, including all inherited members.
| assign(const string &s) | bioseq | [inline] |
| bioseq() | bioseq | [inline] |
| bioseq(const bioseq &s) | bioseq | [inline] |
| bioseq(const string &s) | bioseq | [inline] |
| bioseq(const string &n, const string &s) | bioseq | [inline] |
| bioseq(const string &n, const string &s, const string &t) | bioseq | [inline] |
| clear() | bioseq | [inline] |
| code | bioseq | [mutable, protected] |
| codontable | DNA | [protected, static] |
| computeEntropy() const | bioseq | [inline] |
| computeEntropy(int b, int e) const | bioseq | [inline] |
| DNA() | DNA | [inline] |
| DNA(const DNA &s) | DNA | [inline] |
| DNA(const string &s) | DNA | [inline] |
| DNA(const string &n, const string &s) | DNA | [inline] |
| DNA(const string &n, const string &s, const string &t) | DNA | [inline] |
| DNA(const bioseq &s) | DNA | [inline] |
| empty() | bioseq | [inline] |
| entropy(const string &seq) | bioseq | [static] |
| GCContent() const | DNA | |
| GCContent(long int &A, long int &C, long int &G, long int &T, long int &N) const | DNA | |
| getcode() const | bioseq | |
| getcodeNuc() const | DNA | |
| getCodonTable() | DNA | [inline, static] |
| getFrequency() const | bioseq | |
| getName() const | bioseq | [inline] |
| getSequence() const | bioseq | [inline] |
| getSequenceType() const | DNA | [inline, virtual] |
| getTitle() const | bioseq | [inline] |
| importFasta(const string &fas) | bioseq | |
| length() const | bioseq | [inline] |
| longestORF(char strand, int &b, int &e) const | DNA | |
| longestORF(int &b, int &e) const | DNA | |
| longestORF(Protein &p, int &b, int &e) const | DNA | |
| longestORFForward(int &b, int &e) const | DNA | |
| longestORFForward(Protein &p, int &b, int &e) const | DNA | |
| longestORFReverse(int &b, int &e) const | DNA | |
| longestORFReverse(Protein &p, int &b, int &e) const | DNA | |
| name | bioseq | [protected] |
| operator+=(const bioseq &s) | bioseq | [inline] |
| operator<<(ostream &ous, const bioseq &s) | bioseq | [friend] |
| operator=(const DNA &s) | DNA | |
| operator=(const string &str) | DNA | |
| bioseq::operator=(const bioseq &s) | bioseq | |
| operator[](const int i) const | bioseq | [inline] |
| printFasta(ostream &ous, int width=70) | bioseq | |
| printFastaWithHeader(ostream &ous, int width=70) | bioseq | |
| randomize() | bioseq | [inline] |
| read(const string &file) | bioseq | |
| read(istream &ins, string &header) | bioseq | |
| revcomp() | DNA | [inline] |
| rvc() | bioseq | |
| seq | bioseq | [protected] |
| setCodonTable(const int ctid) | DNA | [inline, static] |
| setName(const string &n) | bioseq | [inline] |
| setTitle(const string &t) | bioseq | [inline] |
| subseq(int b, int e) const | DNA | [inline] |
| subsequence(int b, int len=-1) const | bioseq | |
| substr(int b, int e) const | bioseq | |
| substring(const int b, const int len) const | bioseq | [inline] |
| substring(const int b) const | bioseq | [inline] |
| title | bioseq | [protected] |
| toLowerCase() | bioseq | |
| toString() const | bioseq | [inline] |
| toUpperCase() | bioseq | |
| translate() const | DNA | |
| translate(int begin, int end=-1) const | DNA | |
| ~bioseq() | bioseq | [inline] |
| ~DNA() | DNA | [inline] |
