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waitForFile(long)
- Method in class compbio.engine.
FilePuller
waitForJob(String)
- Method in class compbio.engine.cluster.drmaa.
ClusterSession
waitForJob(String, long)
- Method in class compbio.engine.cluster.drmaa.
ClusterSession
waitForResult(ClusterSession, String)
- Static method in class compbio.engine.cluster.drmaa.
ClusterUtil
waitForResult()
- Method in class compbio.engine.cluster.drmaa.
JobRunner
waitForResult()
- Method in class compbio.engine.local.
LocalRunner
waitForResult()
- Method in interface compbio.engine.
SyncExecutor
Call to this method block for as long as it is required for an executable to finish its job.
wasAborted()
- Method in class compbio.engine.cluster.drmaa.
StatisticManager
WHITE_SPACE
- Static variable in class compbio.data.sequence.
SequenceUtil
A whitespace character: [\t\n\x0B\f\r]
write(TreeSet<Score>, Writer)
- Static method in class compbio.data.sequence.
Score
Outputs the List of Score objects into the Output stream.
write(RunConfiguration)
- Static method in class compbio.engine.client.
RunConfiguration
write(Object, OutputStream)
- Method in class compbio.engine.conf.
RunnerConfigMarshaller
writeAndValidate(Object, String, OutputStream)
- Method in class compbio.engine.conf.
RunnerConfigMarshaller
writeClustalAlignment(Writer, Alignment)
- Static method in class compbio.data.sequence.
ClustalAlignmentUtil
Write Clustal formatted alignment Limitations: does not record the consensus.
writeFasta(OutputStream, List<FastaSequence>, int)
- Static method in class compbio.data.sequence.
SequenceUtil
Writes list of FastaSequeces into the outstream formatting the sequence so that it contains width chars on each line
writeFasta(OutputStream, List<FastaSequence>)
- Static method in class compbio.data.sequence.
SequenceUtil
Writes FastaSequence in the file, each sequence will take one line only
writeFastaKeepTheStream(OutputStream, List<FastaSequence>, int)
- Static method in class compbio.data.sequence.
SequenceUtil
writeFile(String, String, String, boolean)
- Static method in class compbio.engine.client.
Util
writeInput(List<FastaSequence>, ConfiguredExecutable<?>)
- Static method in class compbio.runner.
Util
writeMarker(String, JobStatus)
- Static method in class compbio.engine.client.
Util
writeOut(Writer)
- Method in class compbio.data.sequence.
ScoreManager.ScoreHolder
writeOut(Writer)
- Method in class compbio.data.sequence.
ScoreManager
writeStatFile(String, String)
- Static method in class compbio.engine.client.
Util
WrongParameterException
- Exception in
compbio.metadata
WrongParameterException is thrown wherever the
RunnerConfig
object does not match the actual runnable or then attempting to set the value of
Argument
to invalid value.
WrongParameterException(Option<?>)
- Constructor for exception compbio.metadata.
WrongParameterException
WrongParameterException(String)
- Constructor for exception compbio.metadata.
WrongParameterException
WrongParameterException(Throwable)
- Constructor for exception compbio.metadata.
WrongParameterException
WrongParameterException(String, Throwable)
- Constructor for exception compbio.metadata.
WrongParameterException
WrongParameterExceptionBean
- Class in
compbio.data.msa.jaxws
This class was generated by the JAX-WS RI.
WrongParameterExceptionBean()
- Constructor for class compbio.data.msa.jaxws.
WrongParameterExceptionBean
WSTester
- Class in
compbio.ws.client
Class for testing web services
WSTester(String, PrintWriter)
- Constructor for class compbio.ws.client.
WSTester
Construct an instance of JABAWS tester
WSUtil
- Class in
compbio.ws.server
WSUtil()
- Constructor for class compbio.ws.server.
WSUtil
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