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Correct the number of workers

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Former-commit-id: febbccfb853263e0761ecfccb0f09c8c1bf88475
This commit is contained in:
Eric Coissac
2023-11-22 09:46:30 +01:00
parent 8905a16bc0
commit 2e0c1bd801
11 changed files with 206 additions and 39 deletions
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57
pkg/obiseq/worker.go
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@@ -1,5 +1,7 @@
package obiseq
import log "github.com/sirupsen/logrus"
type SeqAnnotator func(*BioSequence)
type SeqWorker func(*BioSequence) *BioSequence
@@ -17,7 +19,8 @@ func AnnotatorToSeqWorker(function SeqAnnotator) SeqWorker {
return f
}
func SeqToSliceWorker(worker SeqWorker, inplace bool) SeqSliceWorker {
func SeqToSliceWorker(worker SeqWorker,
inplace, breakOnError bool) SeqSliceWorker {
var f SeqSliceWorker
if worker == nil {
@@ -25,12 +28,12 @@ func SeqToSliceWorker(worker SeqWorker, inplace bool) SeqSliceWorker {
f = func(input BioSequenceSlice) BioSequenceSlice {
return input
}
} else {
} else {
f = func(input BioSequenceSlice) BioSequenceSlice {
output := MakeBioSequenceSlice(len(input))
copy(output,input)
copy(output, input)
return output
}
}
}
} else {
f = func(input BioSequenceSlice) BioSequenceSlice {
@@ -38,12 +41,21 @@ func SeqToSliceWorker(worker SeqWorker, inplace bool) SeqSliceWorker {
if !inplace {
output = MakeBioSequenceSlice(len(input))
}
for i, s := range input {
output[i] = worker(s)
i := 0
for _, s := range input {
r := worker(s)
if r != nil {
output[i] = r
i++
} else if breakOnError {
log.Fatalf("got an error on sequence %s processing",
r.Id())
}
}
return output
}
return output[0:i]
}
}
return f
@@ -51,10 +63,10 @@ func SeqToSliceWorker(worker SeqWorker, inplace bool) SeqSliceWorker {
func SeqToSliceConditionalWorker(worker SeqWorker,
condition SequencePredicate,
inplace bool) SeqSliceWorker {
inplace, breakOnError bool) SeqSliceWorker {
if condition == nil {
return SeqToSliceWorker(worker,inplace)
return SeqToSliceWorker(worker, inplace, breakOnError)
}
f := func(input BioSequenceSlice) BioSequenceSlice {
@@ -62,15 +74,23 @@ func SeqToSliceConditionalWorker(worker SeqWorker,
if !inplace {
output = MakeBioSequenceSlice(len(input))
}
for i, s := range input {
i := 0
for _, s := range input {
if condition(s) {
output[i] = worker(s)
} else {
output[i] = s
r := worker(s)
if r != nil {
output[i] = r
i++
} else if breakOnError {
log.Fatalf("got an error on sequence %s processing",
r.Id())
}
}
}
return output
return output[0:i]
}
return f
@@ -83,9 +103,12 @@ func (worker SeqWorker) ChainWorkers(next SeqWorker) SeqWorker {
if next == nil {
return worker
}
}
}
f := func(seq *BioSequence) *BioSequence {
if seq == nil {
return nil
}
return next(worker(seq))
}