First commit

pkg/obiseq/biosequence.go

@@ -0,0 +1,185 @@
+package obiseq
+
+import (
+	"bytes"
+	"crypto/md5"
+
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/goutils"
+)
+
+type Quality []uint8
+
+var __default_qualities__ = make(Quality, 0, 500)
+
+func __make_default_qualities__(length int) Quality {
+	cl := len(__default_qualities__)
+	if cl < length {
+		for i := cl; i <= length; i++ {
+			__default_qualities__ = append(__default_qualities__, 40)
+		}
+	}
+	return __default_qualities__[0:length]
+}
+
+type Annotation map[string]interface{}
+
+type __sequence__ struct {
+	id          bytes.Buffer
+	definition  bytes.Buffer
+	sequence    bytes.Buffer
+	qualities   bytes.Buffer
+	feature     bytes.Buffer
+	annotations Annotation
+}
+
+type BioSequence struct {
+	sequence *__sequence__
+}
+
+type BioSequenceSlice []BioSequence
+
+var NilBioSequence = BioSequence{sequence: nil}
+
+func (s BioSequence) IsNil() bool {
+	return s.sequence == nil
+}
+
+func (s BioSequence) Reset() {
+	s.sequence.id.Reset()
+	s.sequence.definition.Reset()
+	s.sequence.sequence.Reset()
+	s.sequence.qualities.Reset()
+	s.sequence.feature.Reset()
+
+	for k := range s.sequence.annotations {
+		delete(s.sequence.annotations, k)
+	}
+
+}
+
+func (s BioSequence) Copy() BioSequence {
+	new_seq := MakeEmptyBioSequence()
+	new_seq.sequence.id.Write(s.sequence.id.Bytes())
+	new_seq.sequence.definition.Write(s.sequence.definition.Bytes())
+	new_seq.sequence.sequence.Write(s.sequence.sequence.Bytes())
+	new_seq.sequence.qualities.Write(s.sequence.qualities.Bytes())
+	new_seq.sequence.feature.Write(s.sequence.feature.Bytes())
+
+	if len(s.sequence.annotations) > 0 {
+		goutils.CopyMap(new_seq.sequence.annotations,
+			s.sequence.annotations)
+	}
+
+	return new_seq
+}
+
+func (s BioSequence) Id() string {
+	return s.sequence.id.String()
+}
+func (s BioSequence) Definition() string {
+	return s.sequence.definition.String()
+}
+
+func (s BioSequence) Sequence() []byte {
+	return s.sequence.sequence.Bytes()
+}
+
+func (s BioSequence) String() string {
+	return s.sequence.sequence.String()
+}
+func (s BioSequence) Length() int {
+	return s.sequence.sequence.Len()
+}
+
+func (s BioSequence) HasQualities() bool {
+	return s.sequence.qualities.Len() > 0
+}
+
+func (s BioSequence) Qualities() Quality {
+	if s.HasQualities() {
+		return s.sequence.qualities.Bytes()
+	} else {
+		return __make_default_qualities__(s.sequence.sequence.Len())
+	}
+}
+
+func (s BioSequence) Features() string {
+	return s.sequence.feature.String()
+}
+
+func (s BioSequence) Annotations() Annotation {
+	return s.sequence.annotations
+}
+
+func (s BioSequence) MD5() [16]byte {
+	return md5.Sum(s.sequence.sequence.Bytes())
+}
+
+func (s BioSequence) Count() int {
+	if s.sequence.annotations == nil {
+		return 1
+	}
+
+	if val, ok := (s.sequence.annotations)["count"]; ok {
+		val, err := goutils.InterfaceToInt(val)
+		if err == nil {
+			return val
+		}
+	}
+	return 1
+}
+
+func (s BioSequence) Taxid() int {
+	if s.sequence.annotations == nil {
+		return 1
+	}
+
+	if val, ok := (s.sequence.annotations)["taxid"]; ok {
+		val, err := goutils.InterfaceToInt(val)
+		if err == nil {
+			return val
+		}
+	}
+	return 1
+}
+
+func (s BioSequence) SetId(id string) {
+	s.sequence.id.Reset()
+	s.sequence.id.WriteString(id)
+}
+
+func (s BioSequence) SetDefinition(definition string) {
+	s.sequence.definition.Reset()
+	s.sequence.definition.WriteString(definition)
+}
+
+func (s BioSequence) SetFeatures(feature string) {
+	s.sequence.feature.Reset()
+	s.sequence.feature.WriteString(feature)
+}
+
+func (s BioSequence) SetSequence(sequence []byte) {
+	s.sequence.sequence.Reset()
+	s.sequence.sequence.Write(sequence)
+}
+
+func (s BioSequence) SetQualities(qualities Quality) {
+	s.sequence.qualities.Reset()
+	s.sequence.qualities.Write(qualities)
+}
+
+func (s BioSequence) Write(data []byte) (int, error) {
+	return s.sequence.sequence.Write(data)
+}
+
+func (s BioSequence) WriteString(data string) (int, error) {
+	return s.sequence.sequence.WriteString(data)
+}
+
+func (s BioSequence) WriteByte(data byte) error {
+	return s.sequence.sequence.WriteByte(data)
+}
+
+func (s BioSequence) WriteRune(data rune) (int, error) {
+	return s.sequence.sequence.WriteRune(data)
+}