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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 <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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113 <B>Field Summary</B></FONT></TH>
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115 <TR BGCOLOR="white" CLASS="TableRowColor">
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116 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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117 <CODE>static org.apache.log4j.Logger</CODE></FONT></TD>
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118 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#log">log</A></B></CODE>
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121 </TD>
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123 <TR BGCOLOR="white" CLASS="TableRowColor">
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124 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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125 <CODE>static <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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126 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#SPACE">SPACE</A></B></CODE>
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138 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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139 <B>Constructor Summary</B></FONT></TH>
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141 <TR BGCOLOR="white" CLASS="TableRowColor">
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142 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#Util()">Util</A></B>()</CODE>
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155 <B>Method Summary</B></FONT></TH>
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161 <TR ALIGN="right" VALIGN="">
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162 <TD NOWRAP><FONT SIZE="-1">
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163 <CODE><T> <A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><T></CODE></FONT></TD>
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166 </CODE></FONT></TD>
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167 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#getPresets(java.lang.Class)">getPresets</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A><? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T>> clazz)</CODE>
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170 </TD>
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172 <TR BGCOLOR="white" CLASS="TableRowColor">
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176 <TR ALIGN="right" VALIGN="">
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177 <TD NOWRAP><FONT SIZE="-1">
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178 <CODE><T> <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><T></CODE></FONT></TD>
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181 </CODE></FONT></TD>
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182 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#getSupportedOptions(java.lang.Class)">getSupportedOptions</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A><? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T>> clazz)</CODE>
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185 </TD>
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187 <TR BGCOLOR="white" CLASS="TableRowColor">
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188 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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189 <CODE>static <A HREF="../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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190 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#readClustalFile(java.lang.String, java.lang.String)">readClustalFile</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> workDirectory,
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191 <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> clustFile)</CODE>
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194 </TD>
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196 <TR BGCOLOR="white" CLASS="TableRowColor">
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197 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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198 <CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A><<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>,<A HREF="../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></CODE></FONT></TD>
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199 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#readJronnFile(java.lang.String, java.lang.String)">readJronnFile</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> workDirectory,
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200 <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> clustFile)</CODE>
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203 </TD>
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205 <TR BGCOLOR="white" CLASS="TableRowColor">
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206 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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207 <CODE>static void</CODE></FONT></TD>
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208 <TD><CODE><B><A HREF="../../compbio/runner/Util.html#writeInput(java.util.List, compbio.engine.client.ConfiguredExecutable)">writeInput</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/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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209 <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> exec)</CODE>
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212 </TD>
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215 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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216 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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217 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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218 <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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220 <TR BGCOLOR="white" CLASS="TableRowColor">
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221 <TD><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>, <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#toString()" title="class or interface in java.lang">toString</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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227 <!-- ============ FIELD DETAIL =========== -->
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230 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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231 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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232 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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233 <B>Field Detail</B></FONT></TH>
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237 <A NAME="log"><!-- --></A><H3>
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240 public static org.apache.log4j.Logger <B>log</B></PRE>
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247 <A NAME="SPACE"><!-- --></A><H3>
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250 public static final <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>SPACE</B></PRE>
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253 <DT><B>See Also:</B><DD><A HREF="../../constant-values.html#compbio.runner.Util.SPACE">Constant Field Values</A></DL>
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256 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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258 <A NAME="constructor_detail"><!-- --></A>
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259 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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260 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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261 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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262 <B>Constructor Detail</B></FONT></TH>
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266 <A NAME="Util()"><!-- --></A><H3>
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269 public <B>Util</B>()</PRE>
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273 <!-- ============ METHOD DETAIL ========== -->
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275 <A NAME="method_detail"><!-- --></A>
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276 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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278 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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279 <B>Method Detail</B></FONT></TH>
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283 <A NAME="getSupportedOptions(java.lang.Class)"><!-- --></A><H3>
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284 getSupportedOptions</H3>
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286 public static <T> <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><T> <B>getSupportedOptions</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A><? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T>> clazz)</PRE>
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294 <A NAME="getPresets(java.lang.Class)"><!-- --></A><H3>
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297 public static <T> <A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><T> <B>getPresets</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A><? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T>> clazz)</PRE>
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305 <A NAME="readClustalFile(java.lang.String, java.lang.String)"><!-- --></A><H3>
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306 readClustalFile</H3>
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308 public static final <A HREF="../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>readClustalFile</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> workDirectory,
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309 <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> clustFile)
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310 throws <A HREF="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>,
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311 <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A>,
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312 <A HREF="http://java.sun.com/javase/6/docs/api/java/io/FileNotFoundException.html?is-external=true" title="class or interface in java.io">FileNotFoundException</A>,
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313 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></PRE>
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318 <DD><CODE><A HREF="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE>
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319 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE>
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320 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/FileNotFoundException.html?is-external=true" title="class or interface in java.io">FileNotFoundException</A></CODE>
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321 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></CODE></DL>
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326 <A NAME="readJronnFile(java.lang.String, java.lang.String)"><!-- --></A><H3>
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329 public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A><<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>,<A HREF="../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>> <B>readJronnFile</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> workDirectory,
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330 <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> clustFile)
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331 throws <A HREF="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>,
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332 <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A>,
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333 <A HREF="http://java.sun.com/javase/6/docs/api/java/io/FileNotFoundException.html?is-external=true" title="class or interface in java.io">FileNotFoundException</A>,
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334 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></PRE>
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339 <DD><CODE><A HREF="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE>
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340 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE>
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341 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/FileNotFoundException.html?is-external=true" title="class or interface in java.io">FileNotFoundException</A></CODE>
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342 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></CODE></DL>
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347 <A NAME="writeInput(java.util.List, compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>
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350 public static void <B>writeInput</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/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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351 <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> exec)
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352 throws <A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>
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357 <DD><CODE><A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>
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360 <!-- ========= END OF CLASS DATA ========= -->
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365 <A NAME="navbar_bottom"><!-- --></A>
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367 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
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384 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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391 <A HREF="../../compbio/runner/OptionCombinator.html" title="class in compbio.runner"><B>PREV CLASS</B></A>
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392 NEXT CLASS</FONT></TD>
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399 document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');
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412 SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
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