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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
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