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7 Uses of Class compbio.metadata.RunnerConfig
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84 <B>Uses of Class<br>compbio.metadata.RunnerConfig</B></H2>
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87 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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88 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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89 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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90 Packages that use <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>
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92 <TR BGCOLOR="white" CLASS="TableRowColor">
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93 <TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>
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94 <TD> </TD>
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96 <TR BGCOLOR="white" CLASS="TableRowColor">
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97 <TD><A HREF="#compbio.data.msa.jaxws"><B>compbio.data.msa.jaxws</B></A></TD>
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98 <TD> </TD>
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100 <TR BGCOLOR="white" CLASS="TableRowColor">
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101 <TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>
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102 <TD>Classes and interfaces representing an input for engines. </TD>
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104 <TR BGCOLOR="white" CLASS="TableRowColor">
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105 <TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>
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106 <TD>A meta-data model for multiple sequence alignment web services
107 Classes in this package have no dependencies to other sources in the project. </TD>
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109 <TR BGCOLOR="white" CLASS="TableRowColor">
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110 <TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>
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111 <TD>Utilities commonly used by all runners. </TD>
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113 <TR BGCOLOR="white" CLASS="TableRowColor">
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114 <TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>
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115 <TD> </TD>
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120 <A NAME="compbio.data.msa"><!-- --></A>
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121 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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122 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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123 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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124 Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>
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130 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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131 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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132 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>
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134 <TR BGCOLOR="white" CLASS="TableRowColor">
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135 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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136 <CODE> <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>></CODE></FONT></TD>
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137 <TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>
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140 Get options supported by a web service</TD>
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145 <A NAME="compbio.data.msa.jaxws"><!-- --></A>
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146 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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147 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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148 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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149 Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A> in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A></FONT></TH>
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155 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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156 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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157 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> that return <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>
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159 <TR BGCOLOR="white" CLASS="TableRowColor">
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160 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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161 <CODE> <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></CODE></FONT></TD>
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162 <TD><CODE><B>GetRunnerOptionsResponse.</B><B><A HREF="../../../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#getReturn()">getReturn</A></B>()</CODE>
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165 </TD>
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171 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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172 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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173 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> with parameters of type <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>
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175 <TR BGCOLOR="white" CLASS="TableRowColor">
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176 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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177 <CODE> void</CODE></FONT></TD>
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178 <TD><CODE><B>GetRunnerOptionsResponse.</B><B><A HREF="../../../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#setReturn(compbio.metadata.RunnerConfig)">setReturn</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A> _return)</CODE>
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181 </TD>
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186 <A NAME="compbio.engine.client"><!-- --></A>
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187 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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188 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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189 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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190 Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A> in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>
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196 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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197 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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198 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that return <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>
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200 <TR BGCOLOR="white" CLASS="TableRowColor">
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201 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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203 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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204 <TR ALIGN="right" VALIGN="">
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205 <TD NOWRAP><FONT SIZE="-1">
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206 <CODE><V> <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><V></CODE></FONT></TD>
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209 </CODE></FONT></TD>
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210 <TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunnerOptions(java.lang.Class)">getRunnerOptions</A></B>(java.lang.Class<? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><V>> clazz)</CODE>
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213 </TD>
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218 <A NAME="compbio.metadata"><!-- --></A>
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219 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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220 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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221 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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222 Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>
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228 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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229 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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230 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>
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232 <TR BGCOLOR="white" CLASS="TableRowColor">
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233 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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234 <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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235 <TD><CODE><B>RunnerConfig.</B><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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238 </TD>
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244 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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245 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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246 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>
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248 <TR BGCOLOR="white" CLASS="TableRowColor">
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249 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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250 <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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251 <TD><CODE><B>RunnerConfig.</B><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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254 </TD>
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256 <TR BGCOLOR="white" CLASS="TableRowColor">
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257 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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258 <CODE> java.util.List<<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>>></CODE></FONT></TD>
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259 <TD><CODE><B>Preset.</B><B><A HREF="../../../compbio/metadata/Preset.html#getArguments(compbio.metadata.RunnerConfig)">getArguments</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>> rconfig)</CODE>
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262 Converts list of options as String to type Option</TD>
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264 <TR BGCOLOR="white" CLASS="TableRowColor">
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265 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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266 <CODE> void</CODE></FONT></TD>
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267 <TD><CODE><B>PresetManager.</B><B><A HREF="../../../compbio/metadata/PresetManager.html#validate(compbio.metadata.RunnerConfig)">validate</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>> options)</CODE>
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270 Checks whether preset option and parameter are defined in RunnerConfig
276 <A NAME="compbio.runner"><!-- --></A>
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277 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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278 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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279 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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280 Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A> in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>
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286 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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287 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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288 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> that return <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>
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290 <TR BGCOLOR="white" CLASS="TableRowColor">
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291 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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293 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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294 <TR ALIGN="right" VALIGN="">
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295 <TD NOWRAP><FONT SIZE="-1">
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296 <CODE><T> <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><T></CODE></FONT></TD>
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299 </CODE></FONT></TD>
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300 <TD><CODE><B>Util.</B><B><A HREF="../../../compbio/runner/Util.html#getSupportedOptions(java.lang.Class)">getSupportedOptions</A></B>(java.lang.Class<? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T>> clazz)</CODE>
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303 </TD>
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309 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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310 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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311 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> with parameters of type <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>
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313 <TR BGCOLOR="white" CLASS="TableRowColor">
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314 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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315 <CODE>static java.util.List<java.lang.String></CODE></FONT></TD>
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316 <TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List, compbio.metadata.RunnerConfig)">argumentsToCommandString</A></B>(java.util.List<? extends <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?>> arguments,
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317 <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?>> rconfig)</CODE>
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320 </TD>
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326 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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327 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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328 <TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> with parameters of type <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>
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330 <TR BGCOLOR="white" CLASS="TableRowColor">
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331 <TD><CODE><B><A HREF="../../../compbio/runner/OptionCombinator.html#OptionCombinator(compbio.metadata.RunnerConfig)">OptionCombinator</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?>> rconfig)</CODE>
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334 </TD>
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339 <A NAME="compbio.ws.server"><!-- --></A>
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340 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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341 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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342 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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343 Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A> in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>
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349 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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350 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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351 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that return <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>
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353 <TR BGCOLOR="white" CLASS="TableRowColor">
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354 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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355 <CODE> <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>></CODE></FONT></TD>
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356 <TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>
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359 </TD>
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361 <TR BGCOLOR="white" CLASS="TableRowColor">
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362 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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363 <CODE> <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>></CODE></FONT></TD>
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364 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>
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367 </TD>
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369 <TR BGCOLOR="white" CLASS="TableRowColor">
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370 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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371 <CODE> <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>></CODE></FONT></TD>
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372 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>
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375 </TD>
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377 <TR BGCOLOR="white" CLASS="TableRowColor">
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378 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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379 <CODE> <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>></CODE></FONT></TD>
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380 <TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>
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383 </TD>
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385 <TR BGCOLOR="white" CLASS="TableRowColor">
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386 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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387 <CODE> <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></FONT></TD>
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388 <TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>
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391 </TD>
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399 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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400 <A NAME="navbar_bottom"><!-- --></A>
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401 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
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408 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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