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+A

+
+
AA - +Static variable in class compbio.data.sequence.SequenceUtil +
Valid Amino acids +
AACON_INFO - +Static variable in enum compbio.ws.client.Services +
  +
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 +
  +
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