align

type AlignChannel struct {
	Achan chan Alignment
	Err   error
}

type Alignment interface {
	SeqBag
	AddGaps(rate, lenprop float64)
	AvgAllelesPerSite() float64
	BuildBootstrap() Alignment
	CharStatsSite(site int) (map[rune]int, error)
	Clone() (Alignment, error)
	CodonAlign(ntseqs SeqBag) (codonAl *align, err error)
	Concat(Alignment) error                             // concatenates the given alignment with this alignment
	Entropy(site int, removegaps bool) (float64, error) // Entropy of the given site
	Length() int                                        // Length of the alignment
	Mask(start, length int) error                       // Masks given positions
	MaxCharStats() ([]rune, []int)
	Mutate(rate float64)                                                                        // Adds uniform substitutions in the alignment (~sequencing errors)
	NbVariableSites() int                                                                       // Nb of variable sites
	Pssm(log bool, pseudocount float64, normalization int) (pssm map[rune][]float64, err error) // Normalization: PSSM_NORM_NONE, PSSM_NORM_UNIF, PSSM_NORM_DATA
	Rarefy(nb int, counts map[string]int) (Alignment, error)                                    // Take a new rarefied sample taking into accounts weights
	RandSubAlign(length int) (Alignment, error)                                                 // Extract a random subalignment with given length from this alignment
	Recombine(rate float64, lenprop float64)
	RemoveGapSeqs(cutoff float64)     // Removes sequences having >= cutoff gaps
	RemoveGapSites(cutoff float64)    // Removes sites having >= cutoff gaps
	Sample(nb int) (Alignment, error) // generate a sub sample of the sequences
	ShuffleSites(rate float64, roguerate float64, randroguefirst bool) []string
	SimulateRogue(prop float64, proplen float64) ([]string, []string) // add "rogue" sequences
	SiteConservation(position int) (int, error)                       // If the site is conserved:
	SubAlign(start, length int) (Alignment, error)                    // Extract a subalignment from this alignment
	Swap(rate float64)
	TrimSequences(trimsize int, fromStart bool) error
}

type PairwiseAligner interface {
	AlignEnds() (int, int)
	AlignStarts() (int, int)
	SetGapOpenScore(open float64)
	SetGapExtendScore(extend float64)
	SetScore(match, mismatch float64)
	MaxScore() float64 // Maximum score of the alignment
	NbMatches() int    // Number of matches
	NbMisMatches() int // Number of mismatches
	NbGaps() int       // Nuber of gaps
	Length() int       // Length of the alignment
	Alignment() (Alignment, error)
	AlignmentStr() string
}

type SeqBag interface {
	AddSequence(name string, sequence string, comment string) error
	AddSequenceChar(name string, sequence []rune, comment string) error
	AppendSeqIdentifier(identifier string, right bool)
	Alphabet() int
	AlphabetStr() string
	AlphabetCharacters() []rune
	AutoAlphabet() // detects and sets alphabet automatically for all the sequences
	CharStats() map[rune]int64
	CleanNames()                            // Clean sequence names (newick special char)
	Clear()                                 // Removes all sequences
	CloneSeqBag() (seqs SeqBag, err error)  // Clones the seqqbag
	Deduplicate() error                     // Remove duplicate sequences
	GetSequence(name string) (string, bool) // Get a sequence by names
	GetSequenceById(ith int) (string, bool)
	GetSequenceChar(name string) ([]rune, bool)
	GetSequenceCharById(ith int) ([]rune, bool)
	GetSequenceNameById(ith int) (string, bool)
	SetSequenceChar(ithAlign, ithSite int, char rune) error
	Sequence(ith int) (Sequence, bool)
	SequenceByName(name string) (Sequence, bool)
	Identical(SeqBag) bool
	Iterate(it func(name string, sequence string))
	IterateChar(it func(name string, sequence []rune))
	IterateAll(it func(name string, sequence []rune, comment string))
	Sequences() []Sequence
	LongestORF(reverse bool) (orf Sequence, err error)
	MaxNameLength() int // maximum sequence name length
	NbSequences() int
	Phase(orfs SeqBag, lencutoff, matchcutoff float64, reverse bool, cutend bool, cpus int) (seqs SeqBag, aaseqs SeqBag, positions []int, removed []string, err error)
	PhaseNt(orf Sequence, lencutoff, matchcutoff float64, reverse bool, cutend bool, cpus int) (seqs SeqBag, positions []int, removed []string, err error)
	Rename(namemap map[string]string)
	RenameRegexp(regex, replace string, namemap map[string]string) error
	ShuffleSequences()               // Shuffle sequence order
	String() string                  // Raw string representation (just write all sequences)
	Translate(phase int) (err error) // Translates nt sequence in aa
	TrimNames(namemap map[string]string, size int) error
	TrimNamesAuto(namemap map[string]string, curid *int) error
	Sort() // Sorts the sequences by name
	Unalign() SeqBag
}

type Sequence interface {
	Sequence() string
	SequenceChar() []rune
	CharAt(int) rune
	Name() string
	SetName(name string)
	Comment() string
	Length() int
	LongestORF() (start, end int) // Detects the longest ORF in forward strand only
	Reverse()
	Complement() error                     // Returns an error if not nucleotide sequence
	Translate(phase int) (Sequence, error) // Translates the sequence using the standard code
	DetectAlphabet() int                   // Try to detect alphabet (nt or aa)
	Clone() Sequence
}