// some standard dna alphabets
// Include nl (\012), and cr (\015) to make sequence parsing eol
// convention independent.
-const Alphabet Alphabet::reduced_dna_alphabet("AaCcGgTtNn\012\015");
-const Alphabet Alphabet::reduced_rna_alphabet("AaCcGgUuNn\012\015");
-const Alphabet Alphabet::reduced_nucleic_alphabet("AaCcGgTtUuNn\012\015");
+const char *Alphabet::reduced_dna_cstr = "AaCcGgTtNn\012\015";
+const char *Alphabet::reduced_rna_cstr = "AaCcGgUuNn\012\015";
+const char *Alphabet::reduced_nucleic_cstr = "AaCcGgTtUuNn\012\015";
//! this is the general iupac alphabet for nucleotides
-const Alphabet Alphabet::nucleic_alphabet(
- "AaCcGgTtUuRrYyMmKkSsWwBbDdHhVvNn-~.?\012\015"
-);
+const char *Alphabet::nucleic_cstr =
+ "AaCcGgTtUuRrYyMmKkSsWwBbDdHhVvNn-~.?\012\015";
//! the protein alphabet
-const Alphabet Alphabet::protein_alphabet(
- "AaCcDdEeFfGgHhIiKkLlMmNnPpQqRrSsTtVvWwYy\012\015"
-);
+const char *Alphabet::protein_cstr =
+ "AaCcDdEeFfGgHhIiKkLlMmNnPpQqRrSsTtVvWwYy\012\015";
+
+const Alphabet& Alphabet::reduced_dna_alphabet() {
+ static Alphabet *a = new Alphabet(reduced_dna_cstr);
+ return *a;
+}
+const Alphabet& Alphabet::reduced_rna_alphabet() {
+ static Alphabet *a = new Alphabet(reduced_rna_cstr);
+ return *a;
+}
+const Alphabet& Alphabet::reduced_nucleic_alphabet() {
+ static Alphabet *a = new Alphabet(reduced_nucleic_cstr);
+ return *a;
+}
+const Alphabet& Alphabet::nucleic_alphabet() {
+ static Alphabet *a = new Alphabet(nucleic_cstr);
+ return *a;
+}
+const Alphabet& Alphabet::protein_alphabet() {
+ static Alphabet *a = new Alphabet(protein_cstr);
+ return *a;
+}
Alphabet::Alphabet(const char *a) :
alphabet(a)
alphabet_set.insert(alphabet.begin(), alphabet.end());
}
-const char *Alphabet::c_str() const
-{
- alphabet.c_str();
-}
-
bool Alphabet::exists(const char c) const
{
return (alphabet_set.find(c) != alphabet_set.end());
-}
\ No newline at end of file
+}