName</A></B>(java.lang.String runnerClassName)</CODE>
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279 </TD>
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281 <TR BGCOLOR="white" CLASS="TableRowColor">
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282 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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283 <CODE> java.lang.String</CODE></FONT></TD>
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284 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#toString()">toString</A></B>()</CODE>
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287 </TD>
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289 <TR BGCOLOR="white" CLASS="TableRowColor">
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290 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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291 <CODE> void</CODE></FONT></TD>
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292 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#validate()">validate</A></B>()</CODE>
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295 Validate the arguments</TD>
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298 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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299 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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300 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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301 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>
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303 <TR BGCOLOR="white" CLASS="TableRowColor">
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304 <TD><CODE>getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>
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310 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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312 <A NAME="constructor_detail"><!-- --></A>
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313 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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314 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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315 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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316 <B>Constructor Detail</B></FONT></TH>
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320 <A NAME="RunnerConfig()"><!-- --></A><H3>
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323 public <B>RunnerConfig</B>()</PRE>
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327 <!-- ============ METHOD DETAIL ========== -->
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329 <A NAME="method_detail"><!-- --></A>
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330 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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331 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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332 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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333 <B>Method Detail</B></FONT></TH>
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337 <A NAME="copyAndValidateRConfig(compbio.metadata.RunnerConfig)"><!-- --></A><H3>
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338 copyAndValidateRConfig</H3>
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340 public <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> <B>copyAndValidateRConfig</B>(<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><?> runnerConf)</PRE>
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348 <A NAME="getOptions()"><!-- --></A><H3>
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351 public java.util.List<<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> <B>getOptions</B>()</PRE>
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355 <DT><B>Returns:</B><DD>list of <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> supported by type T</DL>
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360 <A NAME="addParameter(compbio.metadata.Parameter)"><!-- --></A><H3>
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363 public void <B>addParameter</B>(<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> param)</PRE>
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371 <A NAME="addOption(compbio.metadata.Option)"><!-- --></A><H3>
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374 public void <B>addOption</B>(<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> option)</PRE>
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382 <A NAME="getArguments()"><!-- --></A><H3>
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385 public java.util.List<<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> <B>getArguments</B>()</PRE>
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389 <DT><B>Returns:</B><DD>list of <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> and <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> supported by type T</DL>
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394 <A NAME="getPrmSeparator()"><!-- --></A><H3>
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395 getPrmSeparator</H3>
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397 public java.lang.String <B>getPrmSeparator</B>()</PRE>
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401 <DT><B>Returns:</B><DD>name value separator character</DL>
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406 <A NAME="setPrmSeparator(java.lang.String)"><!-- --></A><H3>
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407 setPrmSeparator</H3>
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409 public void <B>setPrmSeparator</B>(java.lang.String prmSeparator)</PRE>
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417 <A NAME="setOptions(java.util.List)"><!-- --></A><H3>
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420 public void <B>setOptions</B>(java.util.List<<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> parameters)</PRE>
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428 <A NAME="getRunnerClassName()"><!-- --></A><H3>
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429 getRunnerClassName</H3>
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431 public java.lang.String <B>getRunnerClassName</B>()</PRE>
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435 <DT><B>Returns:</B><DD>fully qualified class name for type T</DL>
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440 <A NAME="setRunnerClassName(java.lang.String)"><!-- --></A><H3>
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441 setRunnerClassName</H3>
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443 public void <B>setRunnerClassName</B>(java.lang.String runnerClassName)</PRE>
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451 <A NAME="setParameters(java.util.List)"><!-- --></A><H3>
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454 public void <B>setParameters</B>(java.util.List<<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> parameters)</PRE>
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462 <A NAME="getParameters()"><!-- --></A><H3>
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465 public java.util.List<<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> <B>getParameters</B>()</PRE>
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469 <DT><B>Returns:</B><DD>List of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> supported by type T.</DL>
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474 <A NAME="toString()"><!-- --></A><H3>
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477 public java.lang.String <B>toString</B>()</PRE>
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480 <DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>
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488 <A NAME="equals(java.lang.Object)"><!-- --></A><H3>
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491 public boolean <B>equals</B>(java.lang.Object obj)</PRE>
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494 <DT><B>Overrides:</B><DD><CODE>equals</CODE> in class <CODE>java.lang.Object</CODE></DL>
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502 <A NAME="getArgument(java.lang.String)"><!-- --></A><H3>
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505 public <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> <B>getArgument</B>(java.lang.String name)</PRE>
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507 <DD>Returns the argument by its name if found, NULL otherwise
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510 <DT><B>Parameters:</B><DD><CODE>name</CODE> -
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511 <DT><B>Returns:</B><DD><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A></DL>
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516 <A NAME="removeArgument(java.lang.String)"><!-- --></A><H3>
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517 removeArgument</H3>
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519 public boolean <B>removeArgument</B>(java.lang.String name)</PRE>
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521 <DD>Removes the argument <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> if found.
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524 <DT><B>Parameters:</B><DD><CODE>name</CODE> - of the argument
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525 <DT><B>Returns:</B><DD>true if argument was removed, false otherwise</DL>
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530 <A NAME="getArgumentByOptionName(java.lang.String)"><!-- --></A><H3>
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531 getArgumentByOptionName</H3>
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533 public <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> <B>getArgumentByOptionName</B>(java.lang.String optionName)</PRE>
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535 <DD>Returns the argument by option name, NULL if the argument is not found
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538 <DT><B>Parameters:</B><DD><CODE>optionName</CODE> - - the name of the option
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539 <DT><B>Returns:</B><DD>Option</DL>
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544 <A NAME="removeArgumentByOptionName(java.lang.String)"><!-- --></A><H3>
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545 removeArgumentByOptionName</H3>
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547 public boolean <B>removeArgumentByOptionName</B>(java.lang.String optionName)</PRE>
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549 <DD>Removes the argument
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552 <DT><B>Parameters:</B><DD><CODE>optionName</CODE> -
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553 <DT><B>Returns:</B><DD>true if argument with optionName exists and was removed, false
559 <A NAME="validate()"><!-- --></A><H3>
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562 public void <B>validate</B>()
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563 throws javax.xml.bind.ValidationException</PRE>
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565 <DD>Validate the arguments
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570 <DD><CODE>javax.xml.bind.ValidationException</CODE> - if any of the arguments found invalid which is when
572 <li>Parameter value outside <A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><CODE>ValueConstrain</CODE></A> boundary</li>
573 <li>Parameter name is not listed in possible values</li>
577 <!-- ========= END OF CLASS DATA ========= -->
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