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91 compbio.runner</FONT>
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93 Class OptionCombinator</H2>
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96 <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.OptionCombinator</B>
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100 <DT><PRE><FONT SIZE="-1">@Immutable
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101 </FONT>public final class <B>OptionCombinator</B><DT>extends java.lang.Object</DL>
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105 This class solve the following problems. Given the RunnerConfig
107 1) generate a valid option string with all options and parameters in it
109 2) Permute all possible combinations of options order and parameters values
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114 <DT><B>Author:</B></DT>
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121 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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126 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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127 <B>Constructor Summary</B></FONT></TH>
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129 <TR BGCOLOR="white" CLASS="TableRowColor">
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130 <TD><CODE><B><A HREF="../../compbio/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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133 </TD>
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142 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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143 <B>Method Summary</B></FONT></TH>
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145 <TR BGCOLOR="white" CLASS="TableRowColor">
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146 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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147 <CODE> java.util.List<java.lang.String></CODE></FONT></TD>
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148 <TD><CODE><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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151 </TD>
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153 <TR BGCOLOR="white" CLASS="TableRowColor">
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154 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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155 <CODE>static java.util.List<java.lang.String></CODE></FONT></TD>
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156 <TD><CODE><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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157 <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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160 </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> java.util.Map<<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><?>,java.lang.String></CODE></FONT></TD>
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165 <TD><CODE><B><A HREF="../../compbio/runner/OptionCombinator.html#getAllConstrainedParametersWithBorderValues(boolean)">getAllConstrainedParametersWithBorderValues</A></B>(boolean minValue)</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> java.util.Map<<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><?>,java.lang.String></CODE></FONT></TD>
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173 <TD><CODE><B><A HREF="../../compbio/runner/OptionCombinator.html#getAllConstrainedParametersWithRandomValues()">getAllConstrainedParametersWithRandomValues</A></B>()</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> java.util.List<<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?>></CODE></FONT></TD>
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181 <TD><CODE><B><A HREF="../../compbio/runner/OptionCombinator.html#getAllOptions()">getAllOptions</A></B>()</CODE>
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184 </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> java.util.List<<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><?>></CODE></FONT></TD>
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189 <TD><CODE><B><A HREF="../../compbio/runner/OptionCombinator.html#getAllParameters()">getAllParameters</A></B>()</CODE>
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192 </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> java.util.List<java.lang.String></CODE></FONT></TD>
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197 <TD><CODE><B><A HREF="../../compbio/runner/OptionCombinator.html#getOptionsAtRandom()">getOptionsAtRandom</A></B>()</CODE>
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200 </TD>
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202 <TR BGCOLOR="white" CLASS="TableRowColor">
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203 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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204 <CODE> java.util.List<java.lang.String></CODE></FONT></TD>
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205 <TD><CODE><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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208 </TD>
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210 <TR BGCOLOR="white" CLASS="TableRowColor">
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211 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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212 <CODE> java.util.List<java.lang.String></CODE></FONT></TD>
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213 <TD><CODE><B><A HREF="../../compbio/runner/OptionCombinator.html#parametersToCommandString(java.util.List, java.util.Map)">parametersToCommandString</A></B>(java.util.List<<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><?>> orderedList,
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214 java.util.Map<<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><?>,java.lang.String> prmValue)</CODE>
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217 </TD>
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223 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>
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226 <TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
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238 <B>Constructor Detail</B></FONT></TH>
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242 <A NAME="OptionCombinator(compbio.metadata.RunnerConfig)"><!-- --></A><H3>
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243 OptionCombinator</H3>
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245 public <B>OptionCombinator</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)</PRE>
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254 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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255 <B>Method Detail</B></FONT></TH>
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259 <A NAME="optionsToCommandString(java.util.List)"><!-- --></A><H3>
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260 optionsToCommandString</H3>
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262 public java.util.List<java.lang.String> <B>optionsToCommandString</B>(java.util.List<<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?>> options)</PRE>
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270 <A NAME="getOptionsAtRandom()"><!-- --></A><H3>
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271 getOptionsAtRandom</H3>
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273 public java.util.List<java.lang.String> <B>getOptionsAtRandom</B>()</PRE>
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281 <A NAME="getAllOptions()"><!-- --></A><H3>
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284 public java.util.List<<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?>> <B>getAllOptions</B>()</PRE>
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292 <A NAME="getAllParameters()"><!-- --></A><H3>
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293 getAllParameters</H3>
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295 public java.util.List<<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><?>> <B>getAllParameters</B>()</PRE>
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303 <A NAME="argumentsToCommandString(java.util.List)"><!-- --></A><H3>
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304 argumentsToCommandString</H3>
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306 public java.util.List<java.lang.String> <B>argumentsToCommandString</B>(java.util.List<? extends <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?>> arguments)</PRE>
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314 <A NAME="argumentsToCommandString(java.util.List, compbio.metadata.RunnerConfig)"><!-- --></A><H3>
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315 argumentsToCommandString</H3>
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317 public static java.util.List<java.lang.String> <B>argumentsToCommandString</B>(java.util.List<? extends <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?>> arguments,
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318 <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)</PRE>
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326 <A NAME="parametersToCommandString(java.util.List, java.util.Map)"><!-- --></A><H3>
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327 parametersToCommandString</H3>
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329 public java.util.List<java.lang.String> <B>parametersToCommandString</B>(java.util.List<<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><?>> orderedList,
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330 java.util.Map<<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><?>,java.lang.String> prmValue)</PRE>
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338 <A NAME="getAllConstrainedParametersWithBorderValues(boolean)"><!-- --></A><H3>
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339 getAllConstrainedParametersWithBorderValues</H3>
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341 public java.util.Map<<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><?>,java.lang.String> <B>getAllConstrainedParametersWithBorderValues</B>(boolean minValue)</PRE>
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349 <A NAME="getAllConstrainedParametersWithRandomValues()"><!-- --></A><H3>
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350 getAllConstrainedParametersWithRandomValues</H3>
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352 public java.util.Map<<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><?>,java.lang.String> <B>getAllConstrainedParametersWithRandomValues</B>()</PRE>
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