obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-06-29 16:20:46 +00:00
Code Issues Packages Projects Releases Wiki Activity

small refactoring including doc

Browse Source 
Former-commit-id: 6d6b527d89d77aa571831f7500f841840e280536
This commit is contained in:
Eric Coissac
2023-08-27 15:52:28 +02:00
parent f1025f97b8
commit 7b7128196a
4 changed files with 17 additions and 8 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
pkg/obiseq/class.go
View File

@ -71,7 +71,7 @@ func AnnotationClassifier(key string, na string) *BioSequenceClassifier {
locke.RLock() locke.RLock()
defer locke.RUnlock() defer locke.RUnlock()
if k >= maxcode { if k >= maxcode {
log.Fatalf("value %d not register") log.Fatalf("value %d not register", k)
} }
return decode[k] return decode[k]
} }
@ -154,7 +154,7 @@ func DualAnnotationClassifier(key1, key2 string, na string) *BioSequenceClassifi
locke.RLock() locke.RLock()
defer locke.RUnlock() defer locke.RUnlock()
if k >= maxcode { if k >= maxcode {
log.Fatalf("value %d not register") log.Fatalf("value %d not register", k)
} }
return decode[k] return decode[k]
} }

4
pkg/obitax/lca.go
View File

@ -43,7 +43,7 @@ func (taxonomy *Taxonomy) TaxonomicDistribution(sequence *obiseq.BioSequence) ma
t, et := taxonomy.Taxon(taxid) t, et := taxonomy.Taxon(taxid)
if et != nil { if et != nil {
log.Panic("Taxid %d not defined in taxonomy : %v", k, et) log.Panicf("Taxid %d not defined in taxonomy : %v", k, et)
} }
taxons[t] = v taxons[t] = v
} }
@ -60,7 +60,7 @@ func (taxonomy *Taxonomy) LCA(sequence *obiseq.BioSequence, threshold float64) (
for t, w := range taxons { for t, w := range taxons {
p, ep := t.Path() p, ep := t.Path()
if ep != nil { if ep != nil {
log.Panic("Taxonomic path cannot be retreived from Taxid %d : %v", t.Taxid(), ep) log.Panicf("Taxonomic path cannot be retreived from Taxid %d : %v", t.Taxid(), ep)
} }
obiutils.Reverse(*p, true) obiutils.Reverse(*p, true)

8
pkg/obitools/obiclean/obiclean.go
View File

@ -106,7 +106,7 @@ func IsHead(sequence *obiseq.BioSequence) bool {
case bool: case bool:
ishead = iishead ishead = iishead
default: default:
log.Panic("obiclean_head attribute of sequence %s must be a boolean not : %v", sequence.Id(), iishead) log.Panicf("obiclean_head attribute of sequence %s must be a boolean not : %v", sequence.Id(), iishead)
} }
} }
@ -122,7 +122,7 @@ func HeadCount(sequence *obiseq.BioSequence) int {
if ok { if ok {
value, err = obiutils.InterfaceToInt(value) value, err = obiutils.InterfaceToInt(value)
if err != nil { if err != nil {
log.Panic("obiclean_headcount attribute of sequence %s must be an integer value not : %v", sequence.Id(), ivalue) log.Panicf("obiclean_headcount attribute of sequence %s must be an integer value not : %v", sequence.Id(), ivalue)
} }
} }
@ -138,7 +138,7 @@ func InternalCount(sequence *obiseq.BioSequence) int {
if ok { if ok {
value, err = obiutils.InterfaceToInt(value) value, err = obiutils.InterfaceToInt(value)
if err != nil { if err != nil {
log.Panic("obiclean_internalcount attribute of sequence %s must be an integer value not : %v", sequence.Id(), ivalue) log.Panicf("obiclean_internalcount attribute of sequence %s must be an integer value not : %v", sequence.Id(), ivalue)
} }
} }
@ -154,7 +154,7 @@ func SingletonCount(sequence *obiseq.BioSequence) int {
if ok { if ok {
value, err = obiutils.InterfaceToInt(value) value, err = obiutils.InterfaceToInt(value)
if err != nil { if err != nil {
log.Panic("obiclean_samplecount attribute of sequence %s must be an integer value not : %v", sequence.Id(), ivalue) log.Panicf("obiclean_samplecount attribute of sequence %s must be an integer value not : %v", sequence.Id(), ivalue)
} }
} }

9
pkg/obiutils/array.go
View File

@ -33,6 +33,15 @@ func Make2DArray[T any](rows, cols int) Matrix[T] {
return matrix return matrix
} }
// Make2DNumericArray generates a 2D numeric array with the specified number of rows and columns.
//
// Parameters:
// - rows: the number of rows in the array.
// - cols: the number of columns in the array.
// - zeroed: a boolean indicating whether the array should be initialized with zeros.
//
// Returns:
// - matrix: a 2D numeric array with the specified dimensions.
func Make2DNumericArray[T Numeric](rows, cols int, zeroed bool) Matrix[T] { func Make2DNumericArray[T Numeric](rows, cols int, zeroed bool) Matrix[T] {
matrix := make(Matrix[T], rows) matrix := make(Matrix[T], rows)
data := make([]T, cols*rows) data := make([]T, cols*rows)