-A-Index -

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

-A

AA - -Static variable in class compbio.data.sequence.SequenceUtil -: Valid Amino acids -
AAConClient - Class in compbio.ws.client: A command line client for AACon web service
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 -
addPossibleValues(String...) - -Method in class compbio.metadata.Parameter -: -
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. -
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. -
AnalizeResponse - Class in compbio.data.msa.jaxws
AnalizeResponse() - -Constructor for class compbio.data.msa.jaxws.AnalizeResponse -: -
Argument<T> - Interface in compbio.metadata: An unmodifiable view for the options and parameters, with one exception - it - allows to set a value
asMap() - -Method in class compbio.data.sequence.ScoreManager -: -
asSet() - -Method in class compbio.data.sequence.ScoreManager -: -