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91 compbio.runner</FONT>
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96 <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.Util</B>
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100 <DT><PRE>public final class <B>Util</B><DT>extends java.lang.Object</DL>
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107 <!-- =========== FIELD SUMMARY =========== -->
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117 <CODE>static java.lang.String</CODE></FONT></TD>
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118 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#SPACE">SPACE</A></B></CODE>
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130 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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131 <B>Constructor Summary</B></FONT></TH>
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133 <TR BGCOLOR="white" CLASS="TableRowColor">
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134 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#Util()">Util</A></B>()</CODE>
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147 <B>Method Summary</B></FONT></TH>
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149 <TR BGCOLOR="white" CLASS="TableRowColor">
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153 <TR ALIGN="right" VALIGN="">
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154 <TD NOWRAP><FONT SIZE="-1">
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155 <CODE><T> <A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><T></CODE></FONT></TD>
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158 </CODE></FONT></TD>
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159 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#getLimits(java.lang.Class)">getLimits</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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162 For now just assume that all parameters which came in needs setting it
163 will be a client responsibility to prepare RunnerConfig object then</TD>
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165 <TR BGCOLOR="white" CLASS="TableRowColor">
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169 <TR ALIGN="right" VALIGN="">
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170 <TD NOWRAP><FONT SIZE="-1">
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171 <CODE><T> <A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><T></CODE></FONT></TD>
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174 </CODE></FONT></TD>
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175 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#getPresets(java.lang.Class)">getPresets</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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178 </TD>
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186 <CODE><T> <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><T></CODE></FONT></TD>
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189 </CODE></FONT></TD>
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190 <TD><CODE><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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193 </TD>
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195 <TR BGCOLOR="white" CLASS="TableRowColor">
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196 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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197 <CODE>static <A HREF="../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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198 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#readClustalFile(java.lang.String, java.lang.String)">readClustalFile</A></B>(java.lang.String workDirectory,
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199 java.lang.String clustFile)</CODE>
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202 </TD>
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204 <TR BGCOLOR="white" CLASS="TableRowColor">
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205 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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206 <CODE>static void</CODE></FONT></TD>
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207 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#writeInput(java.util.List, compbio.engine.client.ConfiguredExecutable)">writeInput</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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208 <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> exec)</CODE>
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211 </TD>
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214 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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215 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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216 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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217 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>
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219 <TR BGCOLOR="white" CLASS="TableRowColor">
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220 <TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
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226 <!-- ============ FIELD DETAIL =========== -->
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232 <B>Field Detail</B></FONT></TH>
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236 <A NAME="SPACE"><!-- --></A><H3>
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239 public static final java.lang.String <B>SPACE</B></PRE>
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242 <DT><B>See Also:</B><DD><A HREF="../../constant-values.html#compbio.runner.Util.SPACE">Constant Field Values</A></DL>
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245 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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251 <B>Constructor Detail</B></FONT></TH>
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255 <A NAME="Util()"><!-- --></A><H3>
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258 public <B>Util</B>()</PRE>
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262 <!-- ============ METHOD DETAIL ========== -->
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267 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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268 <B>Method Detail</B></FONT></TH>
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272 <A NAME="getLimits(java.lang.Class)"><!-- --></A><H3>
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275 public static <T> <A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><T> <B>getLimits</B>(java.lang.Class<? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T>> clazz)</PRE>
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277 <DD>For now just assume that all parameters which came in needs setting it
278 will be a client responsibility to prepare RunnerConfig object then
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281 <DT><B>Parameters:</B><DD><CODE>rconfig</CODE> -
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282 <DT><B>Returns:</B><DD>public static List<String> toOptionString(RunnerConfig<?>
283 rconfig) { String option = ""; List<String> options = new
284 ArrayList<String>(); for (Parameter<?> par :
285 rconfig.getParameters()) { if (par.getPossibleValues().isEmpty())
286 { option = par.getOptionName(); } else { option =
287 par.getOptionName() + "=" + par.getPossibleValues().get(0); } //
288 separate options options.add(option); } return options; }</DL>
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293 <A NAME="getSupportedOptions(java.lang.Class)"><!-- --></A><H3>
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294 getSupportedOptions</H3>
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296 public static <T> <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><T> <B>getSupportedOptions</B>(java.lang.Class<? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T>> clazz)</PRE>
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304 <A NAME="getPresets(java.lang.Class)"><!-- --></A><H3>
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307 public static <T> <A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><T> <B>getPresets</B>(java.lang.Class<? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T>> clazz)</PRE>
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315 <A NAME="readClustalFile(java.lang.String, java.lang.String)"><!-- --></A><H3>
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316 readClustalFile</H3>
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318 public static final <A HREF="../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>readClustalFile</B>(java.lang.String workDirectory,
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319 java.lang.String clustFile)
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320 throws <A HREF="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>,
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321 java.io.IOException,
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322 java.io.FileNotFoundException,
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323 java.lang.NullPointerException</PRE>
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328 <DD><CODE><A HREF="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE>
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329 <DD><CODE>java.io.IOException</CODE>
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330 <DD><CODE>java.io.FileNotFoundException</CODE>
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331 <DD><CODE>java.lang.NullPointerException</CODE></DL>
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336 <A NAME="writeInput(java.util.List, compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>
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339 public static void <B>writeInput</B>(java.util.List<<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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340 <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> exec)</PRE>
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