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

A

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

Valid Amino acids

addOption(Option<T>) - Method in class compbio.metadata.RunnerConfig

addOptionNames(String...) - Method in class compbio.metadata.Option

Adds an option to the optionName list

addOptionNames(String...) - Method in class compbio.metadata.Parameter

addParameter(Parameter<T>) - Method in class compbio.metadata.RunnerConfig

addParameter(String) - Method in class compbio.runner._SkeletalCommandBuilder

addParameters(List<String>) - Method in class compbio.engine.client.ConfExecutable

addParameters(List<String>) - Method in interface compbio.engine.client.Executable

Adds parameter to the list of parameters for a native executable

addParameters(List<String>) - Method in class compbio.engine.client.SkeletalExecutable

addParameters(List<String>) - Method in class compbio.runner._impl.NetNglyc

addParameters(String[]) - Method in class compbio.runner._SkeletalCommandBuilder

addParameters(List<String>) - Method in class compbio.runner._SkeletalCommandBuilder

addParameters(List<String>) - Method in class compbio.runner.msa.Mafft

Mafft input must always be the last parameter!

addParams(List<String>) - Method in class compbio.engine.client.CommandBuilder

addPossibleValues(String...) - Method in class compbio.metadata.Parameter

addTask(ConfiguredExecutable<?>, Future<ConfiguredExecutable<?>>) - Static method in class compbio.engine.SubmissionManager

Align - Class in compbio.data.msa.jaxws

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

align(List<FastaSequence>) - Method in interface compbio.data.msa.MsaWS

Align a list of sequences with default settings.

align(List<FastaSequence>) - Method in class compbio.ws.server.ClustalWS

align(List<FastaSequence>) - Method in class compbio.ws.server.MafftWS

align(List<FastaSequence>) - Method in class compbio.ws.server.MuscleWS

align(List<FastaSequence>) - Method in class compbio.ws.server.ProbconsWS

align(List<FastaSequence>) - Method in class compbio.ws.server.TcoffeeWS

align(List<FastaSequence>, ConfiguredExecutable<T>, Logger, WebServiceContext, String, Limit<T>) - Static method in class compbio.ws.server.WSUtil

Alignment - Class in compbio.data.sequence

Multiple sequence alignment.

Alignment(List<FastaSequence>, Program, char) - Constructor for class compbio.data.sequence.Alignment

Alignment(List<FastaSequence>, AlignmentMetadata) - Constructor for class compbio.data.sequence.Alignment

AlignmentMetadata - Class in compbio.data.sequence

Alignment metadata e.g.

AlignmentMetadata(Program, char) - Constructor for class compbio.data.sequence.AlignmentMetadata

AlignResponse - Class in compbio.data.msa.jaxws

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

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

Same as AA pattern but with two additional letters - XU

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

Ambiguous nucleotide

Argument<T> - Interface in compbio.metadata

An unmodifiable view for the options and parameters, with one exception - it allows to set a value

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

argumentsToCommandString(List<? extends Option<?>>, RunnerConfig<? extends Executable<?>>) - Static method in class compbio.runner.OptionCombinator

AsyncExecutor - Interface in compbio.engine

An asynchronous executor engine, capable of running, cancelling, obtaining results calculated by a native executable wrapper in Executable interface.

AsyncJobRunner - Class in compbio.engine.cluster.drmaa

Single cluster job runner class

AsyncJobRunner() - Constructor for class compbio.engine.cluster.drmaa.AsyncJobRunner

AsyncLocalRunner - Class in compbio.engine.local

AsyncLocalRunner() - Constructor for class compbio.engine.local.AsyncLocalRunner

awaitTermination(long, TimeUnit) - Method in class compbio.engine.local._TrackingExecutor