Change the way sequence definition are managed. They are now when present stored as an attribute

Former-commit-id: 6e618377c05b42937d2eace3c9668390980ab68c

pkg/obiseq/biosequence.go

@@ -55,8 +55,8 @@ type Annotation map[string]interface{}
 // A BioSequence is a sequence of bytes with an identifier, a definition, a sequence, qualities,
 // features and annotations. It aims to represent a biological sequence
 type BioSequence struct {
-	id          string // The identidier of the sequence (private accessible through the method Id)
-	definition  string // The documentation of the sequence (private accessible through the method Definition)
+	id string // The identidier of the sequence (private accessible through the method Id)
+	//definition  string // The documentation of the sequence (private accessible through the method Definition)
 	source      string // The filename without directory name and extension from where the sequence was read.
 	sequence    []byte // The sequence itself, it is accessible by the methode Sequence
 	qualities   []byte // The quality scores of the sequence.
@@ -80,8 +80,8 @@ func NewEmptyBioSequence(preallocate int) *BioSequence {
 	}
 
 	return &BioSequence{
-		id:          "",
-		definition:  "",
+		id: "",
+		//definition:  "",
 		source:      "",
 		sequence:    seq,
 		qualities:   nil,
@@ -148,7 +148,7 @@ func (s *BioSequence) Copy() *BioSequence {
 	newSeq := NewEmptyBioSequence(0)
 
 	newSeq.id = s.id
-	newSeq.definition = s.definition
+	//newSeq.definition = s.definition
 
 	newSeq.sequence = CopySlice(s.sequence)
 	newSeq.qualities = CopySlice(s.qualities)
@@ -176,7 +176,16 @@ func (s *BioSequence) Id() string {
 // No parameters.
 // Returns a string.
 func (s *BioSequence) Definition() string {
-	return s.definition
+	definition := ""
+	var err error
+	def, ok := s.GetAttribute("definition")
+	if ok {
+		definition, err = obiutils.InterfaceToString(def)
+		if err != nil {
+			definition = ""
+		}
+	}
+	return definition
 }
 
 // Sequence returns the sequence of the BioSequence.
@@ -315,7 +324,7 @@ func (s *BioSequence) SetId(id string) {
 //
 // It takes a string parameter 'definition' and assigns it to the 'definition' field of the BioSequence struct.
 func (s *BioSequence) SetDefinition(definition string) {
-	s.definition = definition
+	s.SetAttribute("definition", definition)
 }
 
 // SetSource sets the source of the BioSequence.

pkg/obiseq/biosequence_test.go

@@ -143,11 +143,10 @@ func TestBioSequence_Recycle(t *testing.T) {
 // Returns: None.
 func TestCopy(t *testing.T) {
 	seq := &BioSequence{
-		id:         "test",
-		definition: "test sequence",
-		sequence:   []byte("ATCG"),
-		qualities:  []byte("1234"),
-		feature:    []byte("feature1...feature2"),
+		id:        "test",
+		sequence:  []byte("ATCG"),
+		qualities: []byte("1234"),
+		feature:   []byte("feature1...feature2"),
 		annotations: Annotation{
 			"annotation1": "value1",
 			"annotation2": "value2",
@@ -161,10 +160,6 @@ func TestCopy(t *testing.T) {
 	if newSeq.id != seq.id {
 		t.Errorf("Expected id to be %v, got %v", seq.id, newSeq.id)
 	}
-	if newSeq.definition != seq.definition {
-		t.Errorf("Expected definition to be %v, got %v", seq.definition, newSeq.definition)
-	}
-
 	// Test if the sequence, qualities, and feature fields are copied correctly
 	if !reflect.DeepEqual(newSeq.sequence, seq.sequence) {
 		t.Errorf("Expected sequence to be %v, got %v", seq.sequence, newSeq.sequence)

pkg/obiseq/subseq.go

@@ -32,7 +32,7 @@ func (sequence *BioSequence) Subsequence(from, to int, circular bool) (*BioSeque
 		}
 
 		newSeq.id = fmt.Sprintf("%s_sub[%d..%d]", sequence.Id(), from+1, to)
-		newSeq.definition = sequence.definition
+		//	newSeq.definition = sequence.definition
 	} else {
 		newSeq, _ = sequence.Subsequence(from, sequence.Len(), false)
 		newSeq.Write(sequence.Sequence()[0:to])