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adding clustalO documentation
[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
index a54536b..f172cbe 100644 (file)
--- a/website/full_javadoc/index-files/index-10.html
+++ b/website/full_javadoc/index-files/index-10.html
@@ -2,12 +2,12 @@
 <!--NewPage-->\r
 <HTML>\r
 <HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\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="2010-02-17">\r
+<META NAME="date" CONTENT="2011-08-12">\r
 \r
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
 \r
@@ -82,7 +82,10 @@ function windowTitle()
 <A NAME="_J_"><!-- --></A><H2>\r
 <B>J</B></H2>\r
 <DL>\r
-<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
+<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
@@ -95,16 +98,16 @@ Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobExecu
 <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/data/msa/jaxws/JobExecutionExceptionBean.html" title="class in compbio.data.msa.jaxws"><B>JobExecutionExceptionBean</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/JobExecutionExceptionBean.html#JobExecutionExceptionBean()"><B>JobExecutionExceptionBean()</B></A> - \r
-Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/JobExecutionExceptionBean.html" title="class in compbio.data.msa.jaxws">JobExecutionExceptionBean</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/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
+<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
@@ -161,7 +164,15 @@ Constructor for class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpre
  ,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/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 Jalview Web Services version 2<DT><A HREF="../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client"><B>Jws2Client.Services</B></A> - Enum in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>List of web services currently supported by JWS2</DL>\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