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A

AA - Static variable in class compbio.data.sequence.SequenceUtil
Valid Amino acids
addAnnotation(T, ArrayList<Float>) - Method in class compbio.data.sequence.MultiAnnotatedSequence
 
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(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
 
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(List<FastaSequence>) - Method in interface compbio.data.msa.Annotation
Analyse the sequences.
AnnotatedSequence - Class in compbio.data.sequence
 
AnnotatedSequence(String, String, float[]) - Constructor for class compbio.data.sequence.AnnotatedSequence
 
AnnotatedSequence(FastaSequence, float[]) - Constructor for class compbio.data.sequence.AnnotatedSequence
 
Annotation<T> - Interface in compbio.data.msa
Interface for tools that results to one or more annotation to sequence(s)
Argument<T> - Interface in compbio.metadata
An unmodifiable view for the options and parameters, with one exception - it allows to set a value

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