First commit

pkg/obiformats/fastseq_json_header.go

@@ -0,0 +1,66 @@
+package obiformats
+
+import (
+	"strings"
+
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+	"github.com/goccy/go-json"
+)
+
+func _parse_json_header_(header string, annotations obiseq.Annotation) string {
+
+	start := -1
+	stop := -1
+	level := 0
+	lh := len(header)
+
+	for i := 0; (i < lh) && (stop < 0); i++ {
+		// fmt.Printf("[%d,%d-%d] : %d (%c) (%d,%c)\n", i, start, stop, header[i], header[i], '{', '{')
+		if level == 0 && header[i] == '{' {
+			start = i
+		}
+
+		if header[i] == '{' {
+			level++
+		}
+
+		if header[i] == '}' {
+			level--
+		}
+
+		if start >= 0 && level == 0 {
+			stop = i
+		}
+
+	}
+
+	if start < 0 || stop < 0 {
+		return header
+	}
+
+	stop++
+
+	json.Unmarshal([]byte(header)[start:stop], annotations)
+	return strings.TrimSpace(header[stop:])
+}
+
+func ParseFastSeqJsonHeader(sequence obiseq.BioSequence) {
+	sequence.SetDefinition(_parse_json_header_(sequence.Definition(),
+		sequence.Annotations()))
+}
+
+func FormatFastSeqJsonHeader(sequence obiseq.BioSequence) string {
+	annotations := sequence.Annotations()
+
+	if annotations != nil {
+		text, err := json.Marshal(sequence.Annotations())
+
+		if err != nil {
+			panic(err)
+		}
+
+		return string(text)
+	}
+
+	return ""
+}