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5 <!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 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="PsiBlast";
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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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43 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/PsiBlast.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
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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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85 <!-- ========= END OF TOP NAVBAR ========= -->
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88 <!-- ======== START OF CLASS DATA ======== -->
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91 compbio.runner.psiblast</FONT>
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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/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>>
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97 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.psiblast.PsiBlast</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/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>></DD>
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104 <DT><PRE>public class <B>PsiBlast</B><DT>extends <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>></DL>
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111 <!-- ======== NESTED CLASS SUMMARY ======== -->
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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/psiblast/PsiBlast.html#PsiBlast()">PsiBlast</A></B>()</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> <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>></CODE></FONT></TD>
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158 <TD><CODE><B><A HREF="../../../compbio/runner/psiblast/PsiBlast.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String presetName)</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> <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>></CODE></FONT></TD>
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166 <TD><CODE><B><A HREF="../../../compbio/runner/psiblast/PsiBlast.html#getLimits()">getLimits</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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174 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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175 <TR ALIGN="right" VALIGN="">
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176 <TD NOWRAP><FONT SIZE="-1">
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177 <CODE><V> V</CODE></FONT></TD>
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180 </CODE></FONT></TD>
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181 <TD><CODE><B><A HREF="../../../compbio/runner/psiblast/PsiBlast.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String directory)</CODE>
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184 </TD>
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186 <TR BGCOLOR="white" CLASS="TableRowColor">
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187 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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188 <CODE> java.lang.Class<? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?>></CODE></FONT></TD>
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189 <TD><CODE><B><A HREF="../../../compbio/runner/psiblast/PsiBlast.html#getType()">getType</A></B>()</CODE>
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192 </TD>
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195 <A NAME="methods_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>
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196 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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197 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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198 <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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200 <TR BGCOLOR="white" CLASS="TableRowColor">
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201 <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#getClusterSettings()">getClusterSettings</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#getOutput()">getOutput</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#setInput(java.lang.String)">setInput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setOutput(java.lang.String)">setOutput</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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204 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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205 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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206 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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207 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>
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209 <TR BGCOLOR="white" CLASS="TableRowColor">
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210 <TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>
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216 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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218 <A NAME="constructor_detail"><!-- --></A>
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219 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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220 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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221 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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222 <B>Constructor Detail</B></FONT></TH>
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226 <A NAME="PsiBlast()"><!-- --></A><H3>
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229 public <B>PsiBlast</B>()</PRE>
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233 <!-- ============ METHOD DETAIL ========== -->
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235 <A NAME="method_detail"><!-- --></A>
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236 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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237 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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238 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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239 <B>Method Detail</B></FONT></TH>
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243 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>
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246 public <V> V <B>getResults</B>(java.lang.String directory)
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247 throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>
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252 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>
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257 <A NAME="getLimit(java.lang.String)"><!-- --></A><H3>
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260 public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>> <B>getLimit</B>(java.lang.String presetName)</PRE>
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268 <A NAME="getLimits()"><!-- --></A><H3>
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271 public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>> <B>getLimits</B>()</PRE>
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279 <A NAME="getType()"><!-- --></A><H3>
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282 public java.lang.Class<? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?>> <B>getType</B>()</PRE>
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285 <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/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>></CODE></DL>
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291 <!-- ========= END OF CLASS DATA ========= -->
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315 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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321 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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322 PREV CLASS
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323 NEXT CLASS</FONT></TD>
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324 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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325 <A HREF="../../../index.html?compbio/runner/psiblast/PsiBlast.html" target="_top"><B>FRAMES</B></A>
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326 <A HREF="PsiBlast.html" target="_top"><B>NO FRAMES</B></A>
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327 <SCRIPT type="text/javascript">
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330 document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
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342 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
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343 SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
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345 DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
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