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15 function windowTitle()
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17 if (location.href.indexOf('is-external=true') == -1) {
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18 parent.document.title="IUPred";
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27 <BODY BGCOLOR="white" onload="windowTitle();">
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31 <!-- ========= START OF TOP NAVBAR ======= -->
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78 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
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79 SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_compbio.engine.client.SkeletalExecutable">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
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80 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
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81 DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
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84 <A NAME="skip-navbar_top"></A>
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85 <!-- ========= END OF TOP NAVBAR ========= -->
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88 <!-- ======== START OF CLASS DATA ======== -->
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91 compbio.runner.disorder</FONT>
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95 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>
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96 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">compbio.engine.client.SkeletalExecutable</A><<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>>
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97 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.disorder.IUPred</B>
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100 <DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>></DD>
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104 <DT><PRE>public class <B>IUPred</B><DT>extends <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>></DL>
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108 iupred sequenceFile <short long glob >
110 Maximum sequence length is 40000 chars. Single string length max is a 1000
118 <!-- ======== NESTED CLASS SUMMARY ======== -->
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120 <A NAME="nested_class_summary"><!-- --></A>
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121 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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124 <B>Nested Class Summary</B></FONT></TH>
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127 <A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>
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128 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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129 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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130 <TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>
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132 <TR BGCOLOR="white" CLASS="TableRowColor">
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133 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>
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137 <!-- =========== FIELD SUMMARY =========== -->
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142 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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143 <B>Field Summary</B></FONT></TH>
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146 <A NAME="fields_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>
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147 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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148 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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149 <TH ALIGN="left"><B>Fields inherited from class compbio.engine.client.<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A></B></TH>
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151 <TR BGCOLOR="white" CLASS="TableRowColor">
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152 <TD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#ERROR">ERROR</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#INPUT">INPUT</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#OUTPUT">OUTPUT</A></CODE></TD>
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156 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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158 <A NAME="constructor_summary"><!-- --></A>
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159 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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160 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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161 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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162 <B>Constructor Summary</B></FONT></TH>
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164 <TR BGCOLOR="white" CLASS="TableRowColor">
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165 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/IUPred.html#IUPred()">IUPred</A></B>()</CODE>
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168 </TD>
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172 <!-- ========== METHOD SUMMARY =========== -->
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174 <A NAME="method_summary"><!-- --></A>
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175 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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177 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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178 <B>Method Summary</B></FONT></TH>
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180 <TR BGCOLOR="white" CLASS="TableRowColor">
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181 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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182 <CODE> <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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183 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/IUPred.html#getOutput()">getOutput</A></B>()</CODE>
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186 </TD>
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188 <TR BGCOLOR="white" CLASS="TableRowColor">
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189 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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190 <CODE> <A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>
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191 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/IUPred.html#getResults(java.lang.String)">getResults</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)</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> <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><<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>></CODE></FONT></TD>
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199 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/IUPred.html#getType()">getType</A></B>()</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> <A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A></CODE></FONT></TD>
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207 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/IUPred.html#setInput(java.lang.String)">setInput</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> inFile)</CODE>
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210 </TD>
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212 <TR BGCOLOR="white" CLASS="TableRowColor">
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213 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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214 <CODE> <A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A></CODE></FONT></TD>
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215 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/IUPred.html#setOutput(java.lang.String)">setOutput</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> outFile)</CODE>
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218 </TD>
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221 <A NAME="methods_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>
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222 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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223 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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224 <TH ALIGN="left"><B>Methods inherited from class compbio.engine.client.<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A></B></TH>
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226 <TR BGCOLOR="white" CLASS="TableRowColor">
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227 <TD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#equals(java.lang.Object)">equals</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterCpuNum(java.lang.Class)">getClusterCpuNum</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterJobSettings()">getClusterJobSettings</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">getCreatedFiles</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getError()">getError</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getInput()">getInput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#hashCode()">hashCode</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setError(java.lang.String)">setError</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)">setParameter</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#toString()">toString</A></CODE></TD>
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230 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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231 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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232 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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233 <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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235 <TR BGCOLOR="white" CLASS="TableRowColor">
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236 <TD><CODE><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#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#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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242 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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244 <A NAME="constructor_detail"><!-- --></A>
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245 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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246 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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247 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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248 <B>Constructor Detail</B></FONT></TH>
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252 <A NAME="IUPred()"><!-- --></A><H3>
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255 public <B>IUPred</B>()</PRE>
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259 <!-- ============ METHOD DETAIL ========== -->
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261 <A NAME="method_detail"><!-- --></A>
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262 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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263 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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264 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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265 <B>Method Detail</B></FONT></TH>
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269 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>
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272 public <A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A> <B>getResults</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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273 throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>
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278 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>
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283 <A NAME="setInput(java.lang.String)"><!-- --></A><H3>
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286 public <A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A> <B>setInput</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> inFile)</PRE>
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289 <DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setInput(java.lang.String)">setInput</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>></CODE></DL>
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297 <A NAME="setOutput(java.lang.String)"><!-- --></A><H3>
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300 public <A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A> <B>setOutput</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> outFile)</PRE>
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303 <DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setOutput(java.lang.String)">setOutput</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>></CODE></DL>
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311 <A NAME="getOutput()"><!-- --></A><H3>
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314 public <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>getOutput</B>()</PRE>
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317 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getOutput()">getOutput</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getOutput()">getOutput</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>></CODE></DL>
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325 <A NAME="getType()"><!-- --></A><H3>
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328 public <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><<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>> <B>getType</B>()</PRE>
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331 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getType()">getType</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>></CODE></DL>
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335 <DT><B>Returns:</B><DD>subclasses must return their type</DL>
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338 <!-- ========= END OF CLASS DATA ========= -->
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342 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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343 <A NAME="navbar_bottom"><!-- --></A>
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348 <A NAME="navbar_bottom_firstrow"><!-- --></A>
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349 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
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350 <TR ALIGN="center" VALIGN="top">
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351 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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354 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/IUPred.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
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355 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
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362 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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368 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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369 <A HREF="../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder"><B>PREV CLASS</B></A>
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370 <A HREF="../../../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder"><B>NEXT CLASS</B></A></FONT></TD>
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372 <A HREF="../../../index.html?compbio/runner/disorder/IUPred.html" target="_top"><B>FRAMES</B></A>
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374 <SCRIPT type="text/javascript">
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377 document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
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390 SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_compbio.engine.client.SkeletalExecutable">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
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391 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
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392 DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
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