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Rename the Length methods Len to follow GO standart

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This commit is contained in:
Eric Coissac
2022-11-17 11:09:58 +01:00
parent eb32089305
commit 29563aa94e
30 changed files with 134 additions and 130 deletions
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2
pkg/obiseq/biosequence.go
View File

@@ -162,7 +162,7 @@ func (s *BioSequence) String() string {
}
// Returning the length of the sequence.
func (s *BioSequence) Length() int {
func (s *BioSequence) Len() int {
return len(s.sequence)
}

22
pkg/obiseq/predicate.go
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@@ -5,10 +5,8 @@ import (
"fmt"
"regexp"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obieval"
log "github.com/sirupsen/logrus"
"github.com/PaesslerAG/gval"
)
type SequencePredicate func(*BioSequence) bool
@@ -130,7 +128,7 @@ func IsLessAbundantOrEqualTo(count int) SequencePredicate {
func IsLongerOrEqualTo(length int) SequencePredicate {
f := func(sequence *BioSequence) bool {
return sequence.Length() >= length
return sequence.Len() >= length
}
return f
@@ -138,7 +136,7 @@ func IsLongerOrEqualTo(length int) SequencePredicate {
func IsShorterOrEqualTo(length int) SequencePredicate {
f := func(sequence *BioSequence) bool {
return sequence.Length() <= length
return sequence.Len() <= length
}
return f
@@ -203,17 +201,7 @@ func IsIdIn(ids ...string) SequencePredicate {
func ExpressionPredicat(expression string) SequencePredicate {
lang := gval.NewLanguage(
gval.Full(),
gval.Function("len", func(args ...interface{}) (interface{}, error) {
length := goutils.Length(args[0])
return (float64)(length), nil
}),
gval.Function("ismap", func(args ...interface{}) (interface{}, error) {
ismap := goutils.IsAMap(args[0])
return ismap, nil
}))
exp, err := lang.NewEvaluable(expression)
exp, err := obieval.OBILang.NewEvaluable(expression)
if err != nil {
log.Fatalf("Error in the expression : %s", expression)
}
@@ -223,7 +211,7 @@ func ExpressionPredicat(expression string) SequencePredicate {
map[string]interface{}{
"annot": sequence.Annotations(),
"count": sequence.Count(),
"seqlength": sequence.Length(),
"seqlength": sequence.Len(),
"sequence": sequence,
},
)

6
pkg/obiseq/revcomp.go
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@@ -13,7 +13,7 @@ func (sequence *BioSequence) ReverseComplement(inplace bool) *BioSequence {
s := sequence.sequence
for i, j := sequence.Length()-1, 0; i >= j; i-- {
for i, j := sequence.Len()-1, 0; i >= j; i-- {
// ASCII code & 31 -> builds an index in witch (a|A) is 1
// ASCII code & 0x20 -> Foce lower case
@@ -25,7 +25,7 @@ func (sequence *BioSequence) ReverseComplement(inplace bool) *BioSequence {
if sequence.HasQualities() {
s := sequence.qualities
for i, j := sequence.Length()-1, 0; i >= j; i-- {
for i, j := sequence.Len()-1, 0; i >= j; i-- {
s[j], s[i] = s[i], s[j]
j++
}
@@ -49,7 +49,7 @@ func (sequence *BioSequence) _revcmpMutation() *BioSequence {
return string(b)
}
lseq := sequence.Length()
lseq := sequence.Len()
mut, ok := sequence.GetIntMap("pairing_mismatches")
if ok && len(mut) > 0 {

8
pkg/obiseq/subseq.go
View File

@@ -13,11 +13,11 @@ func (sequence *BioSequence) Subsequence(from, to int, circular bool) (*BioSeque
return nil, errors.New("from greater than to")
}
if from < 0 || from >= sequence.Length() {
if from < 0 || from >= sequence.Len() {
return nil, errors.New("from out of bounds")
}
if to <= 0 || to > sequence.Length() {
if to <= 0 || to > sequence.Len() {
return nil, errors.New("to out of bounds")
}
@@ -34,7 +34,7 @@ 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
} else {
newSeq, _ = sequence.Subsequence(from, sequence.Length(), false)
newSeq, _ = sequence.Subsequence(from, sequence.Len(), false)
newSeq.Write(sequence.Sequence()[0:to])
if sequence.HasQualities() {
@@ -52,7 +52,7 @@ func (sequence *BioSequence) Subsequence(from, to int, circular bool) (*BioSeque
func (sequence *BioSequence) _subseqMutation(shift int) *BioSequence {
lseq := sequence.Length()
lseq := sequence.Len()
mut, ok := sequence.GetIntMap("pairing_mismatches")
if ok && len(mut) > 0 {