rename the iterator class

pkg/obiseq/attributes.go

@@ -0,0 +1,193 @@
+package obiseq
+
+import (
+	"fmt"
+	"strconv"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
+	log "github.com/sirupsen/logrus"
+)
+
+// A method that returns the value of the key in the annotation map.
+func (s *BioSequence) GetAttribute(key string) (interface{}, bool) {
+	var val interface{}
+	ok := s.annotations != nil
+
+	if ok {
+		val, ok = s.annotations[key]
+	}
+
+	return val, ok
+}
+
+// A method that sets the value of the key in the annotation map.
+func (s *BioSequence) SetAttribute(key string, value interface{}) {
+	annot := s.Annotations()
+	annot[key] = value
+}
+
+// A method that returns the value of the key in the annotation map.
+func (s *BioSequence) GetIntAttribute(key string) (int, bool) {
+	var val int
+	var err error
+
+	v, ok := s.GetAttribute(key)
+
+	if ok {
+		val, err = goutils.InterfaceToInt(v)
+		ok = err == nil
+	}
+
+	return val, ok
+}
+
+// Deleting the key from the annotation map.
+func (s *BioSequence) DeleteAttribute(key string) {
+	delete(s.Annotations(),key)
+}
+ 
+// Renaming the key in the annotation map.
+func (s *BioSequence) RenameAttribute(newName, oldName string) {
+	val,ok := s.GetAttribute(oldName)
+
+	if (ok) {
+		s.SetAttribute(newName,val)
+		s.DeleteAttribute(oldName)
+	}
+}
+
+// A method that returns the value of the key in the annotation map.
+func (s *BioSequence) GetNumericAttribute(key string) (float64, bool) {
+	var val float64
+	var err error
+
+	v, ok := s.GetAttribute(key)
+
+	if ok {
+		val, err = goutils.InterfaceToFloat64(v)
+		ok = err == nil
+	}
+
+	return val, ok
+}
+
+
+// A method that returns the value of the key in the annotation map.
+func (s *BioSequence) GetStringAttribute(key string) (string, bool) {
+	var val string
+	v, ok := s.GetAttribute(key)
+
+	if ok {
+		val = fmt.Sprint(v)
+	}
+
+	return val, ok
+}
+
+// A method that returns the value of the key in the annotation map.
+func (s *BioSequence) GetBoolAttribute(key string) (bool, bool) {
+	var val bool
+	var err error
+
+	v, ok := s.GetAttribute(key)
+
+	if ok {
+		val, err = goutils.InterfaceToBool(v)
+		ok = err == nil
+	}
+
+	return val, ok
+}
+
+func (s *BioSequence) GetIntMap(key string) (map[string]int, bool) {
+	var val map[string]int
+	var err error
+
+	v, ok := s.GetAttribute(key)
+
+	if ok {
+		val, err = goutils.InterfaceToIntMap(v)
+		ok = err == nil
+	}
+
+	return val, ok
+}
+
+// Returning the number of times the sequence has been observed.
+func (s *BioSequence) Count() int {
+	count, ok := s.GetIntAttribute("count")
+
+	if !ok {
+		count = 1
+	}
+
+	return count
+}
+
+// Setting the number of times the sequence has been observed.
+func (s *BioSequence) SetCount(count int) {
+	annot := s.Annotations()
+	annot["count"] = count
+}
+
+
+// Returning the taxid of the sequence.
+func (s *BioSequence) Taxid() int {
+	taxid, ok := s.GetIntAttribute("taxid")
+
+	if !ok {
+		taxid = 1
+	}
+
+	return taxid
+}
+
+// Setting the taxid of the sequence.
+func (s *BioSequence) SetTaxid(taxid int) {
+	annot := s.Annotations()
+	annot["taxid"] = taxid
+}
+
+
+func (s *BioSequence) OBITagRefIndex() map[int]string {
+
+	var val map[int]string
+
+	i, ok := s.GetAttribute("obitag_ref_index")
+
+	if !ok {
+		return nil
+	}
+
+	switch i := i.(type) {
+	case map[int]string:
+		val = i
+	case map[string]interface{}:
+		val = make(map[int]string, len(i))
+		for k, v := range i {
+			score, err := strconv.Atoi(k)
+			if err != nil {
+				log.Panicln(err)
+			}
+
+			val[score], err = goutils.InterfaceToString(v)
+			if err != nil {
+				log.Panicln(err)
+			}
+		}
+	case map[string]string:
+		val = make(map[int]string, len(i))
+		for k, v := range i {
+			score, err := strconv.Atoi(k)
+			if err != nil {
+				log.Panicln(err)
+			}
+			val[score] = v
+
+		}
+	default:
+		log.Panicln("value of attribute obitag_ref_index cannot be casted to a map[int]string")
+	}
+
+	return val
+}