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

W

waitForFile(long) - Method in class compbio.engine.FilePuller

waitForJob(String) - Method in class compbio.engine.cluster.drmaa.ClusterRunner

waitForJob(String) - Method in class compbio.engine.cluster.drmaa.ClusterSession

waitForJob(String, long) - Method in class compbio.engine.cluster.drmaa.ClusterSession

waitForJob(String) - Method in class compbio.engine.cluster.drmaa.JobRunner

waitForResult(ClusterSession, String) - Static method in class compbio.engine.cluster.drmaa.ClusterEngineUtil

waitForResult() - Method in class compbio.engine.cluster.drmaa.ClusterRunner

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

watcher - Variable in class compbio.engine.FilePuller

webService - Variable in class compbio.stat.collector.JobStat

WHITE_SPACE - Static variable in class compbio.data.sequence.SequenceUtil

A whitespace character: [\t\n\x0B\f\r]

workDirectory - Variable in class compbio.engine.client.ConfExecutable

workDirectory - Variable in class compbio.engine.client.RunConfiguration

Working directory

workDirectory - Variable in class compbio.engine.cluster.drmaa.ClusterRunner

workDirectory - Variable in class compbio.engine.cluster.drmaa.JobRunner

workDirectory - Variable in class compbio.engine.local.LocalRunner

workDirectory - Variable in class compbio.stat.collector.DirCleaner

workingDirectory - Variable in class compbio.stat.collector.ExecutionStatCollector

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

writeClustal(OutputStream, List<FastaSequence>, char) - Static method in class compbio.data.sequence.SequenceUtil

writeClustalAlignment(Writer, Alignment) - Static method in class compbio.data.sequence.ClustalAlignmentUtil

Write Clustal formatted alignment Limitations: does not record the consensus.

writeClustalInput(List<FastaSequence>, ConfiguredExecutable<?>, char) - Static method in class compbio.runner.RunnerUtil

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.EngineUtil

writeFile(String, String, String, boolean) - Static method in class compbio.engine.client.Util

writeInput(List<FastaSequence>, ConfiguredExecutable<?>) - Static method in class compbio.runner.RunnerUtil

writeInput(List<FastaSequence>, ConfiguredExecutable<?>) - Static method in class compbio.runner.Util

writeMarker(String, JobStatus) - Static method in class compbio.engine.client.EngineUtil

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

writeOut(Writer, ScoreManager) - Static method in class compbio.ws.client.AAConClient

Outputs AAcon results into the file represented by the outStream

writeOut(Writer, Alignment) - Static method in class compbio.ws.client.IOHelper

Outputs clustal formatted alignment into the file represented by the outStream

writeOut(Writer, ScoreManager) - Static method in class compbio.ws.client.IOHelper

Outputs AAcon results into the file represented by the outStream

writer - Variable in class compbio.ws.client.WSTester

writeStatFile(String, String) - Static method in class compbio.engine.client.EngineUtil

writeStatFile(String, String) - Static method in class compbio.engine.client.Util

writeStatToDB() - Method in class compbio.stat.collector.ExecutionStatCollector

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

wsContext - Variable in class compbio.ws.server.RegistryWS

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

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