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remove old project javadoc
[jabaws.git] / website / full_javadoc / index-files / index-13.html
diff --git a/website/full_javadoc/index-files/index-13.html b/website/full_javadoc/index-files/index-13.html
deleted file mode 100644 (file)
index 58bd1c0..0000000
--- a/website/full_javadoc/index-files/index-13.html
+++ /dev/null
@@ -1,201 +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
-M-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="M-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
-  <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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="index-12.html"><B>PREV LETTER</B></A>&nbsp;\r
-&nbsp;<A HREF="index-14.html"><B>NEXT LETTER</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../index.html?index-filesindex-13.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="index-13.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&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
-\r
-</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="_M_"><!-- --></A><H2>\r
-<B>M</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa"><B>Mafft</B></A> - Class in <A HREF="../compbio/runner/msa/package-summary.html">compbio.runner.msa</A><DD>&nbsp;<DT><A HREF="../compbio/runner/msa/Mafft.html#Mafft()"><B>Mafft()</B></A> - \r
-Constructor for class compbio.runner.msa.<A HREF="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server"><B>MafftWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/MafftWS.html#MafftWS()"><B>MafftWS()</B></A> - \r
-Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/pipeline/_jpred/BlastBlastComparator.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
-Static method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/BlastBlastComparator.html" title="class in compbio.pipeline._jpred">BlastBlastComparator</A>\r
-<DD>args[0] is assumed to be the name of a Blast output file\r
-<DT><A HREF="../compbio/pipeline/_jpred/BlastHmmerComparator.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
-Static method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/BlastHmmerComparator.html" title="class in compbio.pipeline._jpred">BlastHmmerComparator</A>\r
-<DD>args[0] is assumed to be the name of a Blast output file\r
-<DT><A HREF="../compbio/pipeline/_jpred/BlastParser.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
-Static method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/BlastParser.html" title="class in compbio.pipeline._jpred">BlastParser</A>\r
-<DD>args[0] is assumed to be the name of a Blast output file\r
-<DT><A HREF="../compbio/pipeline/_jpred/JackHmmerHitParser.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
-Static method in 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/pipeline/_jpred/Pairwise.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
-Static method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/Pairwise.html" title="class in compbio.pipeline._jpred">Pairwise</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/OB.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
-Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/stat/collector/ExecutionStatCollector.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
-Static method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/ExecutionStatCollector.html" title="class in compbio.stat.collector">ExecutionStatCollector</A>\r
-<DD>Not in use\r
-<DT><A HREF="../compbio/stat/collector/StatDB.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
-Static method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/client/AAConClient.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
-Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/AAConClient.html" title="class in compbio.ws.client">AAConClient</A>\r
-<DD>Starts command line client, if no parameters are supplied prints help.\r
-<DT><A HREF="../compbio/ws/client/Jws2Client.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
-Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
-<DD>Starts command line client, if no parameter are supported print help.\r
-<DT><A HREF="../compbio/ws/client/WSTester.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
-Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A>\r
-<DD>Test JWS2 web services\r
-<DT><A HREF="../compbio/ws/server/SimpleWSPublisher.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
-Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server">SimpleWSPublisher</A>\r
-<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
-<DT><A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl"><B>Mcl</B></A> - Class in <A HREF="../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A><DD>&nbsp;<DT><A HREF="../compbio/runner/_impl/Mcl.html#Mcl(java.lang.String)"><B>Mcl(String)</B></A> - \r
-Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/engine/client/Util.html#mergeEnvVariables(java.util.Map, java.util.Map)"><B>mergeEnvVariables(Map&lt;String, String&gt;, Map&lt;String, String&gt;)</B></A> - \r
-Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa"><B>Metadata</B></A>&lt;<A HREF="../compbio/data/msa/Metadata.html" title="type parameter in Metadata">T</A>&gt; - Interface in <A HREF="../compbio/data/msa/package-summary.html">compbio.data.msa</A><DD>&nbsp;<DT><A HREF="../compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client"><B>MetadataHelper</B></A> - Class in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>&nbsp;<DT><A HREF="../compbio/ws/client/MetadataHelper.html#MetadataHelper()"><B>MetadataHelper()</B></A> - \r
-Constructor for class compbio.ws.client.<A HREF="../compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client">MetadataHelper</A>\r
-<DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><B>MsaWS</B></A>&lt;<A HREF="../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt; - Interface in <A HREF="../compbio/data/msa/package-summary.html">compbio.data.msa</A><DD>Multiple Sequence Alignment (MSA) Web Services Interface<DT><A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa"><B>Muscle</B></A> - Class in <A HREF="../compbio/runner/msa/package-summary.html">compbio.runner.msa</A><DD>&nbsp;<DT><A HREF="../compbio/runner/msa/Muscle.html#Muscle()"><B>Muscle()</B></A> - \r
-Constructor for class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
-<DD>Default options are
- 
- -clwstrict - write output in clustal format\r
-<DT><A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server"><B>MuscleWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/MuscleWS.html#MuscleWS()"><B>MuscleWS()</B></A> - \r
-Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
-<DD>&nbsp;\r
-</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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="index-12.html"><B>PREV LETTER</B></A>&nbsp;\r
-&nbsp;<A HREF="index-14.html"><B>NEXT LETTER</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-  <A HREF="../index.html?index-filesindex-13.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
-&nbsp;<A HREF="index-13.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
-&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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM 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
-\r
-</BODY>\r
-</HTML>\r