- JABAService - Interface in compbio.data.msa
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This is a marker interface, contains no methods
- JABAWS_VERSION - Static variable in interface compbio.data.msa.JABAService
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- JManagement - Interface in compbio.data.msa
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- Job - Class in compbio.engine
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- Job(String, String, ConfiguredExecutable<?>) - Constructor for class compbio.engine.Job
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- jobdir - Variable in class compbio.stat.collector.JobDirectory
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- JobDirectory - Class in compbio.stat.collector
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- JobDirectory(File) - Constructor for class compbio.stat.collector.JobDirectory
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- JobExecutionException - Exception in compbio.metadata
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JobExecutionException is thrown wherever the results of the calculation
cannot be obtained.
- JobExecutionException(String) - Constructor for exception compbio.metadata.JobExecutionException
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- JobExecutionException(Throwable) - Constructor for exception compbio.metadata.JobExecutionException
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- JobExecutionException(String, Throwable) - Constructor for exception compbio.metadata.JobExecutionException
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- jobId - Variable in class compbio.data.msa.jaxws.CancelJob
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- jobId - Variable in class compbio.data.msa.jaxws.GetAnnotation
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- jobId - Variable in class compbio.data.msa.jaxws.GetJobStatus
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- jobId - Variable in class compbio.data.msa.jaxws.GetResult
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- jobId - Variable in class compbio.data.msa.jaxws.PullExecStatistics
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- jobId - Variable in class compbio.engine.cluster.drmaa.ClusterRunner
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- JOBID - Static variable in class compbio.engine.cluster.drmaa.ClusterSession
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- jobId - Variable in class compbio.engine.cluster.drmaa.JobRunner
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- jobId - Variable in class compbio.engine.ClusterJobId
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- jobId - Variable in class compbio.engine.Job
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- jobinfo - Variable in class compbio.engine.cluster.drmaa.StatisticManager
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- Joblist - Class in compbio.stat.servlet
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- Joblist() - Constructor for class compbio.stat.servlet.Joblist
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- jobname - Variable in class compbio.stat.collector.JobStat
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- JobRunner - Class in compbio.engine.cluster.drmaa
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Single cluster job runner class
- JobRunner(ConfiguredExecutable<?>) - Constructor for class compbio.engine.cluster.drmaa.JobRunner
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- jobs - Static variable in class compbio.engine.cluster.drmaa.ClusterSession
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- JobStat - Class in compbio.stat.collector
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- JobStat(Services, String, String, long, long, long, long, boolean, boolean) - Constructor for class compbio.stat.collector.JobStat
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- JobStat(String) - Constructor for class compbio.stat.collector.JobStat
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- JobStatus - Enum in compbio.metadata
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The status of the job.
- JobStatus() - Constructor for enum compbio.metadata.JobStatus
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- JobSubmissionException - Exception in compbio.metadata
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Exception for generic problems with JobSubmission it is often thrown as a
wrapper for the lower level exceptions like IOException or DrmaaException.
- JobSubmissionException(String) - Constructor for exception compbio.metadata.JobSubmissionException
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- JobSubmissionException(Throwable) - Constructor for exception compbio.metadata.JobSubmissionException
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- JobSubmissionException(String, Throwable) - Constructor for exception compbio.metadata.JobSubmissionException
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- JobSubmissionExceptionBean - Class in compbio.data.msa.jaxws
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This class was generated by the JAX-WS RI.
- JobSubmissionExceptionBean() - Constructor for class compbio.data.msa.jaxws.JobSubmissionExceptionBean
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- jobtempl - Variable in class compbio.engine.cluster.drmaa.ClusterRunner
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- jobtempl - Variable in class compbio.engine.cluster.drmaa.JobRunner
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- Jronn - Class in compbio.runner.disorder
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Command line
java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
- Jronn() - Constructor for class compbio.runner.disorder.Jronn
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- JRONN_INFO - Static variable in enum compbio.ws.client.Services
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- JRONN_WRONG_FORMAT_MESSAGE - Static variable in class compbio.data.sequence.SequenceUtil
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- JronnWS - Class in compbio.ws.server
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- JronnWS() - Constructor for class compbio.ws.server.JronnWS
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- JT_ABANDONED - Static variable in class compbio.stat.servlet.Joblist
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- JT_ALL - Static variable in class compbio.stat.servlet.Joblist
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- JT_CANCELLED - Static variable in class compbio.stat.servlet.Joblist
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- JT_FAILED - Static variable in class compbio.stat.servlet.Joblist
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- JT_INCOMPLETE - Static variable in class compbio.stat.servlet.Joblist
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- justStructP - Static variable in class compbio.data.sequence.RNAStructReader
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- Jws2Client - Class in compbio.ws.client
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A command line client for JAva Bioinformatics Analysis Web Services
- Jws2Client(String[]) - Constructor for class compbio.ws.client.Jws2Client
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Connects to the service and do the job as requested, if something goes
wrong reports or/and prints usage help.