remove old project javadoc
[jabaws.git] / website / full_javadoc / index-files / index-10.html
diff --git a/website/full_javadoc/index-files/index-10.html b/website/full_javadoc/index-files/index-10.html
deleted file mode 100644 (file)
index f172cbe..0000000
+++ /dev/null
@@ -1,232 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:36 BST 2011 -->\r
-<TITLE>\r
-J-Index\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2011-08-12">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
-    if (location.href.indexOf('is-external=true') == -1) {\r
-        parent.document.title="J-Index";\r
-    }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
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-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="index-9.html"><B>PREV LETTER</B></A>&nbsp;\r
-&nbsp;<A HREF="index-11.html"><B>NEXT LETTER</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../index.html?index-filesindex-10.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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-&nbsp;<SCRIPT type="text/javascript">\r
-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
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-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
-<A NAME="_J_"><!-- --></A><H2>\r
-<B>J</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa"><B>JABAService</B></A> - Interface in <A HREF="../compbio/data/msa/package-summary.html">compbio.data.msa</A><DD>This is a marker interface, contains no methods<DT><A HREF="../compbio/pipeline/_jpred/JackHmmerHitParser.html" title="class in compbio.pipeline._jpred"><B>JackHmmerHitParser</B></A> - Class in <A HREF="../compbio/pipeline/_jpred/package-summary.html">compbio.pipeline._jpred</A><DD>Parser for the following files:<DT><A HREF="../compbio/pipeline/_jpred/JackHmmerHitParser.html#JackHmmerHitParser(java.lang.String)"><B>JackHmmerHitParser(String)</B></A> - \r
-Constructor for class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/JackHmmerHitParser.html" title="class in compbio.pipeline._jpred">JackHmmerHitParser</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa"><B>JManagement</B></A> - Interface in <A HREF="../compbio/data/msa/package-summary.html">compbio.data.msa</A><DD>&nbsp;<DT><A HREF="../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure"><B>JnetAnnotation</B></A> - Enum in <A HREF="../compbio/data/_structure/package-summary.html">compbio.data._structure</A><DD>&nbsp;<DT><A HREF="../compbio/engine/Job.html" title="class in compbio.engine"><B>Job</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>&nbsp;<DT><A HREF="../compbio/engine/Job.html#Job(java.lang.String, java.lang.String, compbio.engine.client.ConfiguredExecutable)"><B>Job(String, String, ConfiguredExecutable&lt;?&gt;)</B></A> - \r
-Constructor for class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata"><B>JobExecutionException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>JobExecutionException is thrown wherever the results of the calculation
- cannot be obtained.<DT><A HREF="../compbio/metadata/JobExecutionException.html#JobExecutionException(java.lang.String)"><B>JobExecutionException(String)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/JobExecutionException.html#JobExecutionException(java.lang.Throwable)"><B>JobExecutionException(Throwable)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/JobExecutionException.html#JobExecutionException(java.lang.String, java.lang.Throwable)"><B>JobExecutionException(String, Throwable)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#JOBID"><B>JOBID</B></A> - \r
-Static variable in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/stat/servlet/Joblist.html" title="class in compbio.stat.servlet"><B>Joblist</B></A> - Class in <A HREF="../compbio/stat/servlet/package-summary.html">compbio.stat.servlet</A><DD>&nbsp;<DT><A HREF="../compbio/stat/servlet/Joblist.html#Joblist()"><B>Joblist()</B></A> - \r
-Constructor for class compbio.stat.servlet.<A HREF="../compbio/stat/servlet/Joblist.html" title="class in compbio.stat.servlet">Joblist</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa"><B>JobRunner</B></A> - Class in <A HREF="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A><DD>Single cluster job runner class<DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#JobRunner(compbio.engine.client.ConfiguredExecutable)"><B>JobRunner(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
-Constructor for class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector"><B>JobStat</B></A> - Class in <A HREF="../compbio/stat/collector/package-summary.html">compbio.stat.collector</A><DD>&nbsp;<DT><A HREF="../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><B>JobStatus</B></A> - Enum in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>The status of the job.<DT><A HREF="../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata"><B>JobSubmissionException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Exception for generic problems with JobSubmission it is often thrown as a
- wrapper for the lower level exceptions like IOException or DrmaaException.<DT><A HREF="../compbio/metadata/JobSubmissionException.html#JobSubmissionException(java.lang.String)"><B>JobSubmissionException(String)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/JobSubmissionException.html#JobSubmissionException(java.lang.Throwable)"><B>JobSubmissionException(Throwable)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/JobSubmissionException.html#JobSubmissionException(java.lang.String, java.lang.Throwable)"><B>JobSubmissionException(String, Throwable)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws"><B>JobSubmissionExceptionBean</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>This class was generated by the JAX-WS RI.<DT><A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html#JobSubmissionExceptionBean()"><B>JobSubmissionExceptionBean()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws">JobSubmissionExceptionBean</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/pipeline/_jpred/Jpred4.html" title="class in compbio.pipeline._jpred"><B>Jpred4</B></A> - Class in <A HREF="../compbio/pipeline/_jpred/package-summary.html">compbio.pipeline._jpred</A><DD>jpred --sequence <fasta file> OR --alignment <clustalW alignment> [--db
- <database>] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help]
- jpred4 --sequence <fasta file> The path to the sequence (in FASTA format) you
- want to predict OR
- [--alignment <clustalW alignment>] The alignment which to use for prediction
- [--profile=<path to HMM profile>]
- [--db <database>] Database to use for PSI-BLAST querying.<DT><A HREF="../compbio/pipeline/_jpred/Jpred4.html#Jpred4()"><B>Jpred4()</B></A> - \r
-Constructor for class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/Jpred4.html" title="class in compbio.pipeline._jpred">Jpred4</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure"><B>JpredAnnotation</B></A> - Enum in <A HREF="../compbio/data/_structure/package-summary.html">compbio.data._structure</A><DD>&nbsp;<DT><A HREF="../compbio/data/_structure/JpredResult.html" title="class in compbio.data._structure"><B>JpredResult</B></A> - Class in <A HREF="../compbio/data/_structure/package-summary.html">compbio.data._structure</A><DD>Jnet result
- jnetpred:-,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-,
- -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H
- ,H,H,-,-,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,-,-,H,H,H,H,
- -,-,-,-,-,-,-,-,-,-,-,-,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-
- , JNETCONF:7,3,7,9,9,9,9,9,9,9,7,5,2,6,6,3,6,7,5,1,0,5,3,3,6,4,6,6,7,7,7,7,7,
- 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,6,3,6,8,9,9,9,9,9,9,9
- 7,3,7,7,6,2,4,4,1,5,7,8,7,7,7,7,7,7,7,6,5,3,5,6,6,6,4,0,0,2,1,3,5,7,7,7,7,7,7
- , JNETSOL25:B,B,-,-,-,B,-,B,-,B,B,B,-,-,-,B,-,B,-,-,-,-,-,B,-,B,-,-,-,-,-,-,
- -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,B,-,B,-
- , B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,B,-,-,-,-,B,-,-,B,B,-,-
- ,B,
- JNETSOL5:-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,B,B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,-
- ,-,-
- JNETSOL0:-,-,-,-,-,-,B,-,-,B,-,B,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,
- -,-,- ,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,-,B,-,-,
- JNETHMM:-,H,H,H,H,H,H,H,H,H,H,
- H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-,-,
- -,-,-,-,-,-,-,-,-,-,-,-,-,-,-
- ,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H,
- JNETPROPH:0.0110,0.1125,0.8552,0.0107
- ,0.6245,0.3614,0.0120,0.8702,0.1238,0.0120
- ,0.0193,0.9284,0.0708,0.0278,0.8703,0.1244
- ,0.1591,0.7399,0.1456,0.2488,0.5824,0.1017,
- JNETPROPE:0.0107,0.6245,0.3614,0.0120
- ,0.8702,0.1238,0.0120,0.9335,0.0656,0.0102
- ,0.9586,0.0465,0.0094,0.9662,0.0433,
- ,0.1525,0.7103,0.1088,0.1181,0.7425,0.1784,<DT><A HREF="../compbio/data/_structure/JpredResult.html#JpredResult()"><B>JpredResult()</B></A> - \r
-Constructor for class compbio.data._structure.<A HREF="../compbio/data/_structure/JpredResult.html" title="class in compbio.data._structure">JpredResult</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder"><B>Jronn</B></A> - Class in <A HREF="../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A><DD>Command line
- java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out<DT><A HREF="../compbio/runner/disorder/Jronn.html#Jronn()"><B>Jronn()</B></A> - \r
-Constructor for class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/JronnWS.html" title="class in compbio.ws.server"><B>JronnWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/JronnWS.html#JronnWS()"><B>JronnWS()</B></A> - \r
-Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/JronnWS.html" title="class in compbio.ws.server">JronnWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client"><B>Jws2Client</B></A> - Class in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>A command line client for JAva Bioinformatics Analysis Web Services</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
-  <TR ALIGN="center" VALIGN="top">\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
-  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&nbsp;</TD>\r
-  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
-  </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="index-9.html"><B>PREV LETTER</B></A>&nbsp;\r
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-  <!--\r
-  if(window==top) {\r
-    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
-  }\r
-  //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-  <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
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