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6 Commits

Author SHA1 Message Date
Eric Coissac 930fe5f1ba Release 4.4.43 2026-06-01 13:22:58 +02:00
Eric Coissac dcdaf9e372 feat: support map and slice types in OBI attributes
Extends OBI header parsing to recognize and deserialize JSON-like arrays and objects. Introduces safe conversion utilities in `obiutils` to cast generic interface values into typed maps, and exposes them via new `BioSequence` methods. Header values are now marshaled, quote-normalized, and formatted for map and slice types.
2026-06-01 13:21:11 +02:00
Eric Coissac af7ae3d60c Correct Shannon entropy bias for canonical k-mers
Multiple raw k-mers collapsing into identical circular canonical forms introduce bias into complexity estimates. This change pre-computes `log(class_size)` tables and per-word-size maximum entropy bounds. The `KmerEntropy` function and `KmerEntropyFilter` are updated to apply the corrected formula `(log(N) + Σf·log(s) - Σf·log(f))/N / emax`, ensuring accurate sequence complexity estimation.
2026-05-17 14:54:57 +08:00
Eric Coissac cecf90fa40 feat: add min/max filtering and saturating subtraction utilities
Introduce generic and reflection-based utilities for filtering slices and maps by minimum/maximum thresholds, along with saturating subtraction. The `obiutils` package provides type-safe generic implementations alongside dynamic reflection dispatchers to handle arbitrary ordered and numeric types. These are exposed as GVAL expression functions in `obiseq`, extending the language's built-in filtering and numeric capabilities.
2026-05-14 20:58:24 +08:00
Eric Coissac a186bd1c92 fix: validate non-empty sequence IDs in FASTA and FASTQ writers
Adds a pre-processing guard that checks for empty sequence identifiers before formatting. This prevents malformed FASTA output and stops downstream processing of invalid FASTQ data by terminating early. The check is placed before existing sequence-length validations to enforce non-empty IDs during batch processing.
2026-05-05 18:07:58 +02:00
coissac 46d60c1a44 Merge pull request #115 from metabarcoding/push-lkzqoskvyqtr
[4.4.2] Enhanced taxonomy handling, input robustness & PCR tag validation
2026-04-30 16:59:49 +02:00
11 changed files with 496 additions and 70 deletions
+79 -4
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@@ -146,6 +146,65 @@ func __match__key__(text []byte) []int {
return []int{} // Not a key return []int{} // Not a key
} }
func __match__array__(text []byte) []int {
state := 0
level := 0
start := 0
instring := byte(0)
for i, r := range text {
if state == 2 {
if r == ';' {
return []int{start, i + 1}
}
if r != ' ' && r != '\t' {
return []int{}
}
}
if state == 0 {
if r == '[' {
level++
state++
start = i
continue
}
if r != ' ' && r != '\t' {
return []int{}
}
continue
}
// state == 1: inside the array
if instring != 0 {
if r == instring {
instring = 0
}
continue
}
if r == '"' || r == '\'' {
instring = r
continue
}
if r == '[' || r == '{' {
level++
continue
}
if r == ']' || r == '}' {
level--
if level == 0 {
state++
}
}
}
return []int{}
}
func __match__general__(text []byte) []int { func __match__general__(text []byte) []int {
for i, r := range text { for i, r := range text {
@@ -242,6 +301,21 @@ func ParseOBIFeatures(text string, annotations obiseq.Annotation) string {
stop = m[1] + 1 stop = m[1] + 1
} else { } else {
// array value
m = __match__array__(part)
if len(m) > 0 {
bvalue = bytes.TrimSpace(part[m[0]:(m[1] - 1)])
j := bytes.ReplaceAll(bvalue, []byte("'"), []byte(`"`))
j = __obi_header_map_int_key__.ReplaceAll(j, []byte(`$1"$2":`))
arr, err := _parse_json_array_interface(j)
if err != nil {
value = string(bvalue)
} else {
value = arr
}
stop = m[1] + 1
} else {
// Generic value // Generic value
// m = __obi_header_value_general_pattern__.FindIndex(part) // m = __obi_header_value_general_pattern__.FindIndex(part)
@@ -264,6 +338,7 @@ func ParseOBIFeatures(text string, annotations obiseq.Annotation) string {
// no value // no value
break break
} // End of No value } // End of No value
} // End of not array
} // End of not dict } // End of not dict
} // End of not string } // End of not string
} // End of not numeric } // End of not numeric
@@ -327,9 +402,8 @@ func WriteFastSeqOBIHeade(buffer *bytes.Buffer, sequence *obiseq.BioSequence) {
buffer.WriteString(fmt.Sprintf("%s=", key)) buffer.WriteString(fmt.Sprintf("%s=", key))
buffer.Write(tv) buffer.Write(tv)
buffer.WriteString("; ") buffer.WriteString("; ")
case map[string]int, default:
map[string]string, if obiutils.IsAMap(value) || obiutils.IsASlice(value) || obiutils.IsAnArray(value) {
map[string]interface{}:
tv, err := obiutils.JsonMarshal(t) tv, err := obiutils.JsonMarshal(t)
if err != nil { if err != nil {
log.Fatalf("Cannot convert %v value", value) log.Fatalf("Cannot convert %v value", value)
@@ -338,11 +412,12 @@ func WriteFastSeqOBIHeade(buffer *bytes.Buffer, sequence *obiseq.BioSequence) {
buffer.WriteString(fmt.Sprintf("%s=", key)) buffer.WriteString(fmt.Sprintf("%s=", key))
buffer.Write(tv) buffer.Write(tv)
buffer.WriteString("; ") buffer.WriteString("; ")
default: } else {
buffer.WriteString(fmt.Sprintf("%s=%v; ", key, value)) buffer.WriteString(fmt.Sprintf("%s=%v; ", key, value))
} }
} }
} }
}
if sequence.HasDefinition() { if sequence.HasDefinition() {
buffer.WriteByte(' ') buffer.WriteByte(' ')
+3
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@@ -90,6 +90,9 @@ func FormatFastaBatch(batch obiiter.BioSequenceBatch, formater FormatHeader, ski
log.Debugf("FormatFastaBatch: #%d : %d seqs", batch.Order(), batch.Len()) log.Debugf("FormatFastaBatch: #%d : %d seqs", batch.Order(), batch.Len())
for _, seq := range batch.Slice() { for _, seq := range batch.Slice() {
if len(seq.Id()) == 0 {
log.Fatalf("Sequence identifier is empty")
}
if seq.Len() > 0 { if seq.Len() > 0 {
// Write header directly into bs — no intermediate string // Write header directly into bs — no intermediate string
bs.WriteByte('>') bs.WriteByte('>')
+3
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@@ -64,6 +64,9 @@ func FormatFastqBatch(batch obiiter.BioSequenceBatch,
first := true first := true
for _, seq := range batch.Slice() { for _, seq := range batch.Slice() {
if len(seq.Id()) == 0 {
log.Fatalf("Sequence identifier is empty")
}
if seq.Len() > 0 { if seq.Len() > 0 {
_formatFastq(&bs, seq, formater) _formatFastq(&bs, seq, formater)
+75 -40
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@@ -4,22 +4,21 @@ import "math"
// KmerEntropy computes the entropy of a single encoded k-mer. // KmerEntropy computes the entropy of a single encoded k-mer.
// //
// The algorithm mirrors the lowmask entropy calculation: it decodes the k-mer // The algorithm mirrors the Rust obiskbuilder entropy: it decodes the k-mer
// to a DNA sequence, extracts all sub-words of each size from 1 to levelMax, // to a DNA sequence, extracts all sub-words of each size from 1 to levelMax,
// normalizes them by circular canonical form, counts their frequencies, and // normalizes them by circular canonical form, counts their frequencies, and
// computes Shannon entropy normalized by the maximum possible entropy. // computes Shannon entropy corrected for class sizes, normalized by the
// maximum possible entropy over 4^ws raw bins.
// The returned value is the minimum entropy across all word sizes. // The returned value is the minimum entropy across all word sizes.
// //
// Correction for small sequences: the raw entropy H = log(N) - Σ f·log(f)/N
// under-estimates the true complexity when many raw words collapse to the same
// canonical form. Adding Σ f·log(class_size)/N recovers the entropy of the
// underlying uncollapsed distribution (assuming uniform mixing within each
// equivalence class).
//
// A value close to 0 indicates very low complexity (e.g. "AAAA..."), // A value close to 0 indicates very low complexity (e.g. "AAAA..."),
// while a value close to 1 indicates high complexity. // while a value close to 1 indicates high complexity.
//
// Parameters:
// - kmer: the encoded k-mer (2 bits per base)
// - k: the k-mer size
// - levelMax: maximum sub-word size for entropy (typically 6)
//
// Returns:
// - minimum normalized entropy across all word sizes 1..levelMax
func KmerEntropy(kmer uint64, k int, levelMax int) float64 { func KmerEntropy(kmer uint64, k int, levelMax int) float64 {
if k < 1 || levelMax < 1 { if k < 1 || levelMax < 1 {
return 1.0 return 1.0
@@ -35,7 +34,7 @@ func KmerEntropy(kmer uint64, k int, levelMax int) float64 {
var seqBuf [32]byte var seqBuf [32]byte
seq := DecodeKmer(kmer, k, seqBuf[:]) seq := DecodeKmer(kmer, k, seqBuf[:])
// Pre-compute nLogN lookup (same as lowmask) // Pre-compute nLogN lookup
nLogN := make([]float64, k+1) nLogN := make([]float64, k+1)
for i := 1; i <= k; i++ { for i := 1; i <= k; i++ {
nLogN[i] = float64(i) * math.Log(float64(i)) nLogN[i] = float64(i) * math.Log(float64(i))
@@ -51,6 +50,23 @@ func KmerEntropy(kmer uint64, k int, levelMax int) float64 {
} }
} }
// Build ln(class_size) tables: for each canonical form, how many raw
// words map to it under circular normalization.
classLogSizeTables := make([][]float64, levelMax+1)
for ws := 1; ws <= levelMax; ws++ {
tableSize := 1 << (ws * 2)
classSize := make([]int, tableSize)
for code := 0; code < tableSize; code++ {
classSize[normTables[ws][code]]++
}
classLogSizeTables[ws] = make([]float64, tableSize)
for j := 0; j < tableSize; j++ {
if classSize[j] > 0 {
classLogSizeTables[ws][j] = math.Log(float64(classSize[j]))
}
}
}
minEntropy := math.MaxFloat64 minEntropy := math.MaxFloat64
for ws := 1; ws <= levelMax; ws++ { for ws := 1; ws <= levelMax; ws++ {
@@ -75,23 +91,13 @@ func KmerEntropy(kmer uint64, k int, levelMax int) float64 {
table[normWord]++ table[normWord]++
} }
// Compute Shannon entropy // Compute emax over 4^ws raw bins (uncollapsed distribution).
floatNwords := float64(nwords) floatNwords := float64(nwords)
logNwords := math.Log(floatNwords) logNwords := math.Log(floatNwords)
na := tableSize // 4^ws
var sumNLogN float64
for j := 0; j < tableSize; j++ {
n := table[j]
if n > 0 {
sumNLogN += nLogN[n]
}
}
// Compute emax (maximum possible entropy for this word size)
na := CanonicalCircularKmerCount(ws)
var emax float64 var emax float64
if nwords < na { if nwords < na {
emax = math.Log(float64(nwords)) emax = logNwords
} else { } else {
cov := nwords / na cov := nwords / na
remains := nwords - (na * cov) remains := nwords - (na * cov)
@@ -105,7 +111,19 @@ func KmerEntropy(kmer uint64, k int, levelMax int) float64 {
continue continue
} }
entropy := (logNwords - sumNLogN/floatNwords) / emax // Accumulate Σ f·log(f) and Σ f·log(class_size) over canonical forms.
classLogSize := classLogSizeTables[ws]
var sumNLogN, sumClassLogN float64
for j := 0; j < tableSize; j++ {
n := table[j]
if n > 0 {
sumNLogN += nLogN[n]
sumClassLogN += float64(n) * classLogSize[j]
}
}
// Corrected entropy: H_raw ≈ log(N) + (Σf·log(s) - Σf·log(f)) / N
entropy := (logNwords + sumClassLogN/floatNwords - sumNLogN/floatNwords) / emax
if entropy < 0 { if entropy < 0 {
entropy = 0 entropy = 0
} }
@@ -134,6 +152,7 @@ type KmerEntropyFilter struct {
threshold float64 threshold float64
nLogN []float64 nLogN []float64
normTables [][]int normTables [][]int
classLogSizeTables [][]float64
emaxValues []float64 emaxValues []float64
logNwords []float64 logNwords []float64
// Pre-allocated frequency tables reused across Entropy() calls. // Pre-allocated frequency tables reused across Entropy() calls.
@@ -142,11 +161,6 @@ type KmerEntropyFilter struct {
} }
// NewKmerEntropyFilter creates an entropy filter with pre-computed tables. // NewKmerEntropyFilter creates an entropy filter with pre-computed tables.
//
// Parameters:
// - k: the k-mer size
// - levelMax: maximum sub-word size for entropy (typically 6)
// - threshold: entropy threshold (k-mers with entropy <= threshold are rejected)
func NewKmerEntropyFilter(k, levelMax int, threshold float64) *KmerEntropyFilter { func NewKmerEntropyFilter(k, levelMax int, threshold float64) *KmerEntropyFilter {
if levelMax >= k { if levelMax >= k {
levelMax = k - 1 levelMax = k - 1
@@ -169,20 +183,38 @@ func NewKmerEntropyFilter(k, levelMax int, threshold float64) *KmerEntropyFilter
} }
} }
// ln(class_size) for each canonical form under circular normalization.
classLogSizeTables := make([][]float64, levelMax+1)
for ws := 1; ws <= levelMax; ws++ {
tableSize := 1 << (ws * 2)
classSize := make([]int, tableSize)
for code := 0; code < tableSize; code++ {
classSize[normTables[ws][code]]++
}
classLogSizeTables[ws] = make([]float64, tableSize)
for j := 0; j < tableSize; j++ {
if classSize[j] > 0 {
classLogSizeTables[ws][j] = math.Log(float64(classSize[j]))
}
}
}
// Pre-compute emax and logNwords per word size.
// emax uses 4^ws raw bins to match the corrected entropy.
emaxValues := make([]float64, levelMax+1) emaxValues := make([]float64, levelMax+1)
logNwords := make([]float64, levelMax+1) logNwords := make([]float64, levelMax+1)
for ws := 1; ws <= levelMax; ws++ { for ws := 1; ws <= levelMax; ws++ {
nw := k - ws + 1 nw := k - ws + 1
na := CanonicalCircularKmerCount(ws) na := 1 << (ws * 2) // 4^ws raw bins
floatNw := float64(nw)
logNwords[ws] = math.Log(floatNw)
if nw < na { if nw < na {
logNwords[ws] = math.Log(float64(nw)) emaxValues[ws] = logNwords[ws]
emaxValues[ws] = math.Log(float64(nw))
} else { } else {
cov := nw / na cov := nw / na
remains := nw - (na * cov) remains := nw - (na * cov)
f1 := float64(cov) / float64(nw) f1 := float64(cov) / floatNw
f2 := float64(cov+1) / float64(nw) f2 := float64(cov+1) / floatNw
logNwords[ws] = math.Log(float64(nw))
emaxValues[ws] = -(float64(na-remains)*f1*math.Log(f1) + emaxValues[ws] = -(float64(na-remains)*f1*math.Log(f1) +
float64(remains)*f2*math.Log(f2)) float64(remains)*f2*math.Log(f2))
} }
@@ -200,6 +232,7 @@ func NewKmerEntropyFilter(k, levelMax int, threshold float64) *KmerEntropyFilter
threshold: threshold, threshold: threshold,
nLogN: nLogN, nLogN: nLogN,
normTables: normTables, normTables: normTables,
classLogSizeTables: classLogSizeTables,
emaxValues: emaxValues, emaxValues: emaxValues,
logNwords: logNwords, logNwords: logNwords,
freqTables: freqTables, freqTables: freqTables,
@@ -236,7 +269,7 @@ func (ef *KmerEntropyFilter) Entropy(kmer uint64) float64 {
// Count circular-canonical sub-word frequencies // Count circular-canonical sub-word frequencies
tableSize := 1 << (ws * 2) tableSize := 1 << (ws * 2)
table := ef.freqTables[ws] table := ef.freqTables[ws]
clear(table) // reset to zero clear(table)
mask := (1 << (ws * 2)) - 1 mask := (1 << (ws * 2)) - 1
normTable := ef.normTables[ws] normTable := ef.normTables[ws]
@@ -251,19 +284,21 @@ func (ef *KmerEntropyFilter) Entropy(kmer uint64) float64 {
table[normWord]++ table[normWord]++
} }
// Compute Shannon entropy
floatNwords := float64(nwords) floatNwords := float64(nwords)
logNwords := ef.logNwords[ws] logNwords := ef.logNwords[ws]
classLogSize := ef.classLogSizeTables[ws]
var sumNLogN float64 var sumNLogN, sumClassLogN float64
for j := 0; j < tableSize; j++ { for j := 0; j < tableSize; j++ {
n := table[j] n := table[j]
if n > 0 { if n > 0 {
sumNLogN += ef.nLogN[n] sumNLogN += ef.nLogN[n]
sumClassLogN += float64(n) * classLogSize[j]
} }
} }
entropy := (logNwords - sumNLogN/floatNwords) / emax // Corrected entropy: H_raw ≈ log(N) + (Σf·log(s) - Σf·log(f)) / N
entropy := (logNwords + sumClassLogN/floatNwords - sumNLogN/floatNwords) / emax
if entropy < 0 { if entropy < 0 {
entropy = 0 entropy = 0
} }
+1 -1
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@@ -3,7 +3,7 @@ package obioptions
// Version is automatically updated by the Makefile from version.txt // Version is automatically updated by the Makefile from version.txt
// The patch number (third digit) is incremented on each push to the repository // The patch number (third digit) is incremented on each push to the repository
var _Version = "Release 4.4.42" var _Version = "Release 4.4.43"
// Version returns the version of the obitools package. // Version returns the version of the obitools package.
// //
+18
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@@ -364,6 +364,24 @@ func (s *BioSequence) GetIntSlice(key string) ([]int, bool) {
return val, ok return val, ok
} }
func (s *BioSequence) GetMapOfIntSlice(key string) (map[string][]int, bool) {
v, ok := s.GetAttribute(key)
if !ok {
return nil, false
}
val, err := obiutils.InterfaceToMapOfIntSlice(v)
return val, err == nil
}
func (s *BioSequence) GetMapOfStringSlice(key string) (map[string][]string, bool) {
v, ok := s.GetAttribute(key)
if !ok {
return nil, false
}
val, err := obiutils.InterfaceToMapOfStringSlice(v)
return val, err == nil
}
// Count returns the value of the "count" attribute of the BioSequence. // Count returns the value of the "count" attribute of the BioSequence.
// //
// The count of a sequence is the number of times it has been observed in the dataset. // The count of a sequence is the number of times it has been observed in the dataset.
+1 -1
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@@ -103,7 +103,7 @@ func TestNewBioSequence(t *testing.T) {
// Return type: None. // Return type: None.
func TestNewBioSequenceWithQualities(t *testing.T) { func TestNewBioSequenceWithQualities(t *testing.T) {
id := "123" id := "123"
sequence := []byte("ATGC") sequence := []byte("atgc")
definition := "DNA sequence" definition := "DNA sequence"
qualities := []byte("1234") qualities := []byte("1234")
+13
View File
@@ -141,6 +141,19 @@ var OBILang = gval.NewLanguage(
gval.Function("max", func(args ...interface{}) (interface{}, error) { gval.Function("max", func(args ...interface{}) (interface{}, error) {
return obiutils.Max(args[0]) return obiutils.Max(args[0])
}), }),
gval.Function("filtermin", func(args ...interface{}) (interface{}, error) {
return obiutils.FilterMin(args[0], args[1])
}),
gval.Function("filtermax", func(args ...interface{}) (interface{}, error) {
return obiutils.FilterMax(args[0], args[1])
}),
gval.Function("saturatingsub", func(args ...interface{}) (interface{}, error) {
return obiutils.SaturatingSub(args[0], args[1])
}),
gval.Function("contains", func(args ...interface{}) (interface{}, error) { gval.Function("contains", func(args ...interface{}) (interface{}, error) {
if obiutils.IsAMap(args[0]) { if obiutils.IsAMap(args[0]) {
val := reflect.ValueOf(args[0]).MapIndex(reflect.ValueOf(args[1])) val := reflect.ValueOf(args[0]).MapIndex(reflect.ValueOf(args[1]))
+38
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@@ -276,6 +276,44 @@ func InterfaceToStringMap(i interface{}) (val map[string]string, err error) {
return return
} }
func InterfaceToMapOfIntSlice(i interface{}) (val map[string][]int, err error) {
err = nil
switch m := i.(type) {
case map[string][]int:
val = m
case map[string]interface{}:
val = make(map[string][]int, len(m))
for k, v := range m {
val[k], err = InterfaceToIntSlice(v)
if err != nil {
return
}
}
default:
err = &NotAMapInt{"value attribute cannot be casted to a map[string][]int"}
}
return
}
func InterfaceToMapOfStringSlice(i interface{}) (val map[string][]string, err error) {
err = nil
switch m := i.(type) {
case map[string][]string:
val = m
case map[string]interface{}:
val = make(map[string][]string, len(m))
for k, v := range m {
val[k], err = InterfaceToStringSlice(v)
if err != nil {
return
}
}
default:
err = &NotAMapInt{"value attribute cannot be casted to a map[string][]string"}
}
return
}
func InterfaceToStringSlice(i interface{}) (val []string, err error) { func InterfaceToStringSlice(i interface{}) (val []string, err error) {
err = nil err = nil
+241
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@@ -34,6 +34,26 @@ func MinMaxSlice[T constraints.Ordered](vec []T) (min, max T) {
return return
} }
func FilterMinSlice[T constraints.Ordered](vec []T, minimum T) []T {
result := make([]T, 0, len(vec))
for _, v := range vec {
if v >= minimum {
result = append(result, v)
}
}
return result
}
func FilterMaxSlice[T constraints.Ordered](vec []T, maximum T) []T {
result := make([]T, 0, len(vec))
for _, v := range vec {
if v <= maximum {
result = append(result, v)
}
}
return result
}
func MaxMap[K comparable, T constraints.Ordered](values map[K]T) (K, T, error) { func MaxMap[K comparable, T constraints.Ordered](values map[K]T) (K, T, error) {
var maxKey K var maxKey K
var maxValue T var maxValue T
@@ -73,6 +93,46 @@ func MinMap[K comparable, T constraints.Ordered](values map[K]T) (K, T, error) {
return minKey, minValue, nil return minKey, minValue, nil
} }
func FilterMinMap[K comparable, T constraints.Ordered](values map[K]T, minimum T) map[K]T {
result := make(map[K]T)
for k, v := range values {
if v >= minimum {
result[k] = v
}
}
return result
}
func FilterMaxMap[K comparable, T constraints.Ordered](values map[K]T, maximum T) map[K]T {
result := make(map[K]T)
for k, v := range values {
if v <= maximum {
result[k] = v
}
}
return result
}
func SaturatingSubSlice[T Numeric](vec []T, sub T) []T {
result := make([]T, len(vec))
for i, v := range vec {
if v > sub {
result[i] = v - sub
}
}
return result
}
func SaturatingSubMap[K comparable, T Numeric](values map[K]T, sub T) map[K]T {
result := make(map[K]T)
for k, v := range values {
if v > sub {
result[k] = v - sub
}
}
return result
}
// Min returns the smallest element in a slice/array or map, // Min returns the smallest element in a slice/array or map,
// or the value itself if data is a single comparable value. // or the value itself if data is a single comparable value.
// Returns an error if the container is empty or the type is unsupported. // Returns an error if the container is empty or the type is unsupported.
@@ -135,6 +195,116 @@ func Max(data interface{}) (interface{}, error) {
} }
} }
func FilterMin(data interface{}, minimum interface{}) (interface{}, error) {
v := reflect.ValueOf(data)
switch v.Kind() {
case reflect.Slice, reflect.Array:
if v.Len() == 0 {
return nil, errors.New("empty slice or array")
}
return filterMinFromIterable(v, minimum)
case reflect.Map:
if v.Len() == 0 {
return nil, errors.New("empty map")
}
return filterMinFromMap(v, minimum)
default:
if !isOrderedKind(v.Kind()) {
return nil, fmt.Errorf("unsupported type: %s", v.Kind())
}
return data, nil
}
}
func FilterMax(data interface{}, maximum interface{}) (interface{}, error) {
v := reflect.ValueOf(data)
switch v.Kind() {
case reflect.Slice, reflect.Array:
if v.Len() == 0 {
return nil, errors.New("empty slice or array")
}
return filterMaxFromIterable(v, maximum)
case reflect.Map:
if v.Len() == 0 {
return nil, errors.New("empty map")
}
return filterMaxFromMap(v, maximum)
default:
if !isOrderedKind(v.Kind()) {
return nil, fmt.Errorf("unsupported type: %s", v.Kind())
}
return data, nil
}
}
func SaturatingSub(data interface{}, sub interface{}) (interface{}, error) {
v := reflect.ValueOf(data)
switch v.Kind() {
case reflect.Slice, reflect.Array:
return saturatingSubFromIterable(v, sub)
case reflect.Map:
return saturatingSubFromMap(v, sub)
default:
if !isNumericKind(v.Kind()) {
return nil, fmt.Errorf("unsupported type: %s", v.Kind())
}
r, err := saturatingSubValues(v, reflect.ValueOf(sub))
if err != nil {
return nil, err
}
return r.Interface(), nil
}
}
func saturatingSubFromIterable(v reflect.Value, sub interface{}) (interface{}, error) {
subVal := reflect.ValueOf(sub)
result := reflect.MakeSlice(v.Type(), v.Len(), v.Len())
for i := 0; i < v.Len(); i++ {
r, err := saturatingSubValues(v.Index(i), subVal)
if err != nil {
return nil, err
}
result.Index(i).Set(r)
}
return result.Interface(), nil
}
func saturatingSubFromMap(v reflect.Value, sub interface{}) (interface{}, error) {
subVal := reflect.ValueOf(sub)
result := reflect.MakeMap(v.Type())
for _, key := range v.MapKeys() {
r, err := saturatingSubValues(v.MapIndex(key), subVal)
if err != nil {
return nil, err
}
if !r.IsZero() {
result.SetMapIndex(key, r)
}
}
return result.Interface(), nil
}
func saturatingSubValues(a, b reflect.Value) (reflect.Value, error) {
result := reflect.New(a.Type()).Elem()
switch a.Kind() {
case reflect.Int, reflect.Int8, reflect.Int16, reflect.Int32, reflect.Int64:
if av, bv := a.Int(), b.Int(); av > bv {
result.SetInt(av - bv)
}
case reflect.Uint, reflect.Uint8, reflect.Uint16, reflect.Uint32, reflect.Uint64:
if av, bv := a.Uint(), b.Uint(); av > bv {
result.SetUint(av - bv)
}
case reflect.Float32, reflect.Float64:
if av, bv := a.Float(), b.Float(); av > bv {
result.SetFloat(av - bv)
}
default:
return reflect.Value{}, fmt.Errorf("unsupported type for saturating subtraction: %s", a.Kind())
}
return result, nil
}
// maxFromIterable scans a slice/array to find the maximum. // maxFromIterable scans a slice/array to find the maximum.
func maxFromIterable(v reflect.Value) (interface{}, error) { func maxFromIterable(v reflect.Value) (interface{}, error) {
var best reflect.Value var best reflect.Value
@@ -165,6 +335,66 @@ func minFromIterable(v reflect.Value) (interface{}, error) {
return minVal.Interface(), nil return minVal.Interface(), nil
} }
func filterMinFromIterable(v reflect.Value, minimum interface{}) (interface{}, error) {
minVal := reflect.ValueOf(minimum)
result := reflect.MakeSlice(v.Type(), 0, v.Len())
for i := 0; i < v.Len(); i++ {
elem := v.Index(i)
if !isOrderedKind(elem.Kind()) {
return nil, fmt.Errorf("unsupported element type: %s", elem.Kind())
}
if !less(elem, minVal) { // elem >= minimum
result = reflect.Append(result, elem)
}
}
return result.Interface(), nil
}
func filterMaxFromIterable(v reflect.Value, maximum interface{}) (interface{}, error) {
maxVal := reflect.ValueOf(maximum)
result := reflect.MakeSlice(v.Type(), 0, v.Len())
for i := 0; i < v.Len(); i++ {
elem := v.Index(i)
if !isOrderedKind(elem.Kind()) {
return nil, fmt.Errorf("unsupported element type: %s", elem.Kind())
}
if !greater(elem, maxVal) { // elem <= maximum
result = reflect.Append(result, elem)
}
}
return result.Interface(), nil
}
func filterMinFromMap(v reflect.Value, minimum interface{}) (interface{}, error) {
minVal := reflect.ValueOf(minimum)
result := reflect.MakeMap(v.Type())
for _, key := range v.MapKeys() {
elem := v.MapIndex(key)
if !isOrderedKind(elem.Kind()) {
return nil, fmt.Errorf("unsupported element type: %s", elem.Kind())
}
if !less(elem, minVal) { // elem >= minimum
result.SetMapIndex(key, elem)
}
}
return result.Interface(), nil
}
func filterMaxFromMap(v reflect.Value, maximum interface{}) (interface{}, error) {
maxVal := reflect.ValueOf(maximum)
result := reflect.MakeMap(v.Type())
for _, key := range v.MapKeys() {
elem := v.MapIndex(key)
if !isOrderedKind(elem.Kind()) {
return nil, fmt.Errorf("unsupported element type: %s", elem.Kind())
}
if !greater(elem, maxVal) { // elem <= maximum
result.SetMapIndex(key, elem)
}
}
return result.Interface(), nil
}
// maxFromMap scans map values to find the maximum. // maxFromMap scans map values to find the maximum.
func maxFromMap(v reflect.Value) (interface{}, error) { func maxFromMap(v reflect.Value) (interface{}, error) {
var best reflect.Value var best reflect.Value
@@ -199,6 +429,17 @@ func minFromMap(v reflect.Value) (interface{}, error) {
return minVal.Interface(), nil return minVal.Interface(), nil
} }
func isNumericKind(k reflect.Kind) bool {
switch k {
case reflect.Int, reflect.Int8, reflect.Int16, reflect.Int32, reflect.Int64,
reflect.Uint, reflect.Uint8, reflect.Uint16, reflect.Uint32, reflect.Uint64,
reflect.Float32, reflect.Float64:
return true
default:
return false
}
}
// isOrderedKind reports whether k supports comparison ordering. // isOrderedKind reports whether k supports comparison ordering.
func isOrderedKind(k reflect.Kind) bool { func isOrderedKind(k reflect.Kind) bool {
switch k { switch k {
+1 -1
View File
@@ -1 +1 @@
4.4.42 4.4.43