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Plenty of small bugs

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Former-commit-id: 42c7fab7d65906c80ab4cd32da6867ff21842ea8
This commit is contained in:
Eric Coissac
2024-06-04 16:49:12 +02:00
parent e843d2aa5c
commit 65f5109957
15 changed files with 894 additions and 264 deletions
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15
pkg/obiseq/biosequence.go
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@ -161,7 +161,7 @@ func (sequence *BioSequence) Recycle() {
// Copy returns a new BioSequence that is a copy of the original BioSequence.
//
// It copies the id and definition fields of the original BioSequence to the new BioSequence.
// It copies the id of the original BioSequence to the new BioSequence.
// It also creates new slices and copies the values from the original BioSequence's sequence, qualities, and feature fields to the new BioSequence.
// If the original BioSequence has annotations, it locks the annot_lock and copies the annotations to the new BioSequence.
//
@ -170,15 +170,14 @@ func (s *BioSequence) Copy() *BioSequence {
newSeq := NewEmptyBioSequence(0)
newSeq.id = s.id
//newSeq.definition = s.definition
newSeq.sequence = CopySlice(s.sequence)
newSeq.qualities = CopySlice(s.qualities)
newSeq.feature = CopySlice(s.feature)
if len(s.annotations) > 0 {
defer s.annot_lock.Unlock()
s.annot_lock.Lock()
defer s.annot_lock.Unlock()
newSeq.annotations = GetAnnotation(s.annotations)
}
@ -210,6 +209,10 @@ func (s *BioSequence) Definition() string {
return definition
}
func (s *BioSequence) HasDefinition() bool {
return s.HasAttribute("definition")
}
// HasSequence checks if the BioSequence has a sequence.
//
// No parameters.
@ -420,8 +423,7 @@ func (s *BioSequence) SetSequence(sequence []byte) {
if s.sequence != nil {
RecycleSlice(&s.sequence)
}
s.sequence = GetSlice(len(sequence))[0:len(sequence)]
copy(s.sequence, obiutils.InPlaceToLower(sequence))
s.sequence = CopySlice(obiutils.InPlaceToLower(sequence))
}
// Setting the qualities of the BioSequence.
@ -429,8 +431,7 @@ func (s *BioSequence) SetQualities(qualities Quality) {
if s.qualities != nil {
RecycleSlice(&s.qualities)
}
s.qualities = GetSlice(len(qualities))[0:len(qualities)]
copy(s.qualities, qualities)
s.qualities = CopySlice(qualities)
}
// A method that appends a byte slice to the qualities of the BioSequence.