1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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5 <!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->
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10 <META NAME="date" CONTENT="2010-02-17">
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12 <LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">
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14 <SCRIPT type="text/javascript">
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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="RPSBlast";
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27 <BODY BGCOLOR="white" onload="windowTitle();">
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31 <!-- ========= START OF TOP NAVBAR ======= -->
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32 <A NAME="navbar_top"><!-- --></A>
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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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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/RPSBlast.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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63 <SCRIPT type="text/javascript">
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66 document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
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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 | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
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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._impl</FONT>
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96 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">compbio.runner._SkeletalCommandBuilder</A>
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97 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner._impl.RPSBlast</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/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>></DD>
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104 <DT><PRE>public class <B>RPSBlast</B><DT>extends <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></DL>
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111 <!-- ======== NESTED CLASS SUMMARY ======== -->
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113 <A NAME="nested_class_summary"><!-- --></A>
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114 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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115 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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116 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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117 <B>Nested Class Summary</B></FONT></TH>
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120 <A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>
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121 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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122 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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123 <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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125 <TR BGCOLOR="white" CLASS="TableRowColor">
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126 <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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131 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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133 <A NAME="constructor_summary"><!-- --></A>
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134 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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135 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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136 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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137 <B>Constructor Summary</B></FONT></TH>
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139 <TR BGCOLOR="white" CLASS="TableRowColor">
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140 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/RPSBlast.html#RPSBlast(java.lang.String)">RPSBlast</A></B>(java.lang.String workDirectory)</CODE>
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143 </TD>
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147 <!-- ========== METHOD SUMMARY =========== -->
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149 <A NAME="method_summary"><!-- --></A>
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150 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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151 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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152 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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153 <B>Method Summary</B></FONT></TH>
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155 <TR BGCOLOR="white" CLASS="TableRowColor">
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156 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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157 <CODE> java.lang.String</CODE></FONT></TD>
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158 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/RPSBlast.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</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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161 </TD>
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163 <TR BGCOLOR="white" CLASS="TableRowColor">
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164 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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165 <CODE>static java.lang.String</CODE></FONT></TD>
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166 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/RPSBlast.html#getCommandName()">getCommandName</A></B>()</CODE>
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169 </TD>
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171 <TR BGCOLOR="white" CLASS="TableRowColor">
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172 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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173 <CODE> java.util.List<java.lang.String></CODE></FONT></TD>
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174 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/RPSBlast.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>
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177 </TD>
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179 <TR BGCOLOR="white" CLASS="TableRowColor">
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180 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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181 <CODE> java.lang.String</CODE></FONT></TD>
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182 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/RPSBlast.html#getInput()">getInput</A></B>()</CODE>
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185 </TD>
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187 <TR BGCOLOR="white" CLASS="TableRowColor">
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188 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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189 <CODE>static java.lang.String</CODE></FONT></TD>
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190 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/RPSBlast.html#getTestCommand()">getTestCommand</A></B>()</CODE>
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193 </TD>
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196 <A NAME="methods_inherited_from_class_compbio.runner._SkeletalCommandBuilder"><!-- --></A>
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197 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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198 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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199 <TH ALIGN="left"><B>Methods inherited from class compbio.runner.<A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></B></TH>
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201 <TR BGCOLOR="white" CLASS="TableRowColor">
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202 <TD><CODE><A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)">addParameter</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])">addParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getEmail()">getEmail</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getError()">getError</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getName()">getName</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#getResults(java.lang.String)">getResults</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setEmail(java.lang.String)">setEmail</A>, <A HREF="../../../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)">setName</A></CODE></TD>
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205 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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206 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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207 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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208 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>
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210 <TR BGCOLOR="white" CLASS="TableRowColor">
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211 <TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
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217 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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219 <A NAME="constructor_detail"><!-- --></A>
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220 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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221 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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222 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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223 <B>Constructor Detail</B></FONT></TH>
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227 <A NAME="RPSBlast(java.lang.String)"><!-- --></A><H3>
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230 public <B>RPSBlast</B>(java.lang.String workDirectory)</PRE>
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234 <!-- ============ METHOD DETAIL ========== -->
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236 <A NAME="method_detail"><!-- --></A>
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237 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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238 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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239 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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240 <B>Method Detail</B></FONT></TH>
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244 <A NAME="getCommand(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>
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247 public java.lang.String <B>getCommand</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider)</PRE>
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255 <A NAME="getTestCommand()"><!-- --></A><H3>
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256 getTestCommand</H3>
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258 public static java.lang.String <B>getTestCommand</B>()</PRE>
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266 <A NAME="getCommandName()"><!-- --></A><H3>
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267 getCommandName</H3>
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269 public static java.lang.String <B>getCommandName</B>()</PRE>
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277 <A NAME="getCreatedFiles()"><!-- --></A><H3>
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278 getCreatedFiles</H3>
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280 public java.util.List<java.lang.String> <B>getCreatedFiles</B>()</PRE>
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288 <A NAME="getInput()"><!-- --></A><H3>
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291 public java.lang.String <B>getInput</B>()</PRE>
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297 <!-- ========= END OF CLASS DATA ========= -->
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301 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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302 <A NAME="navbar_bottom"><!-- --></A>
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313 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/RPSBlast.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
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321 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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327 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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328 <A HREF="../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>
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330 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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333 <SCRIPT type="text/javascript">
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336 document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
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349 SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
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351 DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
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