BioArray (BioFSharp)

BioArray Module

Namespace: BioFSharp
Assembly: BioFSharp.dll

This module contains the BioArray type and its according functions. The BioArray type is an array of objects using the IBioItem interface

Types

Type	Description
BioArray<'a>	Array of objects using the IBioItem interface

Functions and values

Function or value	Description
`complement nucs` Full Usage: `complement nucs` Parameters: nucs : `BioArray<Nucleotide>` Returns: `BioArray<Nucleotide>`	Create the complement DNA or cDNA (from RNA) strand. For example, the sequence "ATGC" is converted to "TACG" nucs : `BioArray<Nucleotide>` Returns: `BioArray<Nucleotide>`
`initAverageMass` Full Usage: `initAverageMass` Returns: `BioArray<IBioItem> -> float`	Returns a function to calculate the average mass of the given sequence !memoization Returns: `BioArray<IBioItem> -> float`
`initAverageMassWith state` Full Usage: `initAverageMassWith state` Parameters: state : `float` Returns: `BioArray<IBioItem> -> float`	Returns a function to calculate the average mass of the given sequence and initial value (e.g. H2O) !memoization state : `float` Returns: `BioArray<IBioItem> -> float`
`initMonoisoMass` Full Usage: `initMonoisoMass` Returns: `BioArray<IBioItem> -> float`	Returns a function to calculate the monoisotopic mass of the given sequence !memoization Returns: `BioArray<IBioItem> -> float`
`initMonoisoMassWith state` Full Usage: `initMonoisoMassWith state` Parameters: state : `float` Returns: `BioArray<IBioItem> -> float`	Returns a function to calculate the monoisotopic mass of the given sequence and initial value (e.g. H2O) !memoization state : `float` Returns: `BioArray<IBioItem> -> float`
`initSampleBy rnd compositionVector` Full Usage: `initSampleBy rnd compositionVector` Parameters: rnd : `Random` compositionVector : `int[]` Returns: `unit -> AminoAcidSymbol`	rnd : `Random` compositionVector : `int[]` Returns: `unit -> AminoAcidSymbol`
`isEqual a b` Full Usage: `isEqual a b` Parameters: a : `'a[]` b : `'a[]` Returns: `int`	Compares the elemens of two biosequence a : `'a[]` b : `'a[]` Returns: `int`
`mapInTriplets mapping input` Full Usage: `mapInTriplets mapping input` Parameters: mapping : `'a * 'a * 'a -> 'a0` input : `BioArray<'a>` Returns: `'a0[]`	Builts a new collection whose elements are the result of applying the given function to each triplet of the collection. mapping : `'a * 'a * 'a -> 'a0` input : `BioArray<'a>` Returns: `'a0[]`
`ofAminoAcidString s` Full Usage: `ofAminoAcidString s` Parameters: s : `'a` Returns: `BioArray<AminoAcid>`	Generates amino acid sequence of one-letter-code raw string s : `'a` Returns: `BioArray<AminoAcid>`
`ofAminoAcidStringWithOptionConverter converter s` Full Usage: `ofAminoAcidStringWithOptionConverter converter s` Parameters: converter : `AminoAcidOptionConverter` s : `'a` Returns: `BioArray<AminoAcid>`	Generates amino acid sequence of one-letter-code string using given OptionConverter converter : `AminoAcidOptionConverter` s : `'a` Returns: `BioArray<AminoAcid>`
`ofAminoAcidSymbolString s` Full Usage: `ofAminoAcidSymbolString s` Parameters: s : `'a` Returns: `BioArray<AminoAcidSymbol>`	Generates amino acid symbol sequence of one-letter-code raw string s : `'a` Returns: `BioArray<AminoAcidSymbol>`
`ofNucleotideString s` Full Usage: `ofNucleotideString s` Parameters: s : `'a` Returns: `BioArray<Nucleotide>`	Generates nucleotide sequence of one-letter-code raw string s : `'a` Returns: `BioArray<Nucleotide>`
`ofNucleotideStringWithOptionConverter converter s` Full Usage: `ofNucleotideStringWithOptionConverter converter s` Parameters: converter : `NucleotideOptionConverter` s : `'a` Returns: `BioArray<Nucleotide>`	Generates nucleotide sequence of one-letter-code string using given OptionConverter converter : `NucleotideOptionConverter` s : `'a` Returns: `BioArray<Nucleotide>`
`reverse nucs` Full Usage: `reverse nucs` Parameters: nucs : `BioArray<Nucleotide>` Returns: `BioArray<Nucleotide>`	Create the reverse DNA or RNA strand. For example, the sequence "ATGC" is converted to "CGTA" nucs : `BioArray<Nucleotide>` Returns: `BioArray<Nucleotide>`
`reverseComplement nucs` Full Usage: `reverseComplement nucs` Parameters: nucs : `BioArray<Nucleotide>` Returns: `BioArray<Nucleotide>`	Create the reverse complement strand meaning antiparallel DNA strand or the cDNA (from RNA) respectivly. For example, the sequence "ATGC" is converted to "GCAT". "Antiparallel" combines the two functions "Complement" and "Inverse". nucs : `BioArray<Nucleotide>` Returns: `BioArray<Nucleotide>`
`toAverageMass bs` Full Usage: `toAverageMass bs` Parameters: bs : `BioArray<'a>` Returns: `float`	Returns average mass of the given sequence bs : `BioArray<'a>` Returns: `float`
`toAverageMassWith state bs` Full Usage: `toAverageMassWith state bs` Parameters: state : `float` bs : `BioArray<'a>` Returns: `float`	Returns average mass of the given sequence and initial value (e.g. H2O) state : `float` bs : `BioArray<'a>` Returns: `float`
`toCompositionVector input` Full Usage: `toCompositionVector input` Parameters: input : `BioArray<'a>` Returns: `int[]`	Creates an array with information about the abundacies of the distinct BioItems by converting the symbol of the BioItem to an integer and incrementing the given integer. To decrease the size of the resulting array by still having a fast performance, all indices are shifted by 65. Therefore to call the abundancy of a given BioItem, use "Resultcompositionvector.[(BioItem.symbol bioitem) - 65]" input : `BioArray<'a>` Returns: `int[]`
`toMonoisotopicMass bs` Full Usage: `toMonoisotopicMass bs` Parameters: bs : `BioArray<'a>` Returns: `float`	Returns monoisotopic mass of the given sequence bs : `BioArray<'a>` Returns: `float`
`toMonoisotopicMassWith state bs` Full Usage: `toMonoisotopicMassWith state bs` Parameters: state : `float` bs : `BioArray<'a>` Returns: `float`	Returns monoisotopic mass of the given sequence and initial value (e.g. H2O) state : `float` bs : `BioArray<'a>` Returns: `float`
`toRelCompositionVector input` Full Usage: `toRelCompositionVector input` Parameters: input : `BioArray<'a>` Returns: `float[]`	Creates an array with information about the abundacies of the distinct BioItems by converting the symbol of the BioItem to an integer and incrementing the given integer. To decrease the size of the resulting array by still having a fast performance, all indices are shifted by 65. Therefore to call the abundancy of a given BioItem, use "Resultcompositionvector.[(BioItem.symbol bioitem) - 65]" input : `BioArray<'a>` Returns: `float[]`
`toString bs` Full Usage: `toString bs` Parameters: bs : `BioArray<'a>` Returns: `string`	Returns string of one-letter-code bs : `BioArray<'a>` Returns: `string`
`transcribeCodingStrand nucs` Full Usage: `transcribeCodingStrand nucs` Parameters: nucs : `BioArray<Nucleotide>` Returns: `BioArray<Nucleotide>`	Transcribe a given DNA coding strand (5'-----3') nucs : `BioArray<Nucleotide>` Returns: `BioArray<Nucleotide>`
`transcribeTemplateStrand nucs` Full Usage: `transcribeTemplateStrand nucs` Parameters: nucs : `BioArray<Nucleotide>` Returns: `BioArray<Nucleotide>`	Transcribe a given DNA template strand (3'-----5') nucs : `BioArray<Nucleotide>` Returns: `BioArray<Nucleotide>`
`translate nucleotideOffset rnaSeq` Full Usage: `translate nucleotideOffset rnaSeq` Parameters: nucleotideOffset : `int` rnaSeq : `BioArray<Nucleotide>` Returns: `BioArray<AminoAcid>`	translates nucleotide sequence to aminoacid sequence nucleotideOffset : `int` rnaSeq : `BioArray<Nucleotide>` Returns: `BioArray<AminoAcid>`