A B C D E F G H I J K L M N O P R S T U V W _

J

JABAService - Interface in compbio.data.msa

This is a marker interface, contains no methods

JackHmmerHitParser - Class in compbio.pipeline._jpred

Parser for the following files:

JackHmmerHitParser(String) - Constructor for class compbio.pipeline._jpred.JackHmmerHitParser

JManagement - Interface in compbio.data.msa

JnetAnnotation - Enum in compbio.data._structure

Job - Class in compbio.engine

Job(String, String, ConfiguredExecutable<?>) - Constructor for class compbio.engine.Job

JobExecutionException - Exception in compbio.metadata

JobExecutionException is thrown wherever the results of the calculation cannot be obtained.

JobExecutionException(String) - Constructor for exception compbio.metadata.JobExecutionException

JobExecutionException(Throwable) - Constructor for exception compbio.metadata.JobExecutionException

JobExecutionException(String, Throwable) - Constructor for exception compbio.metadata.JobExecutionException

JOBID - Static variable in class compbio.engine.cluster.drmaa.ClusterSession

Joblist - Class in compbio.stat.servlet

Joblist() - Constructor for class compbio.stat.servlet.Joblist

JobRunner - Class in compbio.engine.cluster.drmaa

Single cluster job runner class

JobRunner(ConfiguredExecutable<?>) - Constructor for class compbio.engine.cluster.drmaa.JobRunner

JobStat - Class in compbio.stat.collector

JobStatus - Enum in compbio.metadata

The status of the job.

JobSubmissionException - Exception in compbio.metadata

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

JobSubmissionException(Throwable) - Constructor for exception compbio.metadata.JobSubmissionException

JobSubmissionException(String, Throwable) - Constructor for exception compbio.metadata.JobSubmissionException

JobSubmissionExceptionBean - Class in compbio.data.msa.jaxws

This class was generated by the JAX-WS RI.

JobSubmissionExceptionBean() - Constructor for class compbio.data.msa.jaxws.JobSubmissionExceptionBean

Jpred4 - Class in compbio.pipeline._jpred

jpred --sequence OR --alignment [--db ] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help] jpred4 --sequence The path to the sequence (in FASTA format) you want to predict OR [--alignment ] The alignment which to use for prediction [--profile=] [--db ] Database to use for PSI-BLAST querying.

Jpred4() - Constructor for class compbio.pipeline._jpred.Jpred4

JpredAnnotation - Enum in compbio.data._structure

JpredResult - Class in compbio.data._structure

Jnet result jnetpred:-,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-, -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H ,H,H,-,-,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,-,-,H,H,H,H, -,-,-,-,-,-,-,-,-,-,-,-,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,- , 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, 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 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 , JNETSOL25:B,B,-,-,-,B,-,B,-,B,B,B,-,-,-,B,-,B,-,-,-,-,-,B,-,B,-,-,-,-,-,-, -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,B,-,B,- , B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,B,-,-,-,-,B,-,-,B,B,-,- ,B, JNETSOL5:-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,B,B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,- ,-,- JNETSOL0:-,-,-,-,-,-,B,-,-,B,-,B,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-, -,-,- ,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,-,B,-,-, JNETHMM:-,H,H,H,H,H,H,H,H,H,H, H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-,-, -,-,-,-,-,-,-,-,-,-,-,-,-,-,- ,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H, JNETPROPH:0.0110,0.1125,0.8552,0.0107 ,0.6245,0.3614,0.0120,0.8702,0.1238,0.0120 ,0.0193,0.9284,0.0708,0.0278,0.8703,0.1244 ,0.1591,0.7399,0.1456,0.2488,0.5824,0.1017, JNETPROPE:0.0107,0.6245,0.3614,0.0120 ,0.8702,0.1238,0.0120,0.9335,0.0656,0.0102 ,0.9586,0.0465,0.0094,0.9662,0.0433, ,0.1525,0.7103,0.1088,0.1181,0.7425,0.1784,

JpredResult() - Constructor for class compbio.data._structure.JpredResult

Jronn - Class in compbio.runner.disorder

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

JRONN_INFO - Static variable in enum compbio.ws.client.Services

JronnWS - Class in compbio.ws.server

JronnWS() - Constructor for class compbio.ws.server.JronnWS

Jws2Client - Class in compbio.ws.client

A command line client for JAva Bioinformatics Analysis Web Services