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

type Chainer2 struct {
	// contains filtered or unexported fields
}

type Chaining2Options struct {
	MaxGap   int
	MinScore int // minimum score of a chain

	// only used in Chain2
	MaxDistance int
	Band        int // only check i in range of  i − A < j < i
}

type ChainingOptions struct {
	MaxGap   float64
	MinScore float64
}

type Index struct {

	// k-mer-value searchers
	Searchers []*kv.Searcher
	// contains filtered or unexported fields
}

type IndexBuildingOptions struct {
	// general
	NumCPUs      int
	Verbose      bool // show log
	Log2File     bool // log file
	Force        bool // force overwrite existed index
	MaxOpenFiles int  // maximum opened files, used in merging indexes

	K                int   // k-mer size
	Masks            int   // number of masks
	RandSeed         int64 // random seed
	PrefixForCheckLC int   // length of prefix for checking low-complexity

	Chunks     int // the number of chunks for storing k-mer data
	Partitions int // the number of partitions for indexing k-mer data

	GenomeBatchSize int // the maximum number of genomes of a batch

	ReRefName    *regexp.Regexp   // for extracting genome id from the file name
	ReSeqExclude []*regexp.Regexp // for excluding sequences according to name pattern
}

type IndexInfo struct {
	MainVersion     uint8 `toml:"main-version" comment:"Index format"`
	MinorVersion    uint8 `toml:"minor-version"`
	K               uint8 `toml:"max-K" comment:"LexicHash"`
	Masks           int   `toml:"masks"`
	RandSeed        int64 `toml:"rand-seed"`
	Chunks          int   `toml:"chunks" comment:"Seeds (k-mer-value data) files"`
	Partitions      int   `toml:"index-partitions"`
	Genomes         int   `toml:"genomes" comment:"Genome data"`
	GenomeBatchSize int   `toml:"genome-batch-size"`
	GenomeBatches   int   `toml:"genome-batches"`
}

type IndexSearchingOptions struct {
	// general
	NumCPUs      int
	Verbose      bool // show log
	Log2File     bool // log file
	MaxOpenFiles int  // maximum opened files, used in merging indexes

	// seed searching
	MinPrefix       uint8 // minimum prefix length, e.g., 15
	MaxMismatch     int   // maximum mismatch, e.g., 3
	MinSinglePrefix uint8 // minimum prefix length of the single seed, e.g., 20
	TopN            int   // keep the topN scores, e.g, 10

	// seeds chaining
	MaxGap float64 // e.g., 5000
}

type Options struct {
	NumCPUs int
	Verbose bool

	LogFile  string
	Log2File bool

	Compress         bool
	CompressionLevel int
}

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

type SearchResult struct {
	GenomeBatch int
	GenomeIndex int
	ID          []byte
	GenomeSize  int

	Subs *[]*SubstrPair // matched substring pairs (query,target)

	Score  float64 //  score for soring
	Chains *[]*[]int

	// more about the alignment detail
	SimilarityDetails *[]*SimilarityDetail // sequence comparing
}

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

type SeqComparatorOptions struct {
	// indexing
	K         uint8
	MinPrefix uint8

	// chaining
	Chaining2Options

	// seq similarity
	MinAlignedFraction float64 // percentage
	MinIdentity        float64 // percentage
}

type SeqComparatorResult struct {
	MatchedBases int // The number of matched bases.
	AlignedBases int // The number of aligned bases.
	NumChains    int // The number of chains

	AlignedFraction float64 // aligned fraction, percentage
	Identity        float64 // identity (fraction of same bases), percentage
}

type SimilarityDetail struct {
	TBegin int
	TEnd   int
	RC     bool

	SimilarityScore float64
	Similarity      *SeqComparatorResult
	Chain           *[]int

	// sequence details
	SeqLen int
	SeqID  []byte // seqid of the region
}

type SubstrPair struct {
	QBegin int    // start position of the substring (0-based) in query
	TBegin int    // start position of the substring (0-based) in reference
	Len    int    // prefix length
	Code   uint64 // k-mer, only for debugging

	Mismatch uint8 // number of mismatches

	RC bool // is the substring from the reference seq on the negative strand.
}

type Uint64Slice []uint64