git://source.jalview.org / jabaws.git / blobdiff
? search:
summary | shortlog | log | commit | commitdiff | tree
raw | inline | side by side
remove old project javadoc
[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
deleted file mode 100644 (file)
index 4afad04..0000000
--- a/website/full_javadoc/index-files/index-12.html
+++ /dev/null
@@ -1,216 +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
-L-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="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