repp

type Backbone struct {
	// URL of the backbone fragment's source
	URL string `json:"url"`

	// Seq is the sequence of the backbone (unlinearized)
	Seq string `json:"seq"`

	// Enzymes is the list of enzymes names used to linearize the backbone
	Enzymes []string `json:"enzymes"`

	// cutsites are the indexes where the backbone was cleaved
	Cutsites []int `json:"recognitionIndex"`

	// Strands of each cut direction. True if fwd, False if rev direction
	Strands []bool `json:"strands"`
}

type EnzymeDB struct {
	// contains filtered or unexported fields
}

type FeatureDB struct {
	// contains filtered or unexported fields
}

type Flags struct {
	// contains filtered or unexported fields
}

type Frag struct {
	// ID is a unique identifier for this fragment
	ID string `json:"id,omitempty"`

	// type of the fragment in string representation for export
	Type string `json:"type"`

	// Cost to make the fragment
	Cost float64 `json:"cost"`

	// URL, eg link to a plasmid's addgene page
	URL string `json:"url,omitempty"`

	// fragment/plasmid's sequence
	Seq string `json:"seq,omitempty"`

	// sequence of a pcr fragment after PCR's addition of bp
	PCRSeq string `json:"pcrSeq,omitempty"`

	// primers necessary to create this (if pcr fragment)
	Primers []Primer `json:"primers,omitempty"`
	// contains filtered or unexported fields
}

type Output struct {
	// Target's name. In >example_CDS FASTA its "example_CDS"
	Target string `json:"target"`

	// Target's sequence
	TargetSeq string `json:"seq"`

	// Time, ex: "2018-01-01 20:41:00"
	Time string `json:"time"`

	// Execution is the number of seconds it took to execute the command
	Execution float64 `json:"execution"`

	// Solutions builds
	Solutions []Solution `json:"solutions"`

	// Backbone is the user linearized a backbone fragment
	Backbone *Backbone `json:"backbone,omitempty"`
}

type Primer struct {
	// Seq of the primer (in 5' to 3' direction)
	Seq string `json:"seq"`

	// Strand of the primer; true if top strand, false if complement
	Strand bool `json:"strand"`

	// Penalty score
	Penalty float64 `json:"penalty"`

	// PairPenalty score from primer3
	PairPenalty float64 `json:"pairPenalty"`

	// Tm of the primer
	Tm float64 `json:"tm"`

	// GC % max
	GC float64 `json:"gc"`

	// Range that the primer spans on the fragment
	Range ranged `json:"-"`
}

type Solution struct {
	// Count is the number of fragments in this solution
	Count int `json:"count"`

	// Cost estimated from the primer and sequence lengths
	Cost float64 `json:"cost"`

	// Fragments used to build this solution
	Fragments []*Frag `json:"fragments"`
}