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O

OK - Static variable in class compbio.ws.client.WSTester

oneLineAlignmentLength - Static variable in class compbio.data.sequence.ClustalAlignmentUtil

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

openInputStream(String) - Static method in class compbio.data.sequence.SequenceUtil

Reads and parses Fasta or Clustal formatted file into a list of FastaSequence objects

operating - Static variable in class compbio.ws.server.RegistryWS

Stores tested and passed (the test) services and their testing time

Option<T> - Class in compbio.metadata

Command line option/flag or multiple exclusive options with no value.

Option() - Constructor for class compbio.metadata.Option

Option(String, String) - Constructor for class compbio.metadata.Option

option - Variable in class compbio.metadata.Preset

OptionCombinator - Class in compbio.runner

This class solve the following problems.

OptionCombinator(RunnerConfig<? extends Executable<?>>) - Constructor for class compbio.runner.OptionCombinator

optionNames - Variable in class compbio.metadata.Option

options - Variable in class compbio.data.msa.jaxws.CustomAlign

options - Variable in class compbio.data.msa.jaxws.CustomAnalize

options - Variable in class compbio.data.msa.jaxws.CustomFold

options - Variable in class compbio.metadata.RunnerConfig

optionsToCommandString(List<Option<?>>) - Method in class compbio.runner.OptionCombinator

optionToCommandString(Option<?>) - Static method in class compbio.runner.OptionCombinator

os - Variable in class compbio.engine.local.StreamGobbler

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

Output

OUTPUT - Static variable in class compbio.engine.client.SkeletalExecutable

outputFile - Variable in class compbio.engine.client.SkeletalExecutable

outputkey - Static variable in class compbio.ws.client.Constraints

OutputType() - Constructor for enum compbio.engine.local.StreamGobbler.OutputType

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