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  82 <A NAME="_J_"><!-- --></A><H2>\r
  83 <B>J</B></H2>\r
  84 <DL>\r
  85 <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
  86 Constructor for class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/JackHmmerHitParser.html" title="class in compbio.pipeline._jpred">JackHmmerHitParser</A>\r
  87 <DD>&nbsp;\r
  88 <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
  89 Constructor for class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
  90 <DD>&nbsp;\r
  91 <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
  92  cannot be obtained.<DT><A HREF="../compbio/metadata/JobExecutionException.html#JobExecutionException(java.lang.String)"><B>JobExecutionException(String)</B></A> - \r
  93 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A>\r
  94 <DD>&nbsp;\r
  95 <DT><A HREF="../compbio/metadata/JobExecutionException.html#JobExecutionException(java.lang.Throwable)"><B>JobExecutionException(Throwable)</B></A> - \r
  96 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A>\r
  97 <DD>&nbsp;\r
  98 <DT><A HREF="../compbio/metadata/JobExecutionException.html#JobExecutionException(java.lang.String, java.lang.Throwable)"><B>JobExecutionException(String, Throwable)</B></A> - \r
  99 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A>\r
 100 <DD>&nbsp;\r
 101 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#JOBID"><B>JOBID</B></A> - \r
 102 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
 103 <DD>&nbsp;\r
 104 <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
 105 Constructor for class compbio.stat.servlet.<A HREF="../compbio/stat/servlet/Joblist.html" title="class in compbio.stat.servlet">Joblist</A>\r
 106 <DD>&nbsp;\r
 107 <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
 108 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
 109 <DD>&nbsp;\r
 110 <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
 111  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
 112 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>\r
 113 <DD>&nbsp;\r
 114 <DT><A HREF="../compbio/metadata/JobSubmissionException.html#JobSubmissionException(java.lang.Throwable)"><B>JobSubmissionException(Throwable)</B></A> - \r
 115 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>\r
 116 <DD>&nbsp;\r
 117 <DT><A HREF="../compbio/metadata/JobSubmissionException.html#JobSubmissionException(java.lang.String, java.lang.Throwable)"><B>JobSubmissionException(String, Throwable)</B></A> - \r
 118 Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>\r
 119 <DD>&nbsp;\r
 120 <DT><A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws"><B>JobSubmissionExceptionBean</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/JobSubmissionExceptionBean.html#JobSubmissionExceptionBean()"><B>JobSubmissionExceptionBean()</B></A> - \r
 121 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws">JobSubmissionExceptionBean</A>\r
 122 <DD>&nbsp;\r
 123 <DT><A HREF="../compbio/pipeline/_jpred/Jpred4.html" title="class in compbio.pipeline._jpred"><B>Jpred4</B></A> - Class in <A HREF="../compbio/pipeline/_jpred/package-summary.html">compbio.pipeline._jpred</A><DD>jpred --sequence <fasta file> OR --alignment <clustalW alignment> [--db
 124  <database>] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help]
 125
 126  jpred4 --sequence <fasta file> The path to the sequence (in FASTA format) you
 127  want to predict OR
 128
 129  [--alignment <clustalW alignment>] The alignment which to use for prediction
 130
 131  [--profile=<path to HMM profile>]
 132
 133  [--db <database>] Database to use for PSI-BLAST querying.<DT><A HREF="../compbio/pipeline/_jpred/Jpred4.html#Jpred4()"><B>Jpred4()</B></A> - \r
 134 Constructor for class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/Jpred4.html" title="class in compbio.pipeline._jpred">Jpred4</A>\r
 135 <DD>&nbsp;\r
 136 <DT><A HREF="../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure"><B>JpredAnnotation</B></A> - Enum in <A HREF="../compbio/data/_structure/package-summary.html">compbio.data._structure</A><DD>&nbsp;<DT><A HREF="../compbio/data/_structure/JpredResult.html" title="class in compbio.data._structure"><B>JpredResult</B></A> - Class in <A HREF="../compbio/data/_structure/package-summary.html">compbio.data._structure</A><DD>Jnet result
 137
 138  jnetpred:-,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-,
 139  -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H
 140  ,H,H,-,-,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,-,-,H,H,H,H,
 141  -,-,-,-,-,-,-,-,-,-,-,-,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-
 142  , JNETCONF:7,3,7,9,9,9,9,9,9,9,7,5,2,6,6,3,6,7,5,1,0,5,3,3,6,4,6,6,7,7,7,7,7,
 143  7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,6,3,6,8,9,9,9,9,9,9,9
 144  7,3,7,7,6,2,4,4,1,5,7,8,7,7,7,7,7,7,7,6,5,3,5,6,6,6,4,0,0,2,1,3,5,7,7,7,7,7,7
 145  , JNETSOL25:B,B,-,-,-,B,-,B,-,B,B,B,-,-,-,B,-,B,-,-,-,-,-,B,-,B,-,-,-,-,-,-,
 146  -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,B,-,B,-
 147  , B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,B,-,-,-,-,B,-,-,B,B,-,-
 148  ,B,
 149  JNETSOL5:-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,B,B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,-
 150  ,-,-
 151  JNETSOL0:-,-,-,-,-,-,B,-,-,B,-,B,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,
 152  -,-,- ,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,-,B,-,-,
 153  JNETHMM:-,H,H,H,H,H,H,H,H,H,H,
 154  H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-,-,
 155  -,-,-,-,-,-,-,-,-,-,-,-,-,-,-
 156  ,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H,
 157  JNETPROPH:0.0110,0.1125,0.8552,0.0107
 158  ,0.6245,0.3614,0.0120,0.8702,0.1238,0.0120
 159  ,0.0193,0.9284,0.0708,0.0278,0.8703,0.1244
 160  ,0.1591,0.7399,0.1456,0.2488,0.5824,0.1017,
 161  JNETPROPE:0.0107,0.6245,0.3614,0.0120
 162  ,0.8702,0.1238,0.0120,0.9335,0.0656,0.0102
 163  ,0.9586,0.0465,0.0094,0.9662,0.0433,
 164  ,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
 165 Constructor for class compbio.data._structure.<A HREF="../compbio/data/_structure/JpredResult.html" title="class in compbio.data._structure">JpredResult</A>\r
 166 <DD>&nbsp;\r
 167 <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
 168
 169  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
 170 Constructor for class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>\r
 171 <DD>&nbsp;\r
 172 <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
 173 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/JronnWS.html" title="class in compbio.ws.server">JronnWS</A>\r
 174 <DD>&nbsp;\r
 175 <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
 176 <HR>\r
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