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7 Uses of Class compbio.metadata.Option
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42 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
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84 <B>Uses of Class<br>compbio.metadata.Option</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/Option.html" title="class in compbio.metadata">Option</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/Option.html" title="class in compbio.metadata">Option</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">Method parameters in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> with type arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</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> java.lang.String</CODE></FONT></TD>
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137 <TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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138 java.util.List<<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>>> options)</CODE>
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141 Align a list of sequences with options.</TD>
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146 <A NAME="compbio.data.msa.jaxws"><!-- --></A>
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147 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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148 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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149 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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150 Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A></FONT></TH>
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156 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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157 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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158 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> that return types with arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>
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160 <TR BGCOLOR="white" CLASS="TableRowColor">
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161 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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162 <CODE> java.util.List<<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>></CODE></FONT></TD>
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163 <TD><CODE><B>CustomAlign.</B><B><A HREF="../../../compbio/data/msa/jaxws/CustomAlign.html#getOptions()">getOptions</A></B>()</CODE>
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166 </TD>
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172 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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173 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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174 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> with type arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>
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176 <TR BGCOLOR="white" CLASS="TableRowColor">
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177 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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178 <CODE> void</CODE></FONT></TD>
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179 <TD><CODE><B>CustomAlign.</B><B><A HREF="../../../compbio/data/msa/jaxws/CustomAlign.html#setOptions(java.util.List)">setOptions</A></B>(java.util.List<<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>> options)</CODE>
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182 </TD>
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187 <A NAME="compbio.engine.client"><!-- --></A>
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188 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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189 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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190 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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191 Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>
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197 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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198 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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199 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> with type arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>
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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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204 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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205 <TR ALIGN="right" VALIGN="">
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206 <TD NOWRAP><FONT SIZE="-1">
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207 <CODE><T> <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><T></CODE></FONT></TD>
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210 </CODE></FONT></TD>
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211 <TD><CODE><B>CommandBuilder.</B><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#newCommandBuilder(java.util.List, java.lang.String)">newCommandBuilder</A></B>(java.util.List<? extends <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><T>> arguments,
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212 java.lang.String nameValueSeparator)</CODE>
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215 This produces the same result as getCommands method.</TD>
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220 <A NAME="compbio.metadata"><!-- --></A>
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221 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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222 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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223 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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224 Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>
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230 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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231 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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232 <TH ALIGN="left" COLSPAN="2">Subclasses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>
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234 <TR BGCOLOR="white" CLASS="TableRowColor">
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235 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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236 <CODE> class</CODE></FONT></TD>
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237 <TD><CODE><B><A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter<T></A></B></CODE>
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240 A single value containing option supported by the web service e.g.</TD>
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246 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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247 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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248 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>
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250 <TR BGCOLOR="white" CLASS="TableRowColor">
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251 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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252 <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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253 <TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)">getArgument</A></B>(java.lang.String name)</CODE>
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256 Returns the argument by its name if found, NULL otherwise</TD>
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258 <TR BGCOLOR="white" CLASS="TableRowColor">
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259 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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260 <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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261 <TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)">getArgumentByOptionName</A></B>(java.lang.String optionName)</CODE>
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264 Returns the argument by option name, NULL if the argument is not found</TD>
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270 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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271 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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272 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return types with arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>
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274 <TR BGCOLOR="white" CLASS="TableRowColor">
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275 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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276 <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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277 <TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getArguments()">getArguments</A></B>()</CODE>
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280 </TD>
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282 <TR BGCOLOR="white" CLASS="TableRowColor">
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283 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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284 <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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285 <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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288 Converts list of options as String to type Option</TD>
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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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292 <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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293 <TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getOptions()">getOptions</A></B>()</CODE>
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296 </TD>
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302 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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303 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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304 <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/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>
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306 <TR BGCOLOR="white" CLASS="TableRowColor">
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307 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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308 <CODE> void</CODE></FONT></TD>
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309 <TD><CODE><B>RunnerConfig.</B><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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312 </TD>
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318 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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319 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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320 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with type arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>
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322 <TR BGCOLOR="white" CLASS="TableRowColor">
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323 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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324 <CODE> void</CODE></FONT></TD>
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325 <TD><CODE><B>RunnerConfig.</B><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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328 </TD>
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334 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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335 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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336 <TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>
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338 <TR BGCOLOR="white" CLASS="TableRowColor">
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339 <TD><CODE><B><A HREF="../../../compbio/metadata/WrongParameterException.html#WrongParameterException(compbio.metadata.Option)">WrongParameterException</A></B>(<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?> option)</CODE>
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342 </TD>
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347 <A NAME="compbio.runner"><!-- --></A>
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348 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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349 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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350 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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351 Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>
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357 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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358 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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359 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> that return types with arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>
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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> java.util.List<<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?>></CODE></FONT></TD>
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364 <TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#getAllOptions()">getAllOptions</A></B>()</CODE>
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367 </TD>
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373 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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374 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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375 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> with type arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>
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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> java.util.List<java.lang.String></CODE></FONT></TD>
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380 <TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List)">argumentsToCommandString</A></B>(java.util.List<? extends <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?>> arguments)</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>static java.util.List<java.lang.String></CODE></FONT></TD>
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388 <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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389 <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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392 </TD>
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394 <TR BGCOLOR="white" CLASS="TableRowColor">
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395 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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396 <CODE> java.util.List<java.lang.String></CODE></FONT></TD>
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397 <TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#optionsToCommandString(java.util.List)">optionsToCommandString</A></B>(java.util.List<<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?>> options)</CODE>
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400 </TD>
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405 <A NAME="compbio.ws.server"><!-- --></A>
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406 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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407 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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408 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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409 Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>
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415 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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416 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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417 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> with type arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>
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419 <TR BGCOLOR="white" CLASS="TableRowColor">
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420 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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421 <CODE> java.lang.String</CODE></FONT></TD>
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422 <TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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423 java.util.List<<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>>> options)</CODE>
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426 </TD>
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428 <TR BGCOLOR="white" CLASS="TableRowColor">
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429 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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430 <CODE> java.lang.String</CODE></FONT></TD>
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431 <TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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432 java.util.List<<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>>> options)</CODE>
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435 </TD>
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437 <TR BGCOLOR="white" CLASS="TableRowColor">
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438 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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439 <CODE> java.lang.String</CODE></FONT></TD>
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440 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
441 java.util.List<<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>>> options)</CODE>
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444 </TD>
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446 <TR BGCOLOR="white" CLASS="TableRowColor">
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447 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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448 <CODE> java.lang.String</CODE></FONT></TD>
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449 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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450 java.util.List<<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>>> options)</CODE>
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453 </TD>
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455 <TR BGCOLOR="white" CLASS="TableRowColor">
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456 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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457 <CODE> java.lang.String</CODE></FONT></TD>
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458 <TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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459 java.util.List<<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>>> options)</CODE>
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462 </TD>
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464 <TR BGCOLOR="white" CLASS="TableRowColor">
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465 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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467 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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468 <TR ALIGN="right" VALIGN="">
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469 <TD NOWRAP><FONT SIZE="-1">
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470 <CODE><T> java.util.List<java.lang.String></CODE></FONT></TD>
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473 </CODE></FONT></TD>
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474 <TD><CODE><B>WSUtil.</B><B><A HREF="../../../compbio/ws/server/WSUtil.html#getCommands(java.util.List, java.lang.String)">getCommands</A></B>(java.util.List<<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><T>> options,
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475 java.lang.String keyValueSeparator)</CODE>
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478 </TD>
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486 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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487 <A NAME="navbar_bottom"><!-- --></A>
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488 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
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495 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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496 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
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497 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
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498 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>
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499 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
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