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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="Jronn";
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27 <BODY BGCOLOR="white" onload="windowTitle();">
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31 <!-- ========= START OF TOP NAVBAR ======= -->
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42 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
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43 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Jronn.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
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51 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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57 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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58 <A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder"><B>PREV CLASS</B></A>
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59 NEXT CLASS</FONT></TD>
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60 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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71 <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
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78 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
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79 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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80 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
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81 DETAIL: <A HREF="#field_detail">FIELD</A> | <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/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>>
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97 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.disorder.Jronn</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/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>></DD>
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104 <DT><PRE>public class <B>Jronn</B><DT>extends <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>></DL>
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110 java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
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115 <DT><B>Author:</B></DT>
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121 <!-- ======== NESTED CLASS SUMMARY ======== -->
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123 <A NAME="nested_class_summary"><!-- --></A>
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124 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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125 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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126 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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127 <B>Nested Class Summary</B></FONT></TH>
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130 <A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>
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131 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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132 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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133 <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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135 <TR BGCOLOR="white" CLASS="TableRowColor">
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136 <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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140 <!-- =========== FIELD SUMMARY =========== -->
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142 <A NAME="field_summary"><!-- --></A>
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143 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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144 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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145 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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146 <B>Field Summary</B></FONT></TH>
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148 <TR BGCOLOR="white" CLASS="TableRowColor">
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149 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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150 <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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151 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/Jronn.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></B></CODE>
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154 </TD>
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156 <TR BGCOLOR="white" CLASS="TableRowColor">
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157 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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158 <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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159 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/Jronn.html#STAT_FILE">STAT_FILE</A></B></CODE>
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162 </TD>
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165 <A NAME="fields_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>
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166 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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167 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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168 <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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170 <TR BGCOLOR="white" CLASS="TableRowColor">
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171 <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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175 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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177 <A NAME="constructor_summary"><!-- --></A>
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178 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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179 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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180 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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181 <B>Constructor Summary</B></FONT></TH>
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183 <TR BGCOLOR="white" CLASS="TableRowColor">
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184 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/Jronn.html#Jronn()">Jronn</A></B>()</CODE>
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187 </TD>
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191 <!-- ========== METHOD SUMMARY =========== -->
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193 <A NAME="method_summary"><!-- --></A>
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194 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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195 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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196 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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197 <B>Method Summary</B></FONT></TH>
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199 <TR BGCOLOR="white" CLASS="TableRowColor">
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200 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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201 <CODE> <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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202 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/Jronn.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>
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205 This method cannot really tell whether the files has actually been
206 created or not.</TD>
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208 <TR BGCOLOR="white" CLASS="TableRowColor">
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209 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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210 <CODE> <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>></CODE></FONT></TD>
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211 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/Jronn.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</CODE>
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214 </TD>
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216 <TR BGCOLOR="white" CLASS="TableRowColor">
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217 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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218 <CODE> <A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>
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219 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/Jronn.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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222 </TD>
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224 <TR BGCOLOR="white" CLASS="TableRowColor">
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225 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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226 <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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227 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/Jronn.html#getStatFile()">getStatFile</A></B>()</CODE>
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230 </TD>
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232 <TR BGCOLOR="white" CLASS="TableRowColor">
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233 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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234 <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/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>></CODE></FONT></TD>
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235 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/Jronn.html#getType()">getType</A></B>()</CODE>
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238 </TD>
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240 <TR BGCOLOR="white" CLASS="TableRowColor">
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241 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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242 <CODE> <A HREF="../../../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A></CODE></FONT></TD>
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243 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/Jronn.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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246 </TD>
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248 <TR BGCOLOR="white" CLASS="TableRowColor">
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249 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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250 <CODE> void</CODE></FONT></TD>
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251 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/Jronn.html#setNCore(int)">setNCore</A></B>(int ncoreNumber)</CODE>
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254 </TD>
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256 <TR BGCOLOR="white" CLASS="TableRowColor">
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257 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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258 <CODE> <A HREF="../../../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A></CODE></FONT></TD>
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259 <TD><CODE><B><A HREF="../../../compbio/runner/disorder/Jronn.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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262 </TD>
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265 <A NAME="methods_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>
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266 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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267 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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268 <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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270 <TR BGCOLOR="white" CLASS="TableRowColor">
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271 <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#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#getOutput()">getOutput</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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274 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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275 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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276 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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277 <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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279 <TR BGCOLOR="white" CLASS="TableRowColor">
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280 <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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286 <!-- ============ FIELD DETAIL =========== -->
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288 <A NAME="field_detail"><!-- --></A>
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289 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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290 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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291 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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292 <B>Field Detail</B></FONT></TH>
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296 <A NAME="KEY_VALUE_SEPARATOR"><!-- --></A><H3>
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297 KEY_VALUE_SEPARATOR</H3>
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299 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>KEY_VALUE_SEPARATOR</B></PRE>
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302 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.runner.disorder.Jronn.KEY_VALUE_SEPARATOR">Constant Field Values</A></DL>
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306 <A NAME="STAT_FILE"><!-- --></A><H3>
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309 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>STAT_FILE</B></PRE>
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312 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.runner.disorder.Jronn.STAT_FILE">Constant Field Values</A></DL>
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315 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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317 <A NAME="constructor_detail"><!-- --></A>
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318 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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319 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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320 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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321 <B>Constructor Detail</B></FONT></TH>
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325 <A NAME="Jronn()"><!-- --></A><H3>
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328 public <B>Jronn</B>()</PRE>
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332 <!-- ============ METHOD DETAIL ========== -->
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334 <A NAME="method_detail"><!-- --></A>
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335 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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336 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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337 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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338 <B>Method Detail</B></FONT></TH>
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342 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>
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345 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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346 throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>
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351 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>
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356 <A NAME="getCreatedFiles()"><!-- --></A><H3>
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357 getCreatedFiles</H3>
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359 public <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>getCreatedFiles</B>()</PRE>
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361 <DD><B>Description copied from class: <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">SkeletalExecutable</A></CODE></B></DD>
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362 <DD>This method cannot really tell whether the files has actually been
363 created or not. It must be overridden as required.
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366 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</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/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">getCreatedFiles</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/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>></CODE></DL>
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369 <DT><B>See Also:</B><DD><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()"><CODE>Executable.getCreatedFiles()</CODE></A></DL>
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374 <A NAME="setInput(java.lang.String)"><!-- --></A><H3>
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377 public <A HREF="../../../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</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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380 <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/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>></CODE></DL>
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388 <A NAME="setOutput(java.lang.String)"><!-- --></A><H3>
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391 public <A HREF="../../../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</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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394 <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/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>></CODE></DL>
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402 <A NAME="getType()"><!-- --></A><H3>
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405 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/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>> <B>getType</B>()</PRE>
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408 <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/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>></CODE></DL>
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412 <DT><B>Returns:</B><DD>subclasses must return their type</DL>
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417 <A NAME="getStatFile()"><!-- --></A><H3>
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420 public 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> <B>getStatFile</B>()</PRE>
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428 <A NAME="setNCore(int)"><!-- --></A><H3>
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431 public void <B>setNCore</B>(int ncoreNumber)</PRE>
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439 <A NAME="getParameters(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>
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442 public <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A><<A HREF="../../../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>> <B>getParameters</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</PRE>
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445 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</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/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</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/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>></CODE></DL>
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