gts

package module

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Versions in this module

v0

v0.8.2

Mar 24, 2020

Changes in this version

+ func UserCacheDir() (string, error)

v0.8.1

Mar 19, 2020

v0.8.0

Jan 24, 2020

Changes in this version

+ type Filter func(f Feature) bool

+ func ParseSelector(s string) Filter

+ func (f Filter) And(g Filter) Filter

+ func (f Filter) Or(g Filter) Filter

type QualifierIO

+ func (q QualifierIO) Format(prefix string) QualifierFormatter

+ func (q QualifierIO) String() string

+ func (q QualifierIO) Unpack() (string, string)

v0.7.2

Jan 23, 2020

v0.7.1

Jan 21, 2020

v0.7.0

Jan 21, 2020

Changes in this version

type Fasta

+ func (f Fasta) Bytes() []byte

type GTS

+ func (seq GTS) Bytes() []byte

v0.6.0

Jan 20, 2020

Changes in this version

+ func DefaultWriter(seq Sequence) io.WriterTo

+ func Identical(a, b Sequence) bool

+ func NewRecordWriter(rec Record, filetype FileType) io.WriterTo

+ func NewSequenceWriter(seq Sequence, filetype FileType) io.WriterTo

+ type EncoderWriter struct

+ func NewEncoderWriter(v interface{}, ctor EncoderConstructor) EncoderWriter

+ func (f EncoderWriter) WriteTo(w io.Writer) (int64, error)

+ type Fasta struct

+ Body []byte

+ Desc string

+ func (f *Fasta) Delete(pos, arg int) error

+ func (f *Fasta) Insert(pos int, arg Sequence) error

+ func (f *Fasta) Replace(pos int, arg Sequence) error

+ func (f Fasta) Data() []byte

+ func (f Fasta) Info() interface{}

+ func (f Fasta) String() string

+ func (f Fasta) WriteTo(w io.Writer) (int64, error)

+ type FastaWriter struct

+ func (ff FastaWriter) WriteTo(w io.Writer) (int64, error)

type Feature

+ func (f Feature) Data() []byte

+ func (f Feature) Info() interface{}

type FileType

+ const EMBLFile

+ const FastaFile

+ const FastqFile

+ const GenBankFile

+ type GTS struct

+ func New(info interface{}, data []byte) *GTS

+ func (seq *GTS) Delete(pos, arg int) error

+ func (seq *GTS) Insert(pos int, arg Sequence) error

+ func (seq *GTS) Replace(pos int, arg Sequence) error

+ func (seq GTS) Data() []byte

+ func (seq GTS) Info() interface{}

type GenBank

+ func (gb GenBank) Data() []byte

+ func (gb GenBank) Info() interface{}

+ func (gb GenBank) String() string

+ func (gb GenBank) WriteTo(w io.Writer) (int64, error)

+ type GenBankWriter struct

+ func (gf GenBankWriter) WriteTo(w io.Writer) (int64, error)

type Sequence

+ Data func() []byte

+ Info func() interface{}

type SequenceProxy

+ func (sp SequenceProxy) Data() []byte

+ func (sp SequenceProxy) Info() interface{}

type SequenceServer

+ func (ss SequenceServer) Data() []byte

+ func (ss SequenceServer) Info() interface{}

v0.5.0

Jan 18, 2020

v0.4.0

Jan 16, 2020

Changes in this version

+ func DecoderParser(decCtor DecoderConstructor, objCtor Constructor) pars.Parser

+ type Constructor func() interface

+ type Date struct

+ Day int

+ Month time.Month

+ Year int

+ func FromTime(t time.Time) Date

+ func (d Date) ToTime() time.Time

type Encoder

+ func NewGobEncoder(w io.Writer) Encoder

+ func NewJSONEncoder(w io.Writer) Encoder

+ func NewMsgpackEncoder(w io.Writer) Encoder

+ func NewYAMLEncoder(w io.Writer) Encoder

+ type EncoderFormatter struct

+ func NewEncoderFormatter(v interface{}, ctor EncoderConstructor) EncoderFormatter

+ func (f EncoderFormatter) WriteTo(w io.Writer) (int64, error)

type FeatureIO

+ func (fio FeatureIO) SetFeature(f *Feature) error

+ type FileType int

+ const DefaultFile

+ const GenBankFlat

+ const JSONFile

+ const MsgpackFile

+ const UnknownFile

+ const YAMLFile

+ func Detect(filename string) FileType

+ func ToFileType(name string) FileType

type Formatter

+ func NewRecordFormatter(rec Record, filetype FileType) Formatter

type GenBankIO

+ func (gbio GenBankIO) SetGenBank(gb *GenBank) error

+ type MultiParserScanner struct

+ func NewMultiParserScanner(r io.Reader, ii ...interface{}) *MultiParserScanner

+ func (s *MultiParserScanner) Scan() bool

+ func (s MultiParserScanner) Err() error

+ func (s MultiParserScanner) Value() interface{}

+ type ParserScanner struct

+ func NewParserScanner(r io.Reader, i interface{}) *ParserScanner

+ func (s *ParserScanner) Scan() bool

+ func (s ParserScanner) Err() error

+ func (s ParserScanner) Value() interface{}

type Qualifier

+ func (q Qualifier) Unpack() (string, string)

type RecordScanner

+ func NewRecordFileScanner(f *os.File) *RecordScanner

+ type Scanner interface

+ Err func() error

+ Scan func() bool

+ Value func() interface{}

v0.3.1

Jan 6, 2020

v0.3.0

Jan 5, 2020

Changes in this version

+ func DecodeGob(data []byte, v Decodable) error

+ func DecodeJSON(data []byte, v Decodable) error

+ func EncodeGob(v Encodable) ([]byte, error)

+ func EncodeJSON(v Encodable) ([]byte, error)

+ type Decodable interface

+ DecodeWith func(dec Decoder) error

+ type Decoder interface

+ Decode func(v interface{}) error

+ func NewGobDecoder(r io.Reader) Decoder

+ func NewJSONDecoder(r io.Reader) Decoder

+ func NewMsgpackDecoder(r io.Reader) Decoder

+ func NewYAMLDecoder(r io.Reader) Decoder

+ type DecoderConstructor func(io.Reader) Decoder

+ type Encodable interface

+ EncodeWith func(enc Encoder) error

+ type Encoder interface

+ Encode func(v interface{}) error

+ type EncoderConstructor func(io.Writer) Encoder

type Feature

+ func (f *Feature) DecodeMsgpack(dec *msgpack.Decoder) error

+ func (f *Feature) DecodeWith(dec Decoder) (err error)

+ func (f *Feature) GobDecode(data []byte) error

+ func (f *Feature) UnmarshalJSON(data []byte) error

+ func (f *Feature) UnmarshalYAML(value *yaml.Node) error

+ func (f Feature) EncodeMsgpack(enc *msgpack.Encoder) error

+ func (f Feature) EncodeWith(enc Encoder) error

+ func (f Feature) GobEncode() ([]byte, error)

+ func (f Feature) MarshalJSON() ([]byte, error)

+ func (f Feature) MarshalYAML() (interface{}, error)

+ type FeatureIO struct

+ Key string

+ Location string

+ Qualifiers []Qualifier

+ func NewFeatureIO(f Feature) FeatureIO

type GenBank

+ func (gb *GenBank) DecodeMsgpack(dec *msgpack.Decoder) error

+ func (gb *GenBank) DecodeWith(dec Decoder) error

+ func (gb *GenBank) GobDecode(data []byte) error

+ func (gb *GenBank) UnmarshalJSON(data []byte) error

+ func (gb *GenBank) UnmarshalYAML(value *yaml.Node) error

+ func (gb GenBank) EncodeMsgpack(enc *msgpack.Encoder) error

+ func (gb GenBank) EncodeWith(enc Encoder) error

+ func (gb GenBank) GobEncode() ([]byte, error)

+ func (gb GenBank) MarshalJSON() ([]byte, error)

+ func (gb GenBank) MarshalYAML() (interface{}, error)

+ type GenBankIO struct

+ Features []Feature

+ Fields GenBankFields

+ Origin []byte

+ func NewGenBankIO(gb GenBank) GenBankIO

type Qualifier

+ func (q *Qualifier) DecodeMsgpack(dec *msgpack.Decoder) error

+ func (q *Qualifier) DecodeWith(dec Decoder) error

+ func (q *Qualifier) GobDecode(data []byte) error

+ func (q *Qualifier) UnmarshalJSON(data []byte) error

+ func (q *Qualifier) UnmarshalYAML(value *yaml.Node) error

+ func (q Qualifier) EncodeMsgpack(enc *msgpack.Encoder) error

+ func (q Qualifier) EncodeWith(enc Encoder) error

+ func (q Qualifier) GobEncode() ([]byte, error)

+ func (q Qualifier) MarshalJSON() ([]byte, error)

+ func (q Qualifier) MarshalYAML() (interface{}, error)

+ type QualifierIO [2]string

+ func NewQualifierIO(q Qualifier) QualifierIO

v0.2.0

Jan 3, 2020

Changes in this version

+ func Len(seq Sequence) int

v0.1.0

Jan 3, 2020

Changes in this version

+ type FeatureFilter func(f Feature) bool

type FeatureList

+ func (ff FeatureList) Filter(ss ...FeatureFilter) []Feature

type FeatureTable

+ Filter func(ss ...FeatureFilter) []Feature

type GenBank

+ func (gb GenBank) Filter(ss ...FeatureFilter) []Feature

v0.0.3

Jan 2, 2020

v0.0.2

Dec 30, 2019

v0.0.1

Dec 30, 2019

v0.0.0

Dec 30, 2019

Changes in this version

+ var AmbiguousLocationParser = ...(func(result *pars.Result) error { ... })

+ var BetweenLocationParser = ...(func(result *pars.Result) error { ... })

+ var ComplementLocationParser = ...(func(result *pars.Result) error { ... })

+ var FeatureTableParser = pars.Any(RecordParser.Map(func(result *pars.Result) error { ... }), ...)

+ var JoinLocationParser = ...(func(result *pars.Result) error { ... })

+ var LiteralQualifierNames = []string

+ var LocationParser pars.Parser

+ var OrderLocationParser = ...(func(result *pars.Result) error { ... })

+ var PointLocationParser = pars.Parser(pars.Int).Map(func(result *pars.Result) error { ... })

+ var QuotedQualifierNames = []string

+ var RangeLocationParser = ...(func(result *pars.Result) error { ... })

+ var RecordParser = pars.Any(GenBankParser)

+ var ToggleQualifierNames = []string

+ func AddPrefix(s, prefix string) string

+ func Any(f Feature) bool

+ func Composition(seq Sequence) map[byte]int

+ func Equal(a, b Sequence) bool

+ func FeatureListParser(prefix string) pars.Parser

+ func FlatFileSplit(s string) []string

+ func GenBankParser(state *pars.State, result *pars.Result) error

+ func IsLiteralQualifier(name string) bool

+ func IsQuotedQualifier(name string) bool

+ func IsToggleQualifier(name string) bool

+ func LocationLess(a, b Location) bool

+ func QualifierParser(prefix string) pars.Parser

+ func RegisterLiteralQualifier(names ...string)

+ func RegisterQuotedQualifier(names ...string)

+ func RegisterToggleQualifier(names ...string)

+ func Skew(seq Sequence, nSet, pSet string) float64

+ type AmbiguousLocation struct

+ End int

+ Start int

+ func (loc *AmbiguousLocation) Shift(offset, amount int) (ok bool)

+ func (loc AmbiguousLocation) Len() int

+ func (loc AmbiguousLocation) Locate(seq Sequence) Sequence

+ func (loc AmbiguousLocation) Map(index int) int

+ func (loc AmbiguousLocation) String() string

+ type BasicSequence []byte

+ func Seq(arg interface{}) BasicSequence

+ func Slice(seq Sequence, start, end int) BasicSequence

+ func (s *BasicSequence) Delete(pos, cnt int) error

+ func (s *BasicSequence) Insert(pos int, seq Sequence) error

+ func (s *BasicSequence) Replace(pos int, seq Sequence) error

+ func (s BasicSequence) Bytes() []byte

+ type BetweenLocation struct

+ End int

+ Start int

+ func (loc *BetweenLocation) Shift(offset, amount int) (ok bool)

+ func (loc BetweenLocation) Len() int

+ func (loc BetweenLocation) Locate(seq Sequence) Sequence

+ func (loc BetweenLocation) Map(index int) int

+ func (loc BetweenLocation) String() string

+ type ByLocation []Feature

+ func (ff ByLocation) Len() int

+ func (ff ByLocation) Less(i, j int) bool

+ func (ff ByLocation) Swap(i, j int)

+ type ComplementLocation struct

+ Location Location

+ func (loc *ComplementLocation) Shift(offset, amount int) bool

+ func (loc ComplementLocation) Len() int

+ func (loc ComplementLocation) Locate(seq Sequence) Sequence

+ func (loc ComplementLocation) Map(index int) int

+ func (loc ComplementLocation) String() string

+ type Feature struct

+ Key string

+ Location Location

+ Qualifiers Values

+ func NewFeature(key string, loc Location, qfs Values) Feature

+ func (f Feature) Bytes() []byte

+ func (f Feature) Delete(pos, cnt int)

+ func (f Feature) Format(prefix string, depth int) FeatureFormatter

+ func (f Feature) Insert(pos int, seq Sequence)

+ func (f Feature) Replace(pos int, seq Sequence)

+ func (f Feature) Translation() Sequence

+ type FeatureFormatter struct

+ Depth int

+ Feature Feature

+ Prefix string

+ func (ff FeatureFormatter) String() string

+ func (ff FeatureFormatter) WriteTo(w io.Writer) (int, error)

+ type FeatureList []Feature

+ func ReadFeatureTable(r io.Reader) (FeatureList, error)

+ func (ff *FeatureList) Add(f Feature)

+ func (ff *FeatureList) Insert(i int, f Feature)

+ func (ff FeatureList) Format(prefix string, depth int) FeatureListFormatter

+ func (ff FeatureList) Select(ss ...FeatureSelector) []Feature

+ type FeatureListFormatter struct

+ Depth int

+ FeatureList FeatureList

+ Prefix string

+ func (ff FeatureListFormatter) String() string

+ func (ff FeatureListFormatter) WriteTo(w io.Writer) (int64, error)

+ type FeatureSelector func(f Feature) bool

+ func And(ss ...FeatureSelector) FeatureSelector

+ func Key(key string) FeatureSelector

+ func Not(s FeatureSelector) FeatureSelector

+ func Or(ss ...FeatureSelector) FeatureSelector

+ type FeatureTable interface

+ Add func(f Feature)

+ Select func(ss ...FeatureSelector) []Feature

+ type Formatter interface

+ func DefaultFormatter(rec Record) Formatter

+ type GenBank struct

+ Features FeatureList

+ Fields GenBankFields

+ Origin SequenceServer

+ func (gb GenBank) Add(f Feature)

+ func (gb GenBank) Bytes() []byte

+ func (gb GenBank) Delete(pos, cnt int) error

+ func (gb GenBank) Insert(pos int, seq Sequence) error

+ func (gb GenBank) Metadata() interface{}

+ func (gb GenBank) Replace(pos int, seq Sequence) error

+ func (gb GenBank) Select(ss ...FeatureSelector) []Feature

+ type GenBankFields struct

+ Accession string

+ Comment string

+ DBLink PairList

+ Date time.Time

+ Definition string

+ Division string

+ Keywords []string

+ LocusName string

+ Molecule string

+ References []Reference

+ Source Organism

+ Topology string

+ Version string

+ type GenBankFormatter struct

+ Rec Record

+ func (gf GenBankFormatter) String() string

+ func (gf GenBankFormatter) WriteTo(w io.Writer) (int64, error)

+ type JoinLocation struct

+ Locations []Location

+ func (loc *JoinLocation) Shift(pos, n int) bool

+ func (loc JoinLocation) Len() int

+ func (loc JoinLocation) Locate(seq Sequence) Sequence

+ func (loc JoinLocation) Map(index int) int

+ func (loc JoinLocation) String() string

+ type Location interface

+ Len func() int

+ Locate func(seq Sequence) Sequence

+ Map func(index int) int

+ Shift func(offset, amount int) bool

+ String func() string

+ func AsLocation(s string) (Location, error)

+ func NewAmbiguousLocation(start, end int) Location

+ func NewBetweenLocation(start, end int) Location

+ func NewComplementLocation(loc Location) Location

+ func NewJoinLocation(locs []Location) Location

+ func NewOrderLocation(locs []Location) Location

+ func NewPartialRangeLocation(start, end int, p5, p3 bool) Location

+ func NewPointLocation(pos int) Location

+ func NewRangeLocation(start, end int) Location

+ type Mutable interface

+ Delete func(pos, cnt int)

+ Insert func(pos int, seq Sequence)

+ Replace func(pos int, seq Sequence)

+ type MutableSequence interface

+ Delete func(pos, cnt int) error

+ Insert func(pos int, seq Sequence) error

+ Replace func(pos int, seq Sequence) error

+ type OrderLocation struct

+ Locations []Location

+ func (loc *OrderLocation) Shift(pos, n int) bool

+ func (loc OrderLocation) Len() int

+ func (loc OrderLocation) Locate(seq Sequence) Sequence

+ func (loc OrderLocation) Map(index int) int

+ func (loc OrderLocation) String() string

+ type Organism struct

+ Name string

+ Species string

+ Taxon []string

+ type Pair struct

+ Key string

+ Value string

+ type PairList []Pair

+ func (pl *PairList) Set(key, value string)

+ type PointLocation struct

+ Position int

+ func (loc *PointLocation) Shift(offset, amount int) bool

+ func (loc PointLocation) Len() int

+ func (loc PointLocation) Locate(seq Sequence) Sequence

+ func (loc PointLocation) Map(index int) int

+ func (loc PointLocation) String() string

+ type Qualifier struct

+ Name string

+ Value string

+ func (q Qualifier) Format(prefix string) QualifierFormatter

+ func (q Qualifier) String() string

+ type QualifierFormatter struct

+ Prefix string

+ Qualifier Qualifier

+ func (qf QualifierFormatter) String() string

+ func (qf QualifierFormatter) WriteTo(w io.Writer) (int, error)

+ type QualifierType int

+ const LiteralQualifier

+ const QuotedQualifier

+ const ToggleQualifier

+ const UnknownQualifier

+ func GetQualifierType(name string) QualifierType

+ type Range struct

+ End int

+ Start int

+ type RangeLocation struct

+ End int

+ Partial3 bool

+ Partial5 bool

+ Start int

+ func (loc *RangeLocation) Shift(offset, amount int) (ok bool)

+ func (loc RangeLocation) Len() int

+ func (loc RangeLocation) Locate(seq Sequence) Sequence

+ func (loc RangeLocation) Map(index int) int

+ func (loc RangeLocation) String() string

+ type Record interface

+ Metadata func() interface{}

+ func NewRecord(meta interface{}, ff []Feature, p []byte) Record

+ type RecordScanner struct

+ func NewRecordScanner(r io.Reader) *RecordScanner

+ func (s *RecordScanner) Record() Record

+ func (s *RecordScanner) Scan() bool

+ func (s RecordScanner) Err() error

+ type Reference struct

+ Authors string

+ Comment string

+ Group string

+ Journal string

+ Number int

+ Ranges []Range

+ Title string

+ Xref map[string]string

+ type Sequence interface

+ Bytes func() []byte

+ func Complement(seq Sequence) Sequence

+ func Fragment(seq Sequence, window, slide int) []Sequence

+ type SequenceProxy struct

+ func (sp SequenceProxy) Bytes() []byte

+ func (sp SequenceProxy) Delete(pos, cnt int) error

+ func (sp SequenceProxy) Insert(pos int, seq Sequence) error

+ func (sp SequenceProxy) Replace(pos int, seq Sequence) error

+ type SequenceServer struct

+ func NewSequenceServer(seq Sequence) SequenceServer

+ func (ss *SequenceServer) Close()

+ func (ss *SequenceServer) Delete(pos, cnt int) error

+ func (ss *SequenceServer) Insert(pos int, seq Sequence) error

+ func (ss *SequenceServer) Replace(pos int, seq Sequence) error

+ func (ss *SequenceServer) Spin()

+ func (ss SequenceServer) Bytes() []byte

+ func (ss SequenceServer) Proxy() SequenceProxy

+ type Values map[string][]string

+ func (v Values) Add(name, value string)

+ func (v Values) Del(name string)

+ func (v Values) Get(key string) []string

+ func (v Values) Set(name string, values ...string)

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