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  73 <!--   -->
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  75 <h2 class="title">J</h2>
  76 <dl>
  77 <dt><a href="../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa"><span class="typeNameLink">JABAService</span></a> - Interface in <a href="../compbio/data/msa/package-summary.html">compbio.data.msa</a></dt>
  78 <dd>
  79 <div class="block">This is a marker interface, contains no methods</div>
  80 </dd>
  81 <dt><span class="memberNameLink"><a href="../compbio/data/msa/JABAService.html#JABAWS_VERSION">JABAWS_VERSION</a></span> - Static variable in interface compbio.data.msa.<a href="../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</a></dt>
  82 <dd>&nbsp;</dd>
  83 <dt><a href="../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa"><span class="typeNameLink">JManagement</span></a> - Interface in <a href="../compbio/data/msa/package-summary.html">compbio.data.msa</a></dt>
  84 <dd>&nbsp;</dd>
  85 <dt><a href="../compbio/engine/Job.html" title="class in compbio.engine"><span class="typeNameLink">Job</span></a> - Class in <a href="../compbio/engine/package-summary.html">compbio.engine</a></dt>
  86 <dd>&nbsp;</dd>
  87 <dt><span class="memberNameLink"><a href="../compbio/engine/Job.html#Job-java.lang.String-java.lang.String-compbio.engine.client.ConfiguredExecutable-">Job(String, String, ConfiguredExecutable&lt;?&gt;)</a></span> - Constructor for class compbio.engine.<a href="../compbio/engine/Job.html" title="class in compbio.engine">Job</a></dt>
  88 <dd>&nbsp;</dd>
  89 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobDirectory.html#jobdir">jobdir</a></span> - Variable in class compbio.stat.collector.<a href="../compbio/stat/collector/JobDirectory.html" title="class in compbio.stat.collector">JobDirectory</a></dt>
  90 <dd>&nbsp;</dd>
  91 <dt><a href="../compbio/stat/collector/JobDirectory.html" title="class in compbio.stat.collector"><span class="typeNameLink">JobDirectory</span></a> - Class in <a href="../compbio/stat/collector/package-summary.html">compbio.stat.collector</a></dt>
  92 <dd>&nbsp;</dd>
  93 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobDirectory.html#JobDirectory-java.io.File-">JobDirectory(File)</a></span> - Constructor for class compbio.stat.collector.<a href="../compbio/stat/collector/JobDirectory.html" title="class in compbio.stat.collector">JobDirectory</a></dt>
  94 <dd>&nbsp;</dd>
  95 <dt><a href="../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata"><span class="typeNameLink">JobExecutionException</span></a> - Exception in <a href="../compbio/metadata/package-summary.html">compbio.metadata</a></dt>
  96 <dd>
  97 <div class="block">JobExecutionException is thrown wherever the results of the calculation
  98  cannot be obtained.</div>
  99 </dd>
 100 <dt><span class="memberNameLink"><a href="../compbio/metadata/JobExecutionException.html#JobExecutionException-java.lang.String-">JobExecutionException(String)</a></span> - Constructor for exception compbio.metadata.<a href="../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</a></dt>
 101 <dd>&nbsp;</dd>
 102 <dt><span class="memberNameLink"><a href="../compbio/metadata/JobExecutionException.html#JobExecutionException-java.lang.Throwable-">JobExecutionException(Throwable)</a></span> - Constructor for exception compbio.metadata.<a href="../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</a></dt>
 103 <dd>&nbsp;</dd>
 104 <dt><span class="memberNameLink"><a href="../compbio/metadata/JobExecutionException.html#JobExecutionException-java.lang.String-java.lang.Throwable-">JobExecutionException(String, Throwable)</a></span> - Constructor for exception compbio.metadata.<a href="../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</a></dt>
 105 <dd>&nbsp;</dd>
 106 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/CancelJob.html#jobId">jobId</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws">CancelJob</a></dt>
 107 <dd>&nbsp;</dd>
 108 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetAnnotation.html#jobId">jobId</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetAnnotation.html" title="class in compbio.data.msa.jaxws">GetAnnotation</a></dt>
 109 <dd>&nbsp;</dd>
 110 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetJobStatus.html#jobId">jobId</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws">GetJobStatus</a></dt>
 111 <dd>&nbsp;</dd>
 112 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/GetResult.html#jobId">jobId</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws">GetResult</a></dt>
 113 <dd>&nbsp;</dd>
 114 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/PullExecStatistics.html#jobId">jobId</a></span> - Variable in class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</a></dt>
 115 <dd>&nbsp;</dd>
 116 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterRunner.html#jobId">jobId</a></span> - Variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterRunner.html" title="class in compbio.engine.cluster.drmaa">ClusterRunner</a></dt>
 117 <dd>&nbsp;</dd>
 118 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterSession.html#JOBID">JOBID</a></span> - 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></dt>
 119 <dd>&nbsp;</dd>
 120 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/JobRunner.html#jobId">jobId</a></span> - Variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</a></dt>
 121 <dd>&nbsp;</dd>
 122 <dt><span class="memberNameLink"><a href="../compbio/engine/ClusterJobId.html#jobId">jobId</a></span> - Variable in class compbio.engine.<a href="../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</a></dt>
 123 <dd>&nbsp;</dd>
 124 <dt><span class="memberNameLink"><a href="../compbio/engine/Job.html#jobId">jobId</a></span> - Variable in class compbio.engine.<a href="../compbio/engine/Job.html" title="class in compbio.engine">Job</a></dt>
 125 <dd>&nbsp;</dd>
 126 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/StatisticManager.html#jobinfo">jobinfo</a></span> - Variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</a></dt>
 127 <dd>&nbsp;</dd>
 128 <dt><a href="../compbio/stat/servlet/Joblist.html" title="class in compbio.stat.servlet"><span class="typeNameLink">Joblist</span></a> - Class in <a href="../compbio/stat/servlet/package-summary.html">compbio.stat.servlet</a></dt>
 129 <dd>&nbsp;</dd>
 130 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/Joblist.html#Joblist--">Joblist()</a></span> - Constructor for class compbio.stat.servlet.<a href="../compbio/stat/servlet/Joblist.html" title="class in compbio.stat.servlet">Joblist</a></dt>
 131 <dd>&nbsp;</dd>
 132 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#jobname">jobname</a></span> - Variable in class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 133 <dd>&nbsp;</dd>
 134 <dt><a href="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa"><span class="typeNameLink">JobRunner</span></a> - Class in <a href="../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</a></dt>
 135 <dd>
 136 <div class="block">Single cluster job runner class</div>
 137 </dd>
 138 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/JobRunner.html#JobRunner-compbio.engine.client.ConfiguredExecutable-">JobRunner(ConfiguredExecutable&lt;?&gt;)</a></span> - Constructor for class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</a></dt>
 139 <dd>&nbsp;</dd>
 140 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterSession.html#jobs">jobs</a></span> - 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></dt>
 141 <dd>&nbsp;</dd>
 142 <dt><a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector"><span class="typeNameLink">JobStat</span></a> - Class in <a href="../compbio/stat/collector/package-summary.html">compbio.stat.collector</a></dt>
 143 <dd>&nbsp;</dd>
 144 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#JobStat-compbio.ws.client.Services-java.lang.String-java.lang.String-long-long-long-long-boolean-boolean-">JobStat(Services, String, String, long, long, long, long, boolean, boolean)</a></span> - Constructor for class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 145 <dd>&nbsp;</dd>
 146 <dt><span class="memberNameLink"><a href="../compbio/stat/collector/JobStat.html#JobStat-java.lang.String-">JobStat(String)</a></span> - Constructor for class compbio.stat.collector.<a href="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</a></dt>
 147 <dd>&nbsp;</dd>
 148 <dt><a href="../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><span class="typeNameLink">JobStatus</span></a> - Enum in <a href="../compbio/metadata/package-summary.html">compbio.metadata</a></dt>
 149 <dd>
 150 <div class="block">The status of the job.</div>
 151 </dd>
 152 <dt><span class="memberNameLink"><a href="../compbio/metadata/JobStatus.html#JobStatus--">JobStatus()</a></span> - Constructor for enum compbio.metadata.<a href="../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</a></dt>
 153 <dd>&nbsp;</dd>
 154 <dt><a href="../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata"><span class="typeNameLink">JobSubmissionException</span></a> - Exception in <a href="../compbio/metadata/package-summary.html">compbio.metadata</a></dt>
 155 <dd>
 156 <div class="block">Exception for generic problems with JobSubmission it is often thrown as a
 157  wrapper for the lower level exceptions like IOException or DrmaaException.</div>
 158 </dd>
 159 <dt><span class="memberNameLink"><a href="../compbio/metadata/JobSubmissionException.html#JobSubmissionException-java.lang.String-">JobSubmissionException(String)</a></span> - Constructor for exception compbio.metadata.<a href="../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></dt>
 160 <dd>&nbsp;</dd>
 161 <dt><span class="memberNameLink"><a href="../compbio/metadata/JobSubmissionException.html#JobSubmissionException-java.lang.Throwable-">JobSubmissionException(Throwable)</a></span> - Constructor for exception compbio.metadata.<a href="../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></dt>
 162 <dd>&nbsp;</dd>
 163 <dt><span class="memberNameLink"><a href="../compbio/metadata/JobSubmissionException.html#JobSubmissionException-java.lang.String-java.lang.Throwable-">JobSubmissionException(String, Throwable)</a></span> - Constructor for exception compbio.metadata.<a href="../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></dt>
 164 <dd>&nbsp;</dd>
 165 <dt><a href="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws"><span class="typeNameLink">JobSubmissionExceptionBean</span></a> - Class in <a href="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></dt>
 166 <dd>
 167 <div class="block">This class was generated by the JAX-WS RI.</div>
 168 </dd>
 169 <dt><span class="memberNameLink"><a href="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html#JobSubmissionExceptionBean--">JobSubmissionExceptionBean()</a></span> - Constructor for class compbio.data.msa.jaxws.<a href="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws">JobSubmissionExceptionBean</a></dt>
 170 <dd>&nbsp;</dd>
 171 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/ClusterRunner.html#jobtempl">jobtempl</a></span> - Variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/ClusterRunner.html" title="class in compbio.engine.cluster.drmaa">ClusterRunner</a></dt>
 172 <dd>&nbsp;</dd>
 173 <dt><span class="memberNameLink"><a href="../compbio/engine/cluster/drmaa/JobRunner.html#jobtempl">jobtempl</a></span> - Variable in class compbio.engine.cluster.drmaa.<a href="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</a></dt>
 174 <dd>&nbsp;</dd>
 175 <dt><a href="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder"><span class="typeNameLink">Jronn</span></a> - Class in <a href="../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</a></dt>
 176 <dd>
 177 <div class="block">Command line
 178
 179  java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out</div>
 180 </dd>
 181 <dt><span class="memberNameLink"><a href="../compbio/runner/disorder/Jronn.html#Jronn--">Jronn()</a></span> - Constructor for class compbio.runner.disorder.<a href="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</a></dt>
 182 <dd>&nbsp;</dd>
 183 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Services.html#JRONN_INFO">JRONN_INFO</a></span> - Static variable in enum compbio.ws.client.<a href="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</a></dt>
 184 <dd>&nbsp;</dd>
 185 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/SequenceUtil.html#JRONN_WRONG_FORMAT_MESSAGE">JRONN_WRONG_FORMAT_MESSAGE</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></dt>
 186 <dd>&nbsp;</dd>
 187 <dt><a href="../compbio/ws/server/JronnWS.html" title="class in compbio.ws.server"><span class="typeNameLink">JronnWS</span></a> - Class in <a href="../compbio/ws/server/package-summary.html">compbio.ws.server</a></dt>
 188 <dd>&nbsp;</dd>
 189 <dt><span class="memberNameLink"><a href="../compbio/ws/server/JronnWS.html#JronnWS--">JronnWS()</a></span> - Constructor for class compbio.ws.server.<a href="../compbio/ws/server/JronnWS.html" title="class in compbio.ws.server">JronnWS</a></dt>
 190 <dd>&nbsp;</dd>
 191 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/Joblist.html#JT_ABANDONED">JT_ABANDONED</a></span> - Static variable in class compbio.stat.servlet.<a href="../compbio/stat/servlet/Joblist.html" title="class in compbio.stat.servlet">Joblist</a></dt>
 192 <dd>&nbsp;</dd>
 193 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/Joblist.html#JT_ALL">JT_ALL</a></span> - Static variable in class compbio.stat.servlet.<a href="../compbio/stat/servlet/Joblist.html" title="class in compbio.stat.servlet">Joblist</a></dt>
 194 <dd>&nbsp;</dd>
 195 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/Joblist.html#JT_CANCELLED">JT_CANCELLED</a></span> - Static variable in class compbio.stat.servlet.<a href="../compbio/stat/servlet/Joblist.html" title="class in compbio.stat.servlet">Joblist</a></dt>
 196 <dd>&nbsp;</dd>
 197 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/Joblist.html#JT_FAILED">JT_FAILED</a></span> - Static variable in class compbio.stat.servlet.<a href="../compbio/stat/servlet/Joblist.html" title="class in compbio.stat.servlet">Joblist</a></dt>
 198 <dd>&nbsp;</dd>
 199 <dt><span class="memberNameLink"><a href="../compbio/stat/servlet/Joblist.html#JT_INCOMPLETE">JT_INCOMPLETE</a></span> - Static variable in class compbio.stat.servlet.<a href="../compbio/stat/servlet/Joblist.html" title="class in compbio.stat.servlet">Joblist</a></dt>
 200 <dd>&nbsp;</dd>
 201 <dt><span class="memberNameLink"><a href="../compbio/data/sequence/RNAStructReader.html#justStructP">justStructP</a></span> - Static variable in class compbio.data.sequence.<a href="../compbio/data/sequence/RNAStructReader.html" title="class in compbio.data.sequence">RNAStructReader</a></dt>
 202 <dd>&nbsp;</dd>
 203 <dt><a href="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client"><span class="typeNameLink">Jws2Client</span></a> - Class in <a href="../compbio/ws/client/package-summary.html">compbio.ws.client</a></dt>
 204 <dd>
 205 <div class="block">A command line client for JAva Bioinformatics Analysis Web Services</div>
 206 </dd>
 207 <dt><span class="memberNameLink"><a href="../compbio/ws/client/Jws2Client.html#Jws2Client-java.lang.String:A-">Jws2Client(String[])</a></span> - Constructor for class compbio.ws.client.<a href="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</a></dt>
 208 <dd>
 209 <div class="block">Connects to the service and do the job as requested, if something goes
 210  wrong reports or/and prints usage help.</div>
 211 </dd>
 212 </dl>
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