A first version of obigrep. Normally fully functionnal, but not fully tested

pkg/obiseq/predicate.go

@@ -2,6 +2,9 @@ package obiseq
 
 import (
 	"context"
+	"fmt"
+	"regexp"
+
 	log "github.com/sirupsen/logrus"
 
 	"github.com/PaesslerAG/gval"
@@ -10,37 +13,55 @@ import (
 type SequencePredicate func(*BioSequence) bool
 
 func (predicate1 SequencePredicate) And(predicate2 SequencePredicate) SequencePredicate {
-	f := func(sequence *BioSequence) bool {
-		return predicate1(sequence) && predicate2(sequence)
+	switch {
+	case predicate1 == nil:
+		return predicate2
+	case predicate2 == nil:
+		return predicate1
+	default:
+		return func(sequence *BioSequence) bool {
+			return predicate1(sequence) && predicate2(sequence)
+		}
 	}
-
-	return f
 }
 
 func (predicate1 SequencePredicate) Or(predicate2 SequencePredicate) SequencePredicate {
-	f := func(sequence *BioSequence) bool {
-		return predicate1(sequence) || predicate2(sequence)
+	switch {
+	case predicate1 == nil:
+		return predicate2
+	case predicate2 == nil:
+		return predicate1
+	default:
+		return func(sequence *BioSequence) bool {
+			return predicate1(sequence) || predicate2(sequence)
+		}
 	}
-
-	return f
 }
 
 func (predicate1 SequencePredicate) Xor(predicate2 SequencePredicate) SequencePredicate {
-	f := func(sequence *BioSequence) bool {
-		p1 := predicate1(sequence)
-		p2 := predicate2(sequence)
-		return (p1 && !p2) || (p2 && !p1)
+	switch {
+	case predicate1 == nil:
+		return predicate2
+	case predicate2 == nil:
+		return predicate1
+	default:
+		return func(sequence *BioSequence) bool {
+			p1 := predicate1(sequence)
+			p2 := predicate2(sequence)
+			return (p1 && !p2) || (p2 && !p1)
+		}
 	}
-
-	return f
 }
 
 func (predicate1 SequencePredicate) Not() SequencePredicate {
-	f := func(sequence *BioSequence) bool {
-		return !predicate1(sequence)
+	switch {
+	case predicate1 == nil:
+		return nil
+	default:
+		return func(sequence *BioSequence) bool {
+			return !predicate1(sequence)
+		}
 	}
-
-	return f
 }
 
 func HasAttribute(name string) SequencePredicate {
@@ -57,9 +78,43 @@ func HasAttribute(name string) SequencePredicate {
 	return f
 }
 
-func MoreAbundantThan(count int) SequencePredicate {
+func IsAttributeMatch(name string, pattern string) SequencePredicate {
+	pat, err := regexp.Compile(pattern)
+
+	if err != nil {
+		log.Fatalf("error in atribute %s regular pattern syntax : %v", name, err)
+	}
+
 	f := func(sequence *BioSequence) bool {
-		return sequence.Count() > count
+		if sequence.HasAnnotation() {
+			val, ok := (sequence.Annotations())[name]
+			if ok {
+				switch val := val.(type) {
+				case string:
+					return pat.MatchString(val)
+				default:
+					return pat.MatchString(fmt.Sprint(val))
+				}
+			}
+		}
+
+		return false
+	}
+
+	return f
+}
+
+func IsMoreAbundantOrEqualTo(count int) SequencePredicate {
+	f := func(sequence *BioSequence) bool {
+		return sequence.Count() >= count
+	}
+
+	return f
+}
+
+func IsLessAbundantOrEqualTo(count int) SequencePredicate {
+	f := func(sequence *BioSequence) bool {
+		return sequence.Count() <= count
 	}
 
 	return f
@@ -81,7 +136,64 @@ func IsShorterOrEqualTo(length int) SequencePredicate {
 	return f
 }
 
-func ExrpessionPredicat(expression string) SequencePredicate {
+func IsSequenceMatch(pattern string) SequencePredicate {
+	pat, err := regexp.Compile("(?i)" + pattern)
+
+	if err != nil {
+		log.Fatalf("error in sequence regular pattern syntax : %v", err)
+	}
+
+	f := func(sequence *BioSequence) bool {
+		return pat.Match(sequence.Sequence())
+	}
+
+	return f
+}
+
+func IsDefinitionMatch(pattern string) SequencePredicate {
+	pat, err := regexp.Compile(pattern)
+
+	if err != nil {
+		log.Fatalf("error in definition regular pattern syntax : %v", err)
+	}
+
+	f := func(sequence *BioSequence) bool {
+		return pat.MatchString(sequence.Definition())
+	}
+
+	return f
+}
+
+func IsIdMatch(pattern string) SequencePredicate {
+	pat, err := regexp.Compile(pattern)
+
+	if err != nil {
+		log.Fatalf("error in identifier regular pattern syntax : %v", err)
+	}
+
+	f := func(sequence *BioSequence) bool {
+		return pat.MatchString(sequence.Id())
+	}
+
+	return f
+}
+
+func IsIdIn(ids ...string) SequencePredicate {
+	idset := make(map[string]bool)
+
+	for _, v := range ids {
+		idset[v] = true
+	}
+
+	f := func(sequence *BioSequence) bool {
+		_, ok := idset[sequence.Id()]
+		return ok
+	}
+
+	return f
+}
+
+func ExpressionPredicat(expression string) SequencePredicate {
 
 	exp, err := gval.Full().NewEvaluable(expression)