Update the expression language

pkg/obiseq/language.go

@@ -1,6 +1,7 @@
 package obiseq
 
 import (
+	"errors"
 	"fmt"
 	"reflect"
 	"regexp"
@@ -145,14 +146,14 @@ var OBILang = gval.NewLanguage(
 		ismap := obiutils.IsAMap(args[0])
 		return ismap, nil
 	}),
+	gval.Function("isvector", func(args ...interface{}) (interface{}, error) {
+		isvector := obiutils.IsASlice(args[0])
+		return isvector, nil
+	}),
 	gval.Function("sprintf", func(args ...interface{}) (interface{}, error) {
 		text := fmt.Sprintf(args[0].(string), args[1:]...)
 		return text, nil
 	}),
-	gval.Function("gsub", func(args ...interface{}) (interface{}, error) {
-		text := strings.ReplaceAll(args[0].(string), args[1].(string), args[2].(string))
-		return text, nil
-	}),
 	gval.Function("subspc", func(args ...interface{}) (interface{}, error) {
 		text := strings.ReplaceAll(args[0].(string), " ", "_")
 		return text, nil
@@ -181,6 +182,14 @@ var OBILang = gval.NewLanguage(
 		}
 		return val, nil
 	}),
+	gval.Function("string", func(args ...interface{}) (interface{}, error) {
+		val, err := obiutils.InterfaceToString(args[0])
+
+		if err != nil {
+			log.Fatalf("%v cannot be converted to a string value", args[0])
+		}
+		return val, nil
+	}),
 	gval.Function("ifelse", func(args ...interface{}) (interface{}, error) {
 		if args[0].(bool) {
 			return args[1], nil
@@ -192,13 +201,52 @@ var OBILang = gval.NewLanguage(
 		composition := (args[0].(*BioSequence)).Composition()
 		return float64(composition['g']-composition['c']) / float64(composition['g']+composition['c']), nil
 	}),
+	gval.Function("qualities", func(args ...interface{}) (interface{}, error) {
+		qualities := (args[0].(*BioSequence)).Qualities()
+		rep := make([]interface{}, len(qualities))
+		for i, q := range qualities {
+			rep[i] = float64(q)
+		}
+		return rep, nil
+	}),
+	gval.Function("elementof", func(args ...interface{}) (interface{}, error) {
+		if obiutils.IsASlice(args[0]) {
+			pos, err := obiutils.InterfaceToInt(args[1])
+			if err != nil {
+				return nil, err
+			}
+			if slice, ok := args[0].([]interface{}); ok {
+				return slice[pos], nil
+			} else {
+				return nil, errors.New("obi: first argument incorrect slice")
+			}
+
+		} else if obiutils.IsAMap(args[0]) {
+			pos, err := obiutils.InterfaceToString(args[1])
+			if err != nil {
+				return nil, err
+			}
+			if m, ok := args[0].(map[string]interface{}); ok {
+				return m[pos], nil
+			} else {
+				return nil, errors.New("obi: first argument incorrect map")
+			}
+		} else if s, ok := args[0].(string); ok {
+			pos, err := obiutils.InterfaceToInt(args[1])
+			if err != nil {
+				return nil, err
+			}
+			return string(s[pos]), nil
+		}
+		return nil, fmt.Errorf("invalid arguments")
+	}),
 	gval.Function("gc", func(args ...interface{}) (interface{}, error) {
 		composition := (args[0].(*BioSequence)).Composition()
-		return float64(composition['g']+composition['c']) / float64(args[0].(*BioSequence).Len()), nil
+		return float64(composition['g']+composition['c']) / float64(args[0].(*BioSequence).Len()-composition['o']), nil
 	}),
 	gval.Function("composition", func(args ...interface{}) (interface{}, error) {
 		comp := (args[0].(*BioSequence)).Composition()
-		scomp := make(map[string]float64)
+		scomp := make(map[string]interface{}, 5)
 		for k, v := range comp {
 			scomp[string(k)] = float64(v)
 		}
@@ -209,4 +257,22 @@ var OBILang = gval.NewLanguage(
 		results := pattern.ReplaceAllString(args[0].(string), args[2].(string))
 		return results, nil
 	}),
+	gval.Function("substr", func(args ...interface{}) (interface{}, error) {
+		str, ok1 := args[0].(string)
+		start, ok2 := args[1].(float64) // Gval utilise float64 pour les nombres
+		length, ok3 := args[2].(float64)
+
+		if !ok1 || !ok2 || !ok3 {
+			return nil, fmt.Errorf("invalid arguments")
+		}
+
+		startIndex := int(start)
+		endIndex := startIndex + int(length)
+
+		if startIndex < 0 || endIndex > len(str) {
+			return nil, fmt.Errorf("index out of range")
+		}
+
+		return str[startIndex:endIndex], nil
+	}),
 )