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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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81 DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">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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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.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 <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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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.
108 The lists is defined in and loaded from <ExecutableName>Parameters.xml file.
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113 <DT><B>Version:</B></DT>
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114 <DD>1.0 October 2009</DD>
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115 <DT><B>Author:</B></DT>
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122 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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124 <A NAME="constructor_summary"><!-- --></A>
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125 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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126 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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127 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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128 <B>Constructor Summary</B></FONT></TH>
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130 <TR BGCOLOR="white" CLASS="TableRowColor">
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131 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#RunnerConfig()">RunnerConfig</A></B>()</CODE>
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134 </TD>
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138 <!-- ========== METHOD SUMMARY =========== -->
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140 <A NAME="method_summary"><!-- --></A>
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141 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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142 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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143 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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144 <B>Method Summary</B></FONT></TH>
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146 <TR BGCOLOR="white" CLASS="TableRowColor">
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147 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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148 <CODE> void</CODE></FONT></TD>
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149 <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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152 Adds Option to the internal list of options</TD>
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154 <TR BGCOLOR="white" CLASS="TableRowColor">
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155 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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156 <CODE> void</CODE></FONT></TD>
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157 <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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160 Adds parameter to the internal parameter list</TD>
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162 <TR BGCOLOR="white" CLASS="TableRowColor">
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163 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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164 <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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165 <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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168 </TD>
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170 <TR BGCOLOR="white" CLASS="TableRowColor">
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171 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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172 <CODE> boolean</CODE></FONT></TD>
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173 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.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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176 </TD>
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178 <TR BGCOLOR="white" CLASS="TableRowColor">
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179 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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180 <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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181 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)">getArgument</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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184 Returns the argument by its name if found, NULL otherwise.</TD>
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186 <TR BGCOLOR="white" CLASS="TableRowColor">
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187 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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188 <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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189 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)">getArgumentByOptionName</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> optionName)</CODE>
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192 Returns the argument by option name, NULL if the argument is not found</TD>
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194 <TR BGCOLOR="white" CLASS="TableRowColor">
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195 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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196 <CODE> <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="../../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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197 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getArguments()">getArguments</A></B>()</CODE>
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200 Returns list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> supported by current
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/util/List.html?is-external=true" title="class or interface in java.util">List</A><<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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206 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getOptions()">getOptions</A></B>()</CODE>
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209 Returns the list of the Options supported by the executable of type T</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> <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="../../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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214 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getParameters()">getParameters</A></B>()</CODE>
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217 Returns the list of parameters supported executable of type T.</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> <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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222 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getPrmSeparator()">getPrmSeparator</A></B>()</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> <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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230 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getRunnerClassName()">getRunnerClassName</A></B>()</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> boolean</CODE></FONT></TD>
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238 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#removeArgument(java.lang.String)">removeArgument</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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241 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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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> boolean</CODE></FONT></TD>
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246 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#removeArgumentByOptionName(java.lang.String)">removeArgumentByOptionName</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> optionName)</CODE>
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249 Removes the argument which can be a Parameter or an Option instance by
250 the value in <optionNames> element of the runner configuration
253 <TR BGCOLOR="white" CLASS="TableRowColor">
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254 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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255 <CODE> void</CODE></FONT></TD>
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256 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#setOptions(java.util.List)">setOptions</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="../../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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259 Adds the list of options or parameters to the internal list of options</TD>
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261 <TR BGCOLOR="white" CLASS="TableRowColor">
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262 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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263 <CODE> void</CODE></FONT></TD>
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264 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#setParameters(java.util.List)">setParameters</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="../../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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267 Sets the list of parameters as internal list</TD>
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269 <TR BGCOLOR="white" CLASS="TableRowColor">
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270 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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271 <CODE> void</CODE></FONT></TD>
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272 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#setPrmSeparator(java.lang.String)">setPrmSeparator</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> prmSeparator)</CODE>
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275 Sets name value separator character</TD>
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277 <TR BGCOLOR="white" CLASS="TableRowColor">
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278 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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279 <CODE> void</CODE></FONT></TD>
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280 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#setRunnerClassName(java.lang.String)">setRunnerClassName</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> runnerClassName)</CODE>
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283 Set the name of a runner class</TD>
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285 <TR BGCOLOR="white" CLASS="TableRowColor">
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286 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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287 <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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288 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#toString()">toString</A></B>()</CODE>
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291 </TD>
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293 <TR BGCOLOR="white" CLASS="TableRowColor">
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294 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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295 <CODE> void</CODE></FONT></TD>
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296 <TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#validate()">validate</A></B>()</CODE>
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299 Validate the value of the argument.</TD>
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302 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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303 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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304 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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305 <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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307 <TR BGCOLOR="white" CLASS="TableRowColor">
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308 <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#hashCode()" title="class or interface in java.lang">hashCode</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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314 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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316 <A NAME="constructor_detail"><!-- --></A>
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317 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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318 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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319 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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320 <B>Constructor Detail</B></FONT></TH>
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324 <A NAME="RunnerConfig()"><!-- --></A><H3>
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327 public <B>RunnerConfig</B>()</PRE>
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331 <!-- ============ METHOD DETAIL ========== -->
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333 <A NAME="method_detail"><!-- --></A>
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334 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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335 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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336 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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337 <B>Method Detail</B></FONT></TH>
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341 <A NAME="copyAndValidateRConfig(compbio.metadata.RunnerConfig)"><!-- --></A><H3>
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342 copyAndValidateRConfig</H3>
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344 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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352 <A NAME="getOptions()"><!-- --></A><H3>
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355 public <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="../../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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357 <DD>Returns the list of the Options supported by the executable of type T
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361 <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<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A></DL>
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366 <A NAME="addParameter(compbio.metadata.Parameter)"><!-- --></A><H3>
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369 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 <DD>Adds parameter to the internal parameter list
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374 <DT><B>Parameters:</B><DD><CODE>param</CODE> - the <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> to add<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A></DL>
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379 <A NAME="addOption(compbio.metadata.Option)"><!-- --></A><H3>
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382 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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384 <DD>Adds Option to the internal list of options
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387 <DT><B>Parameters:</B><DD><CODE>option</CODE> - the <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> to add</DL>
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392 <A NAME="getArguments()"><!-- --></A><H3>
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395 public <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="../../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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397 <DD>Returns list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> supported by current
402 <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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407 <A NAME="getPrmSeparator()"><!-- --></A><H3>
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408 getPrmSeparator</H3>
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410 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>getPrmSeparator</B>()</PRE>
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414 <DT><B>Returns:</B><DD>name value separator character</DL>
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419 <A NAME="setPrmSeparator(java.lang.String)"><!-- --></A><H3>
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420 setPrmSeparator</H3>
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422 public void <B>setPrmSeparator</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> prmSeparator)</PRE>
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424 <DD>Sets name value separator character
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427 <DT><B>Parameters:</B><DD><CODE>prmSeparator</CODE> - the separator char</DL>
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432 <A NAME="setOptions(java.util.List)"><!-- --></A><H3>
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435 public void <B>setOptions</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="../../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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437 <DD>Adds the list of options or parameters to the internal list of options
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440 <DT><B>Parameters:</B><DD><CODE>parameters</CODE> - the list of parameters to add</DL>
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445 <A NAME="getRunnerClassName()"><!-- --></A><H3>
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446 getRunnerClassName</H3>
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448 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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452 <DT><B>Returns:</B><DD>fully qualified class name for type T</DL>
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457 <A NAME="setRunnerClassName(java.lang.String)"><!-- --></A><H3>
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458 setRunnerClassName</H3>
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460 public void <B>setRunnerClassName</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> runnerClassName)</PRE>
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462 <DD>Set the name of a runner class
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465 <DT><B>Parameters:</B><DD><CODE>runnerClassName</CODE> - the name of the executable wrapping class</DL>
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470 <A NAME="setParameters(java.util.List)"><!-- --></A><H3>
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473 public void <B>setParameters</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="../../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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475 <DD>Sets the list of parameters as internal list
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478 <DT><B>Parameters:</B><DD><CODE>parameters</CODE> - the list of parameters</DL>
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483 <A NAME="getParameters()"><!-- --></A><H3>
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486 public <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="../../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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488 <DD>Returns the list of parameters supported executable of type T. Where
489 <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> is an <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> with value.
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493 <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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498 <A NAME="toString()"><!-- --></A><H3>
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501 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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504 <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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512 <A NAME="equals(java.lang.Object)"><!-- --></A><H3>
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515 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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518 <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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526 <A NAME="getArgument(java.lang.String)"><!-- --></A><H3>
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529 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>(<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)</PRE>
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531 <DD>Returns the argument by its name if found, NULL otherwise. Where the
532 Argument is a common interface for <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>
533 therefore this method can return either. If you need to retrieve the
534 Option by its optionNames use @link
535 <A HREF="../../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)"><CODE>getArgumentByOptionName(String)</CODE></A> method. The
536 difference between option name and optionName is explained by the
540 <name>Sequence type</name>
542 --nuc - Assume the sequences are nucleotide.
543 --amino - Assume the sequences are amino acid. </description>
544 <optionNames>--amino</optionNames>
545 <optionNames>--nuc</optionNames>
546 <optionNames>--auto</optionNames>
549 In the example, the "Sequence type" is a name whereas --amino, --nuc and
550 --auto are all optionNames. This dichotomy only manifests in
551 <code>Option</code> never in <code>Parameters</code> as the latter can
552 only have single <optioNames> element
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555 <DT><B>Parameters:</B><DD><CODE>name</CODE> - the Parameter of Option name
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556 <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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561 <A NAME="removeArgument(java.lang.String)"><!-- --></A><H3>
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562 removeArgument</H3>
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564 public boolean <B>removeArgument</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)</PRE>
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566 <DD>Removes the argument <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> if found. Where Argument is either
567 <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> or <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>.
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570 <DT><B>Parameters:</B><DD><CODE>name</CODE> - of the argument
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571 <DT><B>Returns:</B><DD>true if argument was removed, false otherwise</DL>
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576 <A NAME="getArgumentByOptionName(java.lang.String)"><!-- --></A><H3>
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577 getArgumentByOptionName</H3>
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579 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>(<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> optionName)</PRE>
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581 <DD>Returns the argument by option name, NULL if the argument is not found
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584 <DT><B>Parameters:</B><DD><CODE>optionName</CODE> - - the optionName. This is not the same as an Option name.
589 <name>Output sequences order</name>
590 <description>--inputorder - Output order: same as input.
591 --reorder - Output order: aligned. Default: same as input</description>
592 <optionNames>--inputorder</optionNames>
593 <optionNames>--reorder</optionNames>
596 The name of the option in the example is
597 "Output sequences order" whereas optionNames are
598 "--inputorder" and "--reorder". If you need to retrieve the
599 Option or Parameter by its names use
600 <A HREF="../../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)"><CODE>getArgument(String)</CODE></A> method
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601 <DT><B>Returns:</B><DD>Option</DL>
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606 <A NAME="removeArgumentByOptionName(java.lang.String)"><!-- --></A><H3>
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607 removeArgumentByOptionName</H3>
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609 public boolean <B>removeArgumentByOptionName</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> optionName)</PRE>
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611 <DD>Removes the argument which can be a Parameter or an Option instance by
612 the value in <optionNames> element of the runner configuration
616 <DT><B>Parameters:</B><DD><CODE>optionName</CODE> - the optionName of the option, do not confuse with the name!
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617 <DT><B>Returns:</B><DD>true if argument with optionName exists and was removed, false
618 otherwise<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)"><CODE>for destinctions
619 between optionNames and the name of the Option</CODE></A></DL>
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624 <A NAME="validate()"><!-- --></A><H3>
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627 public void <B>validate</B>()
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628 throws <A HREF="http://java.sun.com/javase/6/docs/api/javax/xml/bind/ValidationException.html?is-external=true" title="class or interface in javax.xml.bind">ValidationException</A></PRE>
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630 <DD>Validate the value of the argument. Checks whether the argument value is
631 in the valid values range.
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636 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/javax/xml/bind/ValidationException.html?is-external=true" title="class or interface in javax.xml.bind">ValidationException</A></CODE> - if any of the arguments found invalid which is when
638 <li>Parameter value outside <A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><CODE>ValueConstrain</CODE></A> boundary</li>
639 <li>Parameter name is not listed in possible values</li>
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