patch the Taxid method

pkg/obiseq/biosequence.go

@@ -1,3 +1,13 @@
+// A package that defines a BioSequence struct.
+//
+// BioSequence are used to représente biological DNA sequences.
+// The structure stores not only the sequence itself, but also some
+// complementaty information. Among them:
+//   - an identifier
+//   - a definition
+//   - the sequence quality scores
+//   - the features
+//   - the annotations
 package obiseq
 
 import (
@@ -260,7 +270,7 @@ func (s *BioSequence) Count() int {
 
 // Returning the taxid of the sequence.
 func (s *BioSequence) Taxid() int {
-	taxid, ok := s.GetInt("count")
+	taxid, ok := s.GetInt("taxid")
 
 	if !ok {
 		taxid = 1
@@ -269,6 +279,11 @@ func (s *BioSequence) Taxid() int {
 	return taxid
 }
 
+func (s *BioSequence) SetTaxid(taxid int) {
+	annot := s.Annotations()
+	annot["taxid"] = taxid
+}
+
 // Setting the id of the BioSequence.
 func (s *BioSequence) SetId(id string) {
 	s.id = id

pkg/obiseq/biosequenceslice.go

@@ -1,9 +1,14 @@
 package obiseq
 
 import (
+	log "github.com/sirupsen/logrus"
 	"sync"
 )
 
+// BioSequenceSlice represents a collection or a set of BioSequence.
+//
+// BioSequenceSlice is used to define BioSequenceBatch
+// a memory pool of BioSequenceSlice is managed to limit allocations.
 type BioSequenceSlice []*BioSequence
 
 var _BioSequenceSlicePool = sync.Pool{
@@ -13,32 +18,54 @@ var _BioSequenceSlicePool = sync.Pool{
 	},
 }
 
+// > This function returns a pointer to a new `BioSequenceSlice` object
 func NewBioSequenceSlice() *BioSequenceSlice {
 	return _BioSequenceSlicePool.Get().(*BioSequenceSlice)
 }
 
+// `MakeBioSequenceSlice()` returns a pointer to a new `BioSequenceSlice` struct
 func MakeBioSequenceSlice() BioSequenceSlice {
 	return *NewBioSequenceSlice()
 }
 
 func (s *BioSequenceSlice) Recycle() {
-	// if s == nil {
+	if s == nil {
-	// 	log.Panicln("Trying too recycle a nil pointer")
+		log.Panicln("Trying too recycle a nil pointer")
-	// }
+	}
 
-	// // Code added to potentially limit memory leaks
+	// Code added to potentially limit memory leaks
-	// for i := range *s {
+	for i := range *s {
-	// 	(*s)[i] = nil
+		(*s)[i] = nil
-	// }
+	}
 
-	// *s = (*s)[:0]
+	*s = (*s)[:0]
-	// _BioSequenceSlicePool.Put(s)
+	_BioSequenceSlicePool.Put(s)
 }
 
+// Making sure that the slice has enough capacity to hold the number of elements that are being added
+// to it.
+func (s *BioSequenceSlice) InsureCapacity(capacity int) *BioSequenceSlice {
+	var c int
+	if s != nil {
+		c = cap(*s)	
+	} else {
+		c = 0
+	}
+
+	if c < capacity {
+		sl := make(BioSequenceSlice, 0,capacity)
+		s = &sl
+	}
+
+	return s
+}
+
+// Appending the sequence to the slice.
 func (s *BioSequenceSlice) Push(sequence *BioSequence) {
 	*s = append(*s, sequence)
 }
 
+// Returning the last element of the slice and removing it from the slice.
 func (s *BioSequenceSlice) Pop() *BioSequence {
 	_s := (*s)[len(*s)-1]
 	(*s)[len(*s)-1] = nil
@@ -46,6 +73,7 @@ func (s *BioSequenceSlice) Pop() *BioSequence {
 	return _s
 }
 
+// Returning the first element of the slice and removing it from the slice.
 func (s *BioSequenceSlice) Pop0() *BioSequence {
 	_s := (*s)[0]
 	(*s)[0] = nil
@@ -53,6 +81,7 @@ func (s *BioSequenceSlice) Pop0() *BioSequence {
 	return _s
 }
 
+// Test that a slice of sequences contains at least a sequence.
 func (s BioSequenceSlice) NotEmpty() bool {
 	return len(s) > 0
 }