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91 compbio.ws.server</FONT>
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96 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.server.WSUtil</B>
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100 <DT><PRE>public final class <B>WSUtil</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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108 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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114 <B>Constructor Summary</B></FONT></TH>
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116 <TR BGCOLOR="white" CLASS="TableRowColor">
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117 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#WSUtil()">WSUtil</A></B>()</CODE>
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130 <B>Method Summary</B></FONT></TH>
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138 <CODE><T> <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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141 </CODE></FONT></TD>
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142 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#align(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, java.lang.String, compbio.metadata.Limit)">align</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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143 <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><T> confExec,
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144 org.apache.log4j.Logger logger,
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145 <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> callingMethod,
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146 <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><T> limit)</CODE>
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149 </TD>
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151 <TR BGCOLOR="white" CLASS="TableRowColor">
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152 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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155 <TR ALIGN="right" VALIGN="">
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156 <TD NOWRAP><FONT SIZE="-1">
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157 <CODE><T> <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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160 </CODE></FONT></TD>
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161 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#analize(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, java.lang.String, compbio.metadata.Limit)">analize</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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162 <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><T> confExec,
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163 org.apache.log4j.Logger log,
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164 <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> method,
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165 <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><T> limit)</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>static boolean</CODE></FONT></TD>
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173 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#cancelJob(java.lang.String)">cancelJob</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> jobId)</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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181 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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182 <TR ALIGN="right" VALIGN="">
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183 <TD NOWRAP><FONT SIZE="-1">
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184 <CODE><T> <A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>
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187 </CODE></FONT></TD>
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188 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#getAnnotation(java.lang.String, org.apache.log4j.Logger)">getAnnotation</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> jobId,
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189 org.apache.log4j.Logger log)</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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197 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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198 <TR ALIGN="right" VALIGN="">
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199 <TD NOWRAP><FONT SIZE="-1">
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200 <CODE><T> <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="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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203 </CODE></FONT></TD>
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204 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#getCommands(java.util.List, java.lang.String)">getCommands</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/metadata/Option.html" title="class in compbio.metadata">Option</A><T>> options,
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205 <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> keyValueSeparator)</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>static <A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></FONT></TD>
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213 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#getEngine(compbio.engine.client.ConfiguredExecutable)">getEngine</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> confClustal)</CODE>
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216 </TD>
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218 <TR BGCOLOR="white" CLASS="TableRowColor">
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219 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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220 <CODE>static <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>
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221 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#getJobStatus(java.lang.String)">getJobStatus</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> jobId)</CODE>
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224 </TD>
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226 <TR BGCOLOR="white" CLASS="TableRowColor">
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227 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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228 <CODE>static byte</CODE></FONT></TD>
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229 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#getProgress(java.lang.String)">getProgress</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> jobId)</CODE>
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232 </TD>
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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>static <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>
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237 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#pullFile(java.lang.String, long)">pullFile</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> file,
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238 long position)</CODE>
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241 </TD>
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243 <TR BGCOLOR="white" CLASS="TableRowColor">
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244 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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245 <CODE>static void</CODE></FONT></TD>
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246 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#validateAAConInput(java.util.List)">validateAAConInput</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)</CODE>
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249 </TD>
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251 <TR BGCOLOR="white" CLASS="TableRowColor">
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252 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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253 <CODE>static void</CODE></FONT></TD>
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254 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#validateFastaInput(java.util.List)">validateFastaInput</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)</CODE>
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257 </TD>
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259 <TR BGCOLOR="white" CLASS="TableRowColor">
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260 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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261 <CODE>static void</CODE></FONT></TD>
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262 <TD><CODE><B><A HREF="../../../compbio/ws/server/WSUtil.html#validateJobId(java.lang.String)">validateJobId</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> jobId)</CODE>
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265 </TD>
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268 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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269 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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270 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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271 <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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273 <TR BGCOLOR="white" CLASS="TableRowColor">
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274 <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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280 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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282 <A NAME="constructor_detail"><!-- --></A>
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283 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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284 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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285 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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286 <B>Constructor Detail</B></FONT></TH>
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290 <A NAME="WSUtil()"><!-- --></A><H3>
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293 public <B>WSUtil</B>()</PRE>
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297 <!-- ============ METHOD DETAIL ========== -->
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299 <A NAME="method_detail"><!-- --></A>
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300 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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301 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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302 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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303 <B>Method Detail</B></FONT></TH>
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307 <A NAME="validateJobId(java.lang.String)"><!-- --></A><H3>
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310 public static final void <B>validateJobId</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> jobId)
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311 throws <A HREF="http://java.sun.com/javase/6/docs/api/java/security/InvalidParameterException.html?is-external=true" title="class or interface in java.security">InvalidParameterException</A></PRE>
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316 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/security/InvalidParameterException.html?is-external=true" title="class or interface in java.security">InvalidParameterException</A></CODE></DL>
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321 <A NAME="validateFastaInput(java.util.List)"><!-- --></A><H3>
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322 validateFastaInput</H3>
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324 public static final void <B>validateFastaInput</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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325 throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>
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330 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>
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335 <A NAME="getJobStatus(java.lang.String)"><!-- --></A><H3>
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338 public static <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</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> jobId)</PRE>
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346 <A NAME="pullFile(java.lang.String, long)"><!-- --></A><H3>
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349 public static <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> <B>pullFile</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> file,
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350 long position)</PRE>
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358 <A NAME="getProgress(java.lang.String)"><!-- --></A><H3>
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361 public static byte <B>getProgress</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> jobId)</PRE>
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369 <A NAME="getEngine(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>
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372 public static <A HREF="../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A> <B>getEngine</B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> confClustal)</PRE>
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380 <A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>
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383 public static boolean <B>cancelJob</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> jobId)</PRE>
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391 <A NAME="align(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, java.lang.String, compbio.metadata.Limit)"><!-- --></A><H3>
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394 public static <T> <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>align</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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395 <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><T> confExec,
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396 org.apache.log4j.Logger logger,
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397 <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> callingMethod,
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398 <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><T> limit)
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399 throws <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,
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400 <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>
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405 <DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE>
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406 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>
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411 <A NAME="analize(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, java.lang.String, compbio.metadata.Limit)"><!-- --></A><H3>
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414 public static <T> <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>analize</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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415 <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><T> confExec,
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416 org.apache.log4j.Logger log,
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417 <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> method,
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418 <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><T> limit)
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419 throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>
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424 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>
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429 <A NAME="getCommands(java.util.List, java.lang.String)"><!-- --></A><H3>
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432 public static final <T> <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="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>getCommands</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/metadata/Option.html" title="class in compbio.metadata">Option</A><T>> options,
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433 <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> keyValueSeparator)</PRE>
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441 <A NAME="validateAAConInput(java.util.List)"><!-- --></A><H3>
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442 validateAAConInput</H3>
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444 public static void <B>validateAAConInput</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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445 throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>
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450 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>
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455 <A NAME="getAnnotation(java.lang.String, org.apache.log4j.Logger)"><!-- --></A><H3>
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458 public static <T> <A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A> <B>getAnnotation</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> jobId,
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459 org.apache.log4j.Logger log)
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460 throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>
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465 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>
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