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5 <!-- Generated by javadoc (build 1.6.0_24) on Wed Dec 07 12:30:41 GMT 2011 -->
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10 <META NAME="date" CONTENT="2011-12-07">
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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="Runners";
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27 <BODY BGCOLOR="white" onload="windowTitle();">
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31 <!-- ========= START OF TOP NAVBAR ======= -->
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40 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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66 document.writeln('<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 | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
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81 DETAIL: FIELD | CONSTR | <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._impl</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 "><B>compbio.runner._impl.Runners</B>
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100 <DT><PRE>public final class <B>Runners</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 <!-- ========== METHOD SUMMARY =========== -->
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112 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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113 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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114 <B>Method Summary</B></FONT></TH>
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116 <TR BGCOLOR="white" CLASS="TableRowColor">
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117 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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118 <CODE>static <A HREF="../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A></CODE></FONT></TD>
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119 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getBlastAllRunnable(java.lang.String)">getBlastAllRunnable</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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122 </TD>
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124 <TR BGCOLOR="white" CLASS="TableRowColor">
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125 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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126 <CODE>static <A HREF="../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A></CODE></FONT></TD>
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127 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getMclRunnable(java.lang.String)">getMclRunnable</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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130 </TD>
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132 <TR BGCOLOR="white" CLASS="TableRowColor">
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133 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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134 <CODE>static <A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A></CODE></FONT></TD>
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135 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getNetNglycRunnable(java.lang.String)">getNetNglycRunnable</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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138 </TD>
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140 <TR BGCOLOR="white" CLASS="TableRowColor">
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141 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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142 <CODE>static <A HREF="../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A></CODE></FONT></TD>
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143 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getOBRunnable(java.lang.String)">getOBRunnable</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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146 </TD>
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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="../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A></CODE></FONT></TD>
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151 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getPSIBlastRunnable(java.lang.String)">getPSIBlastRunnable</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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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="../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A></CODE></FONT></TD>
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159 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getRonnRunnable(java.lang.String)">getRonnRunnable</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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162 </TD>
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164 <TR BGCOLOR="white" CLASS="TableRowColor">
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165 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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166 <CODE>static <A HREF="../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A></CODE></FONT></TD>
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167 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getRPSBlastRunnable(java.lang.String)">getRPSBlastRunnable</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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170 </TD>
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172 <TR BGCOLOR="white" CLASS="TableRowColor">
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173 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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174 <CODE>static compbio.runner._impl.Tmhmm2</CODE></FONT></TD>
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175 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/Runners.html#getTmhmm2Runnable(java.lang.String)">getTmhmm2Runnable</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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178 </TD>
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181 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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182 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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183 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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184 <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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186 <TR BGCOLOR="white" CLASS="TableRowColor">
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187 <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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193 <!-- ============ METHOD DETAIL ========== -->
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198 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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199 <B>Method Detail</B></FONT></TH>
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203 <A NAME="getMclRunnable(java.lang.String)"><!-- --></A><H3>
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204 getMclRunnable</H3>
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206 public static <A HREF="../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A> <B>getMclRunnable</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)</PRE>
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214 <A NAME="getOBRunnable(java.lang.String)"><!-- --></A><H3>
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217 public static <A HREF="../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A> <B>getOBRunnable</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)</PRE>
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225 <A NAME="getNetNglycRunnable(java.lang.String)"><!-- --></A><H3>
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226 getNetNglycRunnable</H3>
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228 public static <A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A> <B>getNetNglycRunnable</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)</PRE>
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236 <A NAME="getRonnRunnable(java.lang.String)"><!-- --></A><H3>
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237 getRonnRunnable</H3>
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239 public static <A HREF="../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A> <B>getRonnRunnable</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)</PRE>
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247 <A NAME="getTmhmm2Runnable(java.lang.String)"><!-- --></A><H3>
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248 getTmhmm2Runnable</H3>
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250 public static compbio.runner._impl.Tmhmm2 <B>getTmhmm2Runnable</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)</PRE>
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258 <A NAME="getRPSBlastRunnable(java.lang.String)"><!-- --></A><H3>
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259 getRPSBlastRunnable</H3>
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261 public static <A HREF="../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A> <B>getRPSBlastRunnable</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)</PRE>
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269 <A NAME="getBlastAllRunnable(java.lang.String)"><!-- --></A><H3>
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270 getBlastAllRunnable</H3>
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272 public static <A HREF="../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A> <B>getBlastAllRunnable</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)</PRE>
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280 <A NAME="getPSIBlastRunnable(java.lang.String)"><!-- --></A><H3>
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281 getPSIBlastRunnable</H3>
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283 public static <A HREF="../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A> <B>getPSIBlastRunnable</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)</PRE>
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