-A-Index -

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-A

AA - -Static variable in class compbio.data.sequence.SequenceUtil -: Valid Amino acids -
AACon - Class in compbio.runner.conservation: Command line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
AACon() - -Constructor for class compbio.runner.conservation.AACon -: -
AAConClient - Class in compbio.ws.client: A command line client for AACon web service
AAConWS - Class in compbio.ws.server
AAConWS() - -Constructor for class compbio.ws.server.AAConWS -: -
addOption(Option<T>) - -Method in class compbio.metadata.RunnerConfig -: Adds Option to the internal list of options -
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 -: Adds parameter to the internal parameter list -
addParameter(String) - -Method in class compbio.runner._SkeletalCommandBuilder -: Deprecated. -
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 -: Deprecated. -
addParameters(List<String>) - -Method in class compbio.runner._SkeletalCommandBuilder -: Deprecated. -
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._MsaService -: -
align(List<FastaSequence>) - -Method in class compbio.ws.server.ClustalOWS -: -
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, 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 -
Analize - Class in compbio.data.msa.jaxws
Analize() - -Constructor for class compbio.data.msa.jaxws.Analize -: -
analize(List<FastaSequence>) - -Method in interface compbio.data.msa.SequenceAnnotation -: Analyse the sequences. -
analize(List<FastaSequence>) - -Method in class compbio.ws.server.AAConWS -: -
analize(List<FastaSequence>) - -Method in class compbio.ws.server.SequenceAnnotationService -: -
analize(List<FastaSequence>, ConfiguredExecutable<T>, Logger, String, Limit<T>) - -Static method in class compbio.ws.server.WSUtil -: -
AnalizeResponse - Class in compbio.data.msa.jaxws
AnalizeResponse() - -Constructor for class compbio.data.msa.jaxws.AnalizeResponse -: -
AnnualStat - Class in compbio.stat.servlet
AnnualStat() - -Constructor for class compbio.stat.servlet.AnnualStat -: -
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 -: -
asMap() - -Method in class compbio.data.sequence.ScoreManager -: -
asSet() - -Method in class compbio.data.sequence.ScoreManager -: -
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 -: -