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rename the iterator class

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This commit is contained in:
Eric Coissac
2023-01-22 22:04:17 +01:00
parent 4592855095
commit f97f92df72
37 changed files with 399 additions and 354 deletions
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10
pkg/obiformats/genbank_read.go
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@ -26,7 +26,7 @@ const (
inSequence gbstate = 4
)
func _ParseGenbankFile(input <-chan _FileChunk, out obiiter.IBioSequenceBatch) {
func _ParseGenbankFile(input <-chan _FileChunk, out obiiter.IBioSequence) {
state := inHeader
@ -107,11 +107,11 @@ func _ParseGenbankFile(input <-chan _FileChunk, out obiiter.IBioSequenceBatch) {
}
func ReadGenbank(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBatch {
func ReadGenbank(reader io.Reader, options ...WithOption) obiiter.IBioSequence {
opt := MakeOptions(options)
entry_channel := make(chan _FileChunk, opt.BufferSize())
newIter := obiiter.MakeIBioSequenceBatch(opt.BufferSize())
newIter := obiiter.MakeIBioSequence(opt.BufferSize())
nworkers := opt.ParallelWorkers()
newIter.Add(nworkers)
@ -130,7 +130,7 @@ func ReadGenbank(reader io.Reader, options ...WithOption) obiiter.IBioSequenceBa
return newIter
}
func ReadGenbankFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) {
func ReadGenbankFromFile(filename string, options ...WithOption) (obiiter.IBioSequence, error) {
var reader io.Reader
var greader io.Reader
var err error
@ -138,7 +138,7 @@ func ReadGenbankFromFile(filename string, options ...WithOption) (obiiter.IBioSe
reader, err = os.Open(filename)
if err != nil {
log.Printf("open file error: %+v", err)
return obiiter.NilIBioSequenceBatch, err
return obiiter.NilIBioSequence, err
}
// Test if the flux is compressed by gzip