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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-3.html
diff --git a/website/full_javadoc/index-files/index-3.html b/website/full_javadoc/index-files/index-3.html
new file mode 100644 (file)
index 0000000..e656e09
--- /dev/null
+++ b/website/full_javadoc/index-files/index-3.html
@@ -0,0 +1,426 @@
+<!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
+C-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="C-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-2.html"><B>PREV LETTER</B></A>&nbsp;\r
+&nbsp;<A HREF="index-4.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+  <A HREF="../index.html?index-filesindex-3.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
+&nbsp;<A HREF="index-3.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="_C_"><!-- --></A><H2>\r
+<B>C</B></H2>\r
+<DL>\r
+<DT><A HREF="../compbio/engine/local/ExecutableWrapper.html#call()"><B>call()</B></A> - \r
+Method in class compbio.engine.local.<A HREF="../compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</A>\r
+<DD>It is vital that output and error streams are captured immediately for
+ this call() to succeed.\r
+<DT><A HREF="../compbio/engine/local/LocalExecutorService.html#canAcceptMoreWork()"><B>canAcceptMoreWork()</B></A> - \r
+Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</A>\r
+<DD>If the Executor queue is empty\r
+<DT><A HREF="../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws"><B>CancelJob</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/CancelJob.html#CancelJob()"><B>CancelJob()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws">CancelJob</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/JManagement.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>\r
+<DD>Stop running the job <code>jobId</code> but leave its output untouched\r
+<DT><A HREF="../compbio/engine/AsyncExecutor.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
+Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>\r
+<DD>Stop running job.\r
+<DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
+Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html#cancelJob(java.lang.String, compbio.engine.cluster.drmaa.ClusterSession)"><B>cancelJob(String, ClusterSession)</B></A> - \r
+Static method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterUtil</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#cancelJob()"><B>cancelJob()</B></A> - \r
+Method in 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/engine/local/AsyncLocalRunner.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
+Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/local/LocalEngineUtil.html#cancelJob(java.util.concurrent.Future, java.lang.String)"><B>cancelJob(Future&lt;ConfiguredExecutable&lt;?&gt;&gt;, String)</B></A> - \r
+Static method in 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/LocalRunner.html#cancelJob()"><B>cancelJob()</B></A> - \r
+Method in 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/engine/SyncExecutor.html#cancelJob()"><B>cancelJob()</B></A> - \r
+Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>\r
+<DD>Stops running job.\r
+<DT><A HREF="../compbio/ws/server/ClustalOWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/ClustalWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/GenericMetadataService.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/MafftWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
+Method in 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/ws/server/MuscleWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/ProbconsWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/TcoffeeWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/WSUtil.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
+Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws"><B>CancelJobResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html#CancelJobResponse()"><B>CancelJobResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws">CancelJobResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/Category.html" title="class in compbio.data.msa"><B>Category</B></A> - Class in <A HREF="../compbio/data/msa/package-summary.html">compbio.data.msa</A><DD>Class that splits <A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client"><CODE>Services</CODE></A> to categories.<DT><A HREF="../compbio/data/msa/Category.html#CATEGORY_ALIGNMENT"><B>CATEGORY_ALIGNMENT</B></A> - \r
+Static variable in class compbio.data.msa.<A HREF="../compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</A>\r
+<DD>All of the Category names\r
+<DT><A HREF="../compbio/data/msa/Category.html#CATEGORY_CONSERVATION"><B>CATEGORY_CONSERVATION</B></A> - \r
+Static variable in class compbio.data.msa.<A HREF="../compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/Category.html#CATEGORY_DISORDER"><B>CATEGORY_DISORDER</B></A> - \r
+Static variable in class compbio.data.msa.<A HREF="../compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/client/WSTester.html#checkService(compbio.ws.client.Services)"><B>checkService(Services)</B></A> - \r
+Method in class compbio.ws.client.<A HREF="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A>\r
+<DD>Test JABA web service\r
+<DT><A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><B>ChunkHolder</B></A> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Represents a chunk of a string data together with the position in a file for
+ the next read operation.<DT><A HREF="../compbio/metadata/ChunkHolder.html#ChunkHolder(java.lang.String, long)"><B>ChunkHolder(String, long)</B></A> - \r
+Constructor for class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/Cleaner.html" title="class in compbio.engine"><B>Cleaner</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD><B>Deprecated.</B>&nbsp;<DT><A HREF="../compbio/engine/Cleaner.html#Cleaner()"><B>Cleaner()</B></A> - \r
+Constructor for class compbio.engine.<A HREF="../compbio/engine/Cleaner.html" title="class in compbio.engine">Cleaner</A>\r
+<DD><B>Deprecated.</B>&nbsp;&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#cleanProteinSequence(java.lang.String)"><B>cleanProteinSequence(String)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Remove all non AA chars from the sequence\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#cleanSequence(java.lang.String)"><B>cleanSequence(String)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Removes all whitespace chars in the sequence string\r
+<DT><A HREF="../compbio/engine/AsyncExecutor.html#cleanup(java.lang.String)"><B>cleanup(String)</B></A> - \r
+Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>\r
+<DD>Remove all files and a job directory for a jobid.\r
+<DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#cleanup(java.lang.String)"><B>cleanup(String)</B></A> - \r
+Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#cleanup()"><B>cleanup()</B></A> - \r
+Method in 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/engine/local/AsyncLocalRunner.html#cleanup(java.lang.String)"><B>cleanup(String)</B></A> - \r
+Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/local/LocalEngineUtil.html#cleanup(compbio.engine.client.ConfiguredExecutable)"><B>cleanup(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
+Static method in 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/LocalRunner.html#cleanup()"><B>cleanup()</B></A> - \r
+Method in 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/engine/SyncExecutor.html#cleanup()"><B>cleanup()</B></A> - \r
+Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>\r
+<DD>Clean up after the job\r
+<DT><A HREF="../compbio/data/sequence/FastaReader.html#close()"><B>close()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaReader.html" title="class in compbio.data.sequence">FastaReader</A>\r
+<DD>Call this method to close the connection to the input file if you want to
+ free up the resources.\r
+<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#close()"><B>close()</B></A> - \r
+Method 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/data/sequence/SequenceUtil.html#closeSilently(java.util.logging.Logger, java.io.Closeable)"><B>closeSilently(Logger, Closeable)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Closes the Closable and logs the exception if any\r
+<DT><A HREF="../compbio/ws/client/Services.html#CLUSTAL_INFO"><B>CLUSTAL_INFO</B></A> - \r
+Static variable in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/client/Services.html#CLUSTAL_OMEGA_INFO"><B>CLUSTAL_OMEGA_INFO</B></A> - \r
+Static variable in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><B>ClustalAlignmentUtil</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Tools to read and write clustal formated files<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#ClustalAlignmentUtil()"><B>ClustalAlignmentUtil()</B></A> - \r
+Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa"><B>ClustalO</B></A> - Class in <A HREF="../compbio/runner/msa/package-summary.html">compbio.runner.msa</A><DD>&nbsp;<DT><A HREF="../compbio/runner/msa/ClustalO.html#ClustalO()"><B>ClustalO()</B></A> - \r
+Constructor for class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>\r
+<DD>--threads=<n> Number of processors to use
+ 
+ -l, --log=<file> Log all non-essential output to this file\r
+<DT><A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server"><B>ClustalOWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/ClustalOWS.html#ClustalOWS()"><B>ClustalOWS()</B></A> - \r
+Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa"><B>ClustalW</B></A> - Class in <A HREF="../compbio/runner/msa/package-summary.html">compbio.runner.msa</A><DD>&nbsp;<DT><A HREF="../compbio/runner/msa/ClustalW.html#ClustalW()"><B>ClustalW()</B></A> - \r
+Constructor for class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server"><B>ClustalWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/ClustalWS.html#ClustalWS()"><B>ClustalWS()</B></A> - \r
+Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html#CLUSTER_STAT_IN_SEC"><B>CLUSTER_STAT_IN_SEC</B></A> - \r
+Static variable in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterUtil</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/client/ConfExecutable.html#CLUSTER_TASK_ID_PREFIX"><B>CLUSTER_TASK_ID_PREFIX</B></A> - \r
+Static variable 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/Configurator.html#CLUSTER_WORK_DIRECTORY"><B>CLUSTER_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/ClusterJobId.html" title="class in compbio.engine"><B>ClusterJobId</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>&nbsp;<DT><A HREF="../compbio/engine/ClusterJobId.html#ClusterJobId(java.lang.String)"><B>ClusterJobId(String)</B></A> - \r
+Constructor for class compbio.engine.<A HREF="../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa"><B>ClusterSession</B></A> - Class in <A HREF="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A><DD>&nbsp;<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa"><B>ClusterUtil</B></A> - Class in <A HREF="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A><DD>&nbsp;<DT><A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html#ClusterUtil()"><B>ClusterUtil()</B></A> - \r
+Constructor for class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterUtil</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/disorder/Disembl.html#COILS_EXPECTATION_THRESHOLD"><B>COILS_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>For the region to be considered disordered the values must exceed these\r
+<DT><A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client"><B>CommandBuilder</B></A>&lt;<A HREF="../compbio/engine/client/CommandBuilder.html" title="type parameter in CommandBuilder">T</A>&gt; - Class in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>&nbsp;<DT><A HREF="../compbio/engine/client/CommandBuilder.html#CommandBuilder(java.lang.String)"><B>CommandBuilder(String)</B></A> - \r
+Constructor for class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/pipeline/_jpred/Hit.EvalueComporator.html#compare(compbio.pipeline._jpred.Hit, compbio.pipeline._jpred.Hit)"><B>compare(Hit, Hit)</B></A> - \r
+Method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/Hit.EvalueComporator.html" title="class in compbio.pipeline._jpred">Hit.EvalueComporator</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/pipeline/_jpred/Hit.NumberComporator.html#compare(compbio.pipeline._jpred.Hit, compbio.pipeline._jpred.Hit)"><B>compare(Hit, Hit)</B></A> - \r
+Method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/Hit.NumberComporator.html" title="class in compbio.pipeline._jpred">Hit.NumberComporator</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/Range.html#compareTo(compbio.data.sequence.Range)"><B>compareTo(Range)</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/Score.html#compareTo(compbio.data.sequence.Score)"><B>compareTo(Score)</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/FilePuller.html#compareTo(java.util.concurrent.Delayed)"><B>compareTo(Delayed)</B></A> - \r
+Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/_structure/package-summary.html"><B>compbio.data._structure</B></A> - package compbio.data._structure<DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/package-summary.html"><B>compbio.data.msa.jaxws</B></A> - package compbio.data.msa.jaxws<DD>&nbsp;<DT><A HREF="../compbio/pipeline/_jpred/package-summary.html"><B>compbio.pipeline._jpred</B></A> - package compbio.pipeline._jpred<DD>&nbsp;<DT><A HREF="../compbio/runner/_jpred/package-summary.html"><B>compbio.runner._jpred</B></A> - package compbio.runner._jpred<DD>&nbsp;<DT><A HREF="../compbio/engine/conf/PropertyHelperManager.html#confDir"><B>confDir</B></A> - \r
+Static variable in class compbio.engine.conf.<A HREF="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client"><B>ConfExecutable</B></A>&lt;<A HREF="../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt; - Class in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>&nbsp;<DT><A HREF="../compbio/engine/client/ConfExecutable.html#ConfExecutable(compbio.engine.client.Executable, java.lang.String)"><B>ConfExecutable(Executable&lt;T&gt;, String)</B></A> - \r
+Constructor for 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/Configurator.html" title="class in compbio.engine"><B>Configurator</B></A> - Class in <A HREF="../compbio/engine/package-summary.html">compbio.engine</A><DD>&nbsp;<DT><A HREF="../compbio/engine/Configurator.html#Configurator()"><B>Configurator()</B></A> - \r
+Constructor for 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/client/ConfiguredExecutable.html" title="interface in compbio.engine.client"><B>ConfiguredExecutable</B></A>&lt;<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="type parameter in ConfiguredExecutable">T</A>&gt; - Interface in <A HREF="../compbio/engine/client/package-summary.html">compbio.engine.client</A><DD>&nbsp;<DT><A HREF="../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable)"><B>configureExecutable(Executable&lt;T&gt;)</B></A> - \r
+Static method 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/Configurator.html#configureExecutable(compbio.engine.client.Executable, java.util.List)"><B>configureExecutable(Executable&lt;T&gt;, List&lt;FastaSequence&gt;)</B></A> - \r
+Static method 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/Configurator.html#configureExecutable(compbio.engine.client.Executable, compbio.engine.client.Executable.ExecProvider)"><B>configureExecutable(Executable&lt;T&gt;, Executable.ExecProvider)</B></A> - \r
+Static method 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/ws/client/AAConClient.html#connect()"><B>connect()</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>Connects to a AACon web service by the host and the service name\r
+<DT><A HREF="../compbio/ws/client/Jws2Client.html#connect(java.lang.String, compbio.ws.client.Services)"><B>connect(String, Services)</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>Connects to a web service by the host and the service name web service
+ type\r
+<DT><A HREF="../compbio/ws/client/Jws2Client.html#connectToRegistry(java.lang.String)"><B>connectToRegistry(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>Get a connection of JABAWS registry\r
+<DT><A HREF="../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence"><B>ConservationMethod</B></A> - Enum in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Enumeration listing of all the supported methods.<DT><A HREF="../compbio/stat/servlet/StatisticCollector.html#contextDestroyed(javax.servlet.ServletContextEvent)"><B>contextDestroyed(ServletContextEvent)</B></A> - \r
+Method in class compbio.stat.servlet.<A HREF="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/SetExecutableFlag.html#contextDestroyed(javax.servlet.ServletContextEvent)"><B>contextDestroyed(ServletContextEvent)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/SetExecutableFlag.html" title="class in compbio.ws.server">SetExecutableFlag</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/ShutdownEngines.html#contextDestroyed(javax.servlet.ServletContextEvent)"><B>contextDestroyed(ServletContextEvent)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ShutdownEngines.html" title="class in compbio.ws.server">ShutdownEngines</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/stat/servlet/StatisticCollector.html#contextInitialized(javax.servlet.ServletContextEvent)"><B>contextInitialized(ServletContextEvent)</B></A> - \r
+Method in class compbio.stat.servlet.<A HREF="../compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/SetExecutableFlag.html#contextInitialized(javax.servlet.ServletContextEvent)"><B>contextInitialized(ServletContextEvent)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/SetExecutableFlag.html" title="class in compbio.ws.server">SetExecutableFlag</A>\r
+<DD>This listener is designed to run only once when the web application is
+ deployed to set executable flag for binaries.\r
+<DT><A HREF="../compbio/ws/server/ShutdownEngines.html#contextInitialized(javax.servlet.ServletContextEvent)"><B>contextInitialized(ServletContextEvent)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ShutdownEngines.html" title="class in compbio.ws.server">ShutdownEngines</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/client/Util.html#convertToAbsolute(java.lang.String)"><B>convertToAbsolute(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/metadata/RunnerConfig.html#copyAndValidateRConfig(compbio.metadata.RunnerConfig)"><B>copyAndValidateRConfig(RunnerConfig&lt;?&gt;)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/FastaSequence.html#countMatchesInSequence(java.lang.String, java.lang.String)"><B>countMatchesInSequence(String, String)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws"><B>CustomAlign</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html#CustomAlign()"><B>CustomAlign()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;T&gt;&gt;)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
+<DD>Align a list of sequences with options.\r
+<DT><A HREF="../compbio/ws/server/_MsaService.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;T&gt;&gt;)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/_MsaService.html" title="class in compbio.ws.server">_MsaService</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/ClustalOWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;ClustalO&gt;&gt;)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/ClustalWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;ClustalW&gt;&gt;)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/MafftWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;Mafft&gt;&gt;)</B></A> - \r
+Method in 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/ws/server/MuscleWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;Muscle&gt;&gt;)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/ProbconsWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;Probcons&gt;&gt;)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/TcoffeeWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;Tcoffee&gt;&gt;)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws"><B>CustomAlignResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html#CustomAlignResponse()"><B>CustomAlignResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws">CustomAlignResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws"><B>CustomAnalize</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/CustomAnalize.html#CustomAnalize()"><B>CustomAnalize()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws">CustomAnalize</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/SequenceAnnotation.html#customAnalize(java.util.List, java.util.List)"><B>customAnalize(List&lt;FastaSequence&gt;, List&lt;Option&lt;T&gt;&gt;)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A>\r
+<DD>Analyse the sequences according to custom settings defined in options
+ list.\r
+<DT><A HREF="../compbio/ws/server/DisemblWS.html#customAnalize(java.util.List, java.util.List)"><B>customAnalize(List&lt;FastaSequence&gt;, List&lt;Option&lt;Disembl&gt;&gt;)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/DisemblWS.html" title="class in compbio.ws.server">DisemblWS</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/GlobPlotWS.html#customAnalize(java.util.List, java.util.List)"><B>customAnalize(List&lt;FastaSequence&gt;, List&lt;Option&lt;GlobPlot&gt;&gt;)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/GlobPlotWS.html" title="class in compbio.ws.server">GlobPlotWS</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/ws/server/SequenceAnnotationService.html#customAnalize(java.util.List, java.util.List)"><B>customAnalize(List&lt;FastaSequence&gt;, List&lt;Option&lt;T&gt;&gt;)</B></A> - \r
+Method in class compbio.ws.server.<A HREF="../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server">SequenceAnnotationService</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/CustomAnalizeResponse.html" title="class in compbio.data.msa.jaxws"><B>CustomAnalizeResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/CustomAnalizeResponse.html#CustomAnalizeResponse()"><B>CustomAnalizeResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalizeResponse.html" title="class in compbio.data.msa.jaxws">CustomAnalizeResponse</A>\r
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