Documentation
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Index ¶
- type Alignment
- func (aln Alignment) Column(p uint) []byte
- func (aln Alignment) Count(bases []byte) map[byte]int
- func (aln Alignment) Frequency(bases []byte) map[byte]float64
- func (aln Alignment) Len() (length int)
- func (aln Alignment) NSeq() uint
- func (aln Alignment) Seq(i uint) string
- func (aln Alignment) String() string
- func (aln Alignment) Subseq(s, e int) Alignment
- type Nexus
- func (nex *Nexus) Alignment() Alignment
- func (nex *Nexus) Charsets() map[string][]Pair
- func (nex *Nexus) DataType() string
- func (nex *Nexus) FillFrom(file io.Reader)
- func (nex *Nexus) Gap() byte
- func (nex *Nexus) Letters() []byte
- func (nex *Nexus) Missing() byte
- func (nex *Nexus) NChar() int
- func (nex *Nexus) NTax() int
- type Pair
Constants ¶
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Variables ¶
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Functions ¶
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Types ¶
type Alignment ¶
type Alignment []string
Alignment is a collection of equal length sequences
func (Alignment) Frequency ¶
Frequency returns the normalized frequency of each base in a set Note that bases that exist in the Alignment, but not in the set are ignored
func (Alignment) Len ¶
Len is the length of the alignment Note that len(alignment) != alignment.Len(), the former equals alignment.NSeq()
func (Alignment) NSeq ¶
NSeq is the number of sequences in the alignment Note: len(alignment) == alignment.NSeq()
type Nexus ¶
type Nexus struct {
// contains filtered or unexported fields
}
Nexus only understands two blocks: DATA and SETS Note: meant for exclusive use in swsc
func New ¶
func New() *Nexus
New creates a new empty Nexus with registered handlers and deferred block creation
func (*Nexus) FillFrom ¶
FillFrom fills in the Nexus with data from a file It overwrites existing values, but does not clear all values
func (*Nexus) Letters ¶
Letters is the known (capital) characters allowed by DataType Missing and Gap characters are NOT appended.
Source Files