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updated javadoc for the system as well as new redirect address for download app
[jabaws.git] / website / full_javadoc / index-files / index-12.html
diff --git a/website/full_javadoc/index-files/index-12.html b/website/full_javadoc/index-files/index-12.html
new file mode 100644 (file)
index 0000000..e0e30e5
--- /dev/null
+++ b/website/full_javadoc/index-files/index-12.html
@@ -0,0 +1,216 @@
+<!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 Wed Dec 07 12:30:43 GMT 2011 -->\r
+<TITLE>\r
+L-Index\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2011-12-07">\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="L-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-11.html"><B>PREV LETTER</B></A>&nbsp;\r
+&nbsp;<A HREF="index-13.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+  <A HREF="../index.html?index-filesindex-12.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
+&nbsp;<A HREF="index-12.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="_L_"><!-- --></A><H2>\r
+<B>L</B></H2>\r
+<DL>\r
+<DT><A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata"><B>Limit</B></A>&lt;<A HREF="../compbio/metadata/Limit.html" title="type parameter in Limit">T</A>&gt; - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>A value object containing a maximum number of sequences and a maximum average
+ sequence length for a preset.<DT><A HREF="../compbio/metadata/Limit.html#Limit(int, int, java.lang.String)"><B>Limit(int, int, String)</B></A> - \r
+Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
+<DD>Instantiate the limit\r
+<DT><A HREF="../compbio/metadata/Limit.html#Limit(int, int, java.lang.String, boolean)"><B>Limit(int, int, String, boolean)</B></A> - \r
+Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><B>LimitExceededException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>This exception is thrown if the task larger in size that the limit that
+ applies to the calculation.<DT><A HREF="../compbio/metadata/LimitExceededException.html#LimitExceededException(java.lang.String)"><B>LimitExceededException(String)</B></A> - \r
+Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws"><B>LimitExceededExceptionBean</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/LimitExceededExceptionBean.html#LimitExceededExceptionBean()"><B>LimitExceededExceptionBean()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><B>LimitsManager</B></A>&lt;<A HREF="../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>&gt; - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>A collection of Limits<DT><A HREF="../compbio/metadata/LimitsManager.html#LimitsManager()"><B>LimitsManager()</B></A> - \r
+Constructor for class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/client/RunConfiguration.html#load(java.io.InputStream)"><B>load(InputStream)</B></A> - \r
+Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/LoadBalancer.html" title="class in compbio.engine"><B>LoadBalancer</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>This class decides where to execute the job.<DT><A HREF="../compbio/engine/client/Util.html#loadExecutable(java.lang.String)"><B>loadExecutable(String)</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/engine/client/ConfExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)"><B>loadRunConfiguration(RunConfiguration)</B></A> - \r
+Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/client/ConfExecutable.html#loadRunConfiguration(java.io.InputStream)"><B>loadRunConfiguration(InputStream)</B></A> - \r
+Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#loadRunConfiguration(java.io.InputStream)"><B>loadRunConfiguration(InputStream)</B></A> - \r
+Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)"><B>loadRunConfiguration(RunConfiguration)</B></A> - \r
+Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)"><B>loadRunConfiguration(RunConfiguration)</B></A> - \r
+Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)"><B>loadRunConfiguration(RunConfiguration)</B></A> - \r
+Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)"><B>loadRunConfiguration(RunConfiguration)</B></A> - \r
+Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
+<DT><A HREF="../compbio/metadata/PresetManager.html#LOCAL_ENGINE_LIMIT_PRESET"><B>LOCAL_ENGINE_LIMIT_PRESET</B></A> - \r
+Static variable in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/Configurator.html#LOCAL_WORK_DIRECTORY"><B>LOCAL_WORK_DIRECTORY</B></A> - \r
+Static variable in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local"><B>LocalEngineUtil</B></A> - Class in <A HREF="../compbio/engine/local/package-summary.html">compbio.engine.local</A><DD>&nbsp;<DT><A HREF="../compbio/engine/local/LocalEngineUtil.html#LocalEngineUtil()"><B>LocalEngineUtil()</B></A> - \r
+Constructor for class compbio.engine.local.<A HREF="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local"><B>LocalExecutorService</B></A> - Class in <A HREF="../compbio/engine/local/package-summary.html">compbio.engine.local</A><DD>&nbsp;<DT><A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local"><B>LocalRunner</B></A> - Class in <A HREF="../compbio/engine/local/package-summary.html">compbio.engine.local</A><DD>&nbsp;<DT><A HREF="../compbio/engine/local/LocalRunner.html#LocalRunner(compbio.engine.client.ConfiguredExecutable)"><B>LocalRunner(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
+Constructor for class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/Util.html#log"><B>log</B></A> - \r
+Static variable in class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/_WSLogger.html#log(compbio.util.Timer, java.lang.String)"><B>log(Timer, String)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/_WSLogger.html" title="class in compbio.ws.server">_WSLogger</A>\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
+<DT><A HREF="../compbio/ws/server/_WSLogger.html#log(compbio.util.Timer, java.lang.String, java.lang.String)"><B>log(Timer, String, String)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/_WSLogger.html" title="class in compbio.ws.server">_WSLogger</A>\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
+<DT><A HREF="../compbio/ws/server/_WSLogger.html#logAll(compbio.util.Timer, java.lang.String)"><B>logAll(Timer, String)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/_WSLogger.html" title="class in compbio.ws.server">_WSLogger</A>\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
+<DT><A HREF="../compbio/ws/server/_WSLogger.html#logFine(compbio.util.Timer, java.lang.String)"><B>logFine(Timer, String)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/_WSLogger.html" title="class in compbio.ws.server">_WSLogger</A>\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
+<DT><A HREF="../compbio/runner/disorder/Disembl.html#LOOPS_EXPECTATION_THRESHOLD"><B>LOOPS_EXPECTATION_THRESHOLD</B></A> - \r
+Variable in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</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-11.html"><B>PREV LETTER</B></A>&nbsp;\r
+&nbsp;<A HREF="index-13.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+  <A HREF="../index.html?index-filesindex-12.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
+&nbsp;<A HREF="index-12.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