Index

Modules: bioseq/alignment, bioseq/aminoAcid, bioseq/biallelic, bioseq/fasta, bioseq/matrix, bioseq/nexus, bioseq/nucleotide, bioseq/parserMacro, bioseq/phylip, bioseq/seqRecord, bioseq/sequence, bioseq/structure, bioseq/twoBitSequence.

API symbols

`$`:

• alignment: `$`[T](a: Alignment[T]): string
• matrix: `$`[T](m: Matrix[T]): string
• seqRecord: `$`[T](s: SeqRecord[T]): string
• twoBitSequence: `$`[T](s: TwoBitSequence[T]): string

`[]=`:

• matrix: `[]=`[T](m: var Matrix[T]; row, col: int; s: T)
• twoBitSequence: `[]=`[T](s: var TwoBitSequence[T]; loc: int; val: T)

`[]`:

• matrix: `[]`[T](m: Matrix[T]; row, col: int): T
• matrix: `[]`[T](m: var Matrix[T]; row, col: int): var T
• twoBitSequence: `[]`[T](s: TwoBitSequence[T]; loc: int): T

aaA:

• AminoAcid.aaA

aaB:

• AminoAcid.aaB

aaC:

• AminoAcid.aaC

aaD:

• AminoAcid.aaD

aaE:

• AminoAcid.aaE

aaF:

• AminoAcid.aaF

aaG:

• AminoAcid.aaG

aaH:

• AminoAcid.aaH

aaI:

• AminoAcid.aaI

aaK:

• AminoAcid.aaK

aaL:

• AminoAcid.aaL

aaM:

• AminoAcid.aaM

aaN:

• AminoAcid.aaN

aaO:

• AminoAcid.aaO

aaP:

• AminoAcid.aaP

aaQ:

• AminoAcid.aaQ

aaR:

• AminoAcid.aaR

aaS:

• AminoAcid.aaS

aaStp:

• AminoAcid.aaStp

aaT:

• AminoAcid.aaT

aaU:

• AminoAcid.aaU

aaV:

• AminoAcid.aaV

aaW:

• AminoAcid.aaW

aaX:

• AminoAcid.aaX

aaY:

• AminoAcid.aaY

aaZ:

• AminoAcid.aaZ

abreviation:

• aminoAcid: abreviation(a: AminoAcid): string

Alignment:

• alignment: Alignment

alleleCount:

• alignment: alleleCount[T: Nucleotide](align: Alignment[T]; col: int): int
• alignment: alleleCount[T: StrictNucleotide](align: Alignment[T]; col: int): int

AminoAcid:

• aminoAcid: AminoAcid

aminoAcidAbreviation:

• aminoAcid: aminoAcidAbreviation

aminoAcidChar:

• aminoAcid: aminoAcidChar

aminoAcidDefinition:

• aminoAcid: aminoAcidDefinition

AnyNucleotide:

• nucleotide: AnyNucleotide

Biallelic:

• biallelic: Biallelic

bitSeq:

• twoBitSequence: bitSeq[T](s: TwoBitSequence[T]): BitArray

byte:

• nucleotide: byte(n: DNA): byte
• nucleotide: byte(n: RNA): byte
• nucleotide: byte(n: StrictDNA): byte
• nucleotide: byte(n: StrictRNA): byte

colCharacterCount:

• alignment: colCharacterCount[T](a: Alignment[T]; col: int; chars: set[T]): int

cols:

• matrix: cols[T](m: Matrix[T]): int

complement:

• nucleotide: complement(n: DNA): DNA
• nucleotide: complement(n: RNA): RNA
• nucleotide: complement(n: StrictDNA): StrictDNA
• nucleotide: complement(n: StrictRNA): StrictRNA
• sequence: complement[T: AnyNucleotide](s: seq[T]): seq[T]
• sequence: complement[T: AnyNucleotide](s: var seq[T])

concat:

• matrix: concat[T](matrices: varargs[Matrix[T]]): Matrix[T]

db0:

• DiploidBiallelic.db0

db1:

• DiploidBiallelic.db1

db2:

• DiploidBiallelic.db2

dbGap:

• DiploidBiallelic.dbGap

dbUnk:

• DiploidBiallelic.dbUnk

definition:

• aminoAcid: definition(a: AminoAcid): string

diffBase:

• nucleotide: diffBase(a, b: AnyNucleotide): bool

dim:

• matrix: dim[T](m: Matrix[T]): (int, int)

DiploidBiallelic:

• biallelic: DiploidBiallelic

diploidBiallelicChar:

• biallelic: diploidBiallelicChar

diploidStructureChar:

• structure: diploidStructureChar

DNA:

• nucleotide: DNA

dnaA:

• DNA.dnaA

dnaB:

• DNA.dnaB

dnaByte:

• nucleotide: dnaByte

dnaC:

• DNA.dnaC

dnaChar:

• nucleotide: dnaChar

dnaComplement:

• nucleotide: dnaComplement

dnaD:

• DNA.dnaD

dnaG:

• DNA.dnaG

dnaGap:

• DNA.dnaGap

dnaH:

• DNA.dnaH

dnaK:

• DNA.dnaK

dnaM:

• DNA.dnaM

dnaN:

• DNA.dnaN

dnaR:

• DNA.dnaR

dnaS:

• DNA.dnaS

dnaT:

• DNA.dnaT

dnaUnambiguousSet:

• nucleotide: dnaUnambiguousSet

dnaUnk:

• DNA.dnaUnk

dnaV:

• DNA.dnaV

dnaW:

• DNA.dnaW

dnaY:

• DNA.dnaY

FastaError:

• fasta: FastaError

filterColumns:

• alignment: filterColumns[T](a: Alignment[T]; filter: set[T]): Alignment[T]

filterSamples:

• alignment: filterSamples[T](a: Alignment[T]; samples: seq[string]): Alignment[T]

gCode1:

• GeneticCode.gCode1

gCode10:

• GeneticCode.gCode10

gCode11:

• GeneticCode.gCode11

gCode12:

• GeneticCode.gCode12

gCode13:

• GeneticCode.gCode13

gCode14:

• GeneticCode.gCode14

gCode16:

• GeneticCode.gCode16

gCode2:

• GeneticCode.gCode2

gCode21:

• GeneticCode.gCode21

gCode22:

• GeneticCode.gCode22

gCode23:

• GeneticCode.gCode23

gCode24:

• GeneticCode.gCode24

gCode25:

• GeneticCode.gCode25

gCode26:

• GeneticCode.gCode26

gCode27:

• GeneticCode.gCode27

gCode28:

• GeneticCode.gCode28

gCode29:

• GeneticCode.gCode29

gCode3:

• GeneticCode.gCode3

gCode30:

• GeneticCode.gCode30

gCode31:

• GeneticCode.gCode31

gCode33:

• GeneticCode.gCode33

gCode4:

• GeneticCode.gCode4

gCode5:

• GeneticCode.gCode5

gCode6:

• GeneticCode.gCode6

gCode9:

• GeneticCode.gCode9

generateParser:

• parserMacro: generateParser(c: char; k: openArray[char]; v: typed): untyped

GeneticCode:

• aminoAcid: GeneticCode

HaploidBiallelic:

• biallelic: HaploidBiallelic

haploidBiallelicChar:

• biallelic: haploidBiallelicChar

haploidStructureChar:

• structure: haploidStructureChar

hb0:

• HaploidBiallelic.hb0

hb1:

• HaploidBiallelic.hb1

hbGap:

• HaploidBiallelic.hbGap

hbUnk:

• HaploidBiallelic.hbUnk

Interleaved:

• PhylipFormat.Interleaved

isAdenine:

• nucleotide: isAdenine(n: AnyNucleotide): bool

isCytosine:

• nucleotide: isCytosine(n: AnyNucleotide): bool

isGuanine:

• nucleotide: isGuanine(n: AnyNucleotide): bool

isPurine:

• nucleotide: isPurine(n: AnyNucleotide): bool

isPyrimidine:

• nucleotide: isPyrimidine(n: AnyNucleotide): bool

isThymine:

• nucleotide: isThymine(n: DNA | StrictDNA): bool

isUracil:

• nucleotide: isUracil(n: RNA | StrictRNA): bool

iterFastaFile:

• fasta: iterFastaFile(path: string; typ: typedesc): SeqRecord[typ]

iterFastaStream:

• fasta: iterFastaStream(stream: Stream; typ: typedesc): SeqRecord[typ]

iterFastaString:

• fasta: iterFastaString(str: string; typ: typedesc): SeqRecord[typ]

iterPhylipFile:

• phylip: iterPhylipFile(path: string; typ: typedesc; fmt: PhylipFormat): Alignment[typ]

iterPhylipStream:

• phylip: iterPhylipStream(stream: Stream; typ: typedesc; fmt: PhylipFormat): Alignment[ typ]

iterPhylipString:

• phylip: iterPhylipString(str: string; typ: typedesc; fmt: PhylipFormat): Alignment[typ]

knownBase:

• nucleotide: knownBase(n: AnyNucleotide): bool

len:

• twoBitSequence: len[T](s: TwoBitSequence[T]): int

Matrix:

• matrix: Matrix

nchars:

• alignment: nchars[T](a: Alignment[T]): int

newAlignment:

• alignment: newAlignment[T](nseqs, nchars: int): Alignment[T]
• alignment: newAlignment[T](nseqs, nchars: int; ids: seq[string]; data: seq[T]): Alignment[T]

newMatrix:

• matrix: newMatrix[T](rows, cols: int): Matrix[T]
• matrix: newMatrix[T](rows, cols: int; data: seq[T]): Matrix[T]

newTwoBitSequence:

• twoBitSequence: newTwoBitSequence[T](len: int): TwoBitSequence[T]

nseqs:

• alignment: nseqs[T](a: Alignment[T]): int

Nucleotide:

• nucleotide: Nucleotide

numPolymorphicSites:

• alignment: numPolymorphicSites[T](align: Alignment[T]): int

parseChar:

• aminoAcid: parseChar(c: char; T: typedesc[AminoAcid]): AminoAcid
• biallelic: parseChar(c: char; typ: typedesc[DiploidBiallelic]): DiploidBiallelic
• biallelic: parseChar(c: char; typ: typedesc[HaploidBiallelic]): HaploidBiallelic
• nucleotide: parseChar(c: char; typ: typedesc[DNA]): DNA
• nucleotide: parseChar(c: char; typ: typedesc[RNA]): RNA
• nucleotide: parseChar(c: char; typ: typedesc[StrictDNA]): StrictDNA
• nucleotide: parseChar(c: char; typ: typedesc[StrictRNA]): StrictRNA

parsePhylipFile:

• phylip: parsePhylipFile(path: string; typ: typedesc; fmt: PhylipFormat): Alignment[typ]

parsePhylipStream:

• phylip: parsePhylipStream(stream: Stream; typ: typedesc; fmt: PhylipFormat): Alignment[ typ]

parsePhylipString:

• phylip: parsePhylipString(str: string; typ: typedesc; fmt: PhylipFormat): Alignment[typ]

PhylipError:

• phylip: PhylipError

PhylipFormat:

• phylip: PhylipFormat

reverseComplement:

• sequence: reverseComplement[T: AnyNucleotide](s: seq[T]): seq[T]
• sequence: reverseComplement[T: AnyNucleotide](s: var seq[T])

RNA:

• nucleotide: RNA

rnaA:

• RNA.rnaA

rnaB:

• RNA.rnaB

rnaByte:

• nucleotide: rnaByte

rnaC:

• RNA.rnaC

rnaChar:

• nucleotide: rnaChar

rnaComplement:

• nucleotide: rnaComplement

rnaD:

• RNA.rnaD

rnaG:

• RNA.rnaG

rnaGap:

• RNA.rnaGap

rnaH:

• RNA.rnaH

rnaK:

• RNA.rnaK

rnaM:

• RNA.rnaM

rnaN:

• RNA.rnaN

rnaR:

• RNA.rnaR

rnaS:

• RNA.rnaS

rnaU:

• RNA.rnaU

rnaUnambiguousSet:

• nucleotide: rnaUnambiguousSet

rnaUnk:

• RNA.rnaUnk

rnaV:

• RNA.rnaV

rnaW:

• RNA.rnaW

rnaY:

• RNA.rnaY

rowCharacterCount:

• alignment: rowCharacterCount[T](a: Alignment[T]; row: int; chars: set[T]): int

rows:

• matrix: rows[T](m: Matrix[T]): int

sameBase:

• nucleotide: sameBase(a, b: AnyNucleotide): bool

sdnaA:

• StrictDNA.sdnaA

sdnaC:

• StrictDNA.sdnaC

sdnaG:

• StrictDNA.sdnaG

sdnaT:

• StrictDNA.sdnaT

SeqRecord:

• seqRecord: SeqRecord

Sequential:

• PhylipFormat.Sequential

srnaA:

• StrictRNA.srnaA

srnaC:

• StrictRNA.srnaC

srnaG:

• StrictRNA.srnaG

srnaU:

• StrictRNA.srnaU

stack:

• matrix: stack[T](matrices: varargs[Matrix[T]]): Matrix[T]

StrictDNA:

• nucleotide: StrictDNA

strictDnaByte:

• nucleotide: strictDnaByte

strictDnaChar:

• nucleotide: strictDnaChar

strictDnaComplement:

• nucleotide: strictDnaComplement

StrictNucleotide:

• nucleotide: StrictNucleotide

StrictRNA:

• nucleotide: StrictRNA

strictRnaByte:

• nucleotide: strictRnaByte

strictRnaChar:

• nucleotide: strictRnaChar

strictRnaComplement:

• nucleotide: strictRnaComplement

toChar:

• aminoAcid: toChar(a: AminoAcid): char
• biallelic: toChar(n: DiploidBiallelic): char
• biallelic: toChar(n: HaploidBiallelic): char
• nucleotide: toChar(n: DNA): char
• nucleotide: toChar(n: RNA): char
• nucleotide: toChar(n: StrictDNA): char
• nucleotide: toChar(n: StrictRNA): char

toCharSeq:

• sequence: toCharSeq[T](data: seq[T]): seq[char]

toDiploidBiallelic:

• biallelic: toDiploidBiallelic(a: Alignment[DNA]; seed: int64 = 1): Alignment[ DiploidBiallelic]

toDNA:

• nucleotide: toDNA(n: RNA): DNA
• nucleotide: toDNA(n: StrictRNA): StrictDNA
• twoBitSequence: toDNA[T](s: var TwoBitSequence[T]): TwoBitSequence[StrictDNA]

toFastaFile:

• fasta: toFastaFile[T](s: seq[SeqRecord[T]]; path: string; mode: FileMode = fmWrite; lineLength = 80)
• fasta: toFastaFile[T](s: SeqRecord[T]; path: string; mode: FileMode = fmWrite; lineLength = 80)

toFastaString:

• fasta: toFastaString[T](s: seq[SeqRecord[T]]; lineLength = 80): string
• fasta: toFastaString[T](s: SeqRecord[T]; lineLength = 80): string

toNexus:

• nexus: toNexus[T](a: Alignment[T]): string

toNexusFile:

• nexus: toNexusFile[T](a: Alignment[T]; path: string; mode: FileMode = fmWrite)

toNexusString:

• nexus: toNexusString[T](a: Alignment[T]): string

toPhylip:

• phylip: toPhylip[T](a: Alignment[T]; fmt: PhylipFormat; lineLength = 80): string

toPhylipFile:

• phylip: toPhylipFile[T](a: Alignment[T]; path: string; fmt: PhylipFormat; lineLength = 80; mode: FileMode = fmWrite)

toPhylipString:

• phylip: toPhylipString[T](a: Alignment[T]; fmt: PhylipFormat; lineLength = 80): string

toRNA:

• nucleotide: toRNA(n: DNA): RNA
• nucleotide: toRNA(n: StrictDNA): StrictRNA
• twoBitSequence: toRNA[T](s: var TwoBitSequence[T]): TwoBitSequence[StrictRNA]

toSeq:

• sequence: toSeq(data: seq[char]; typ: typedesc): seq[typ:type]
• sequence: toSeq(data: string; typ: typedesc): seq[typ:type]

toString:

• matrix: toString[T](m: Matrix[T]): string
• sequence: toString[T](data: seq[T]): string

toStructure:

• structure: toStructure[T: Biallelic](a: Alignment[T]): string

toStructureCharStr:

• structure: toStructureCharStr(n: DiploidBiallelic): string
• structure: toStructureCharStr(n: HaploidBiallelic): string

toStructureFile:

• structure: toStructureFile(a: Alignment[Biallelic]; path: string)

toStructureString:

• structure: toStructureString[T: Biallelic](a: Alignment[T]): string

toUnambiguousSet:

• nucleotide: toUnambiguousSet(n: DNA): set[DNA]
• nucleotide: toUnambiguousSet(n: RNA): set[RNA]

translate:

• sequence: translate[T: AnyNucleotide](s: seq[T]; code: GeneticCode = gCode1): seq[ AminoAcid]

translateCodon:

• aminoAcid: translateCodon(nucleotides: array[3, AnyNucleotide]; code: GeneticCode): AminoAcid

TwoBitSequence:

• twoBitSequence: TwoBitSequence