Add some code refactoring from the blackboard branch

pkg/obiiter/batch.go

@@ -3,50 +3,118 @@ package obiiter
 import "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 
 type BioSequenceBatch struct {
-	slice obiseq.BioSequenceSlice
-	order int
+	source string
+	slice  obiseq.BioSequenceSlice
+	order  int
 }
 
-var NilBioSequenceBatch = BioSequenceBatch{nil, -1}
+var NilBioSequenceBatch = BioSequenceBatch{"", nil, -1}
 
-func MakeBioSequenceBatch(order int,
+// MakeBioSequenceBatch creates a new BioSequenceBatch with the given source, order, and sequences.
+//
+// Parameters:
+// - source: The source of the BioSequenceBatch.
+// - order: The order of the BioSequenceBatch.
+// - sequences: The slice of BioSequence.
+//
+// Returns:
+// - BioSequenceBatch: The newly created BioSequenceBatch.
+func MakeBioSequenceBatch(
+	source string,
+	order int,
 	sequences obiseq.BioSequenceSlice) BioSequenceBatch {
 
 	return BioSequenceBatch{
-		slice: sequences,
-		order: order,
+		source: source,
+		slice:  sequences,
+		order:  order,
 	}
 }
 
+// Order returns the order of the BioSequenceBatch.
+//
+// Returns:
+// - int: The order of the BioSequenceBatch.
 func (batch BioSequenceBatch) Order() int {
 	return batch.order
 }
 
+// Source returns the source of the BioSequenceBatch.
+//
+// Returns:
+// - string: The source of the BioSequenceBatch.
+func (batch BioSequenceBatch) Source() string {
+	return batch.source
+}
+
+// Reorder updates the order of the BioSequenceBatch and returns the updated batch.
+//
+// Parameters:
+// - newOrder: The new order value to assign to the BioSequenceBatch.
+//
+// Returns:
+// - BioSequenceBatch: The updated BioSequenceBatch with the new order value.
 func (batch BioSequenceBatch) Reorder(newOrder int) BioSequenceBatch {
 	batch.order = newOrder
 	return batch
 }
 
+// Slice returns the BioSequenceSlice contained within the BioSequenceBatch.
+//
+// Returns:
+// - obiseq.BioSequenceSlice: The BioSequenceSlice contained within the BioSequenceBatch.
 func (batch BioSequenceBatch) Slice() obiseq.BioSequenceSlice {
 	return batch.slice
 }
 
+// Len returns the number of BioSequence elements in the given BioSequenceBatch.
+//
+// Parameters:
+// - batch: The BioSequenceBatch to get the length from.
+//
+// Return type:
+// - int: The number of BioSequence elements in the BioSequenceBatch.
 func (batch BioSequenceBatch) Len() int {
 	return len(batch.slice)
 }
 
+// NotEmpty returns whether the BioSequenceBatch is empty or not.
+//
+// It checks if the BioSequenceSlice contained within the BioSequenceBatch is not empty.
+//
+// Returns:
+// - bool: True if the BioSequenceBatch is not empty, false otherwise.
 func (batch BioSequenceBatch) NotEmpty() bool {
 	return batch.slice.NotEmpty()
 }
 
+// Pop0 returns and removes the first element of the BioSequenceBatch.
+//
+// It does not take any parameters.
+// It returns a pointer to a BioSequence object.
 func (batch BioSequenceBatch) Pop0() *obiseq.BioSequence {
 	return batch.slice.Pop0()
 }
 
+// IsNil checks if the BioSequenceBatch's slice is nil.
+//
+// This function takes a BioSequenceBatch as a parameter and returns a boolean value indicating whether the slice of the BioSequenceBatch is nil or not.
+//
+// Parameters:
+// - batch: The BioSequenceBatch to check for nil slice.
+//
+// Returns:
+// - bool: True if the BioSequenceBatch's slice is nil, false otherwise.
 func (batch BioSequenceBatch) IsNil() bool {
 	return batch.slice == nil
 }
 
+// Recycle cleans up the BioSequenceBatch by recycling its elements and resetting its slice.
+//
+// If including_seq is true, each element of the BioSequenceBatch's slice is recycled using the Recycle method,
+// and then set to nil. If including_seq is false, each element is simply set to nil.
+//
+// This function does not return anything.
 func (batch BioSequenceBatch) Recycle(including_seq bool) {
 	batch.slice.Recycle(including_seq)
 	batch.slice = nil