, including all inherited members.
| add(const Tblastn &tbn) | Tblastn | |
| addMatch(float identity, int alnlen, int mismatches, int gaps, int qbegin, int qend, int tbegin, int tend, double expect, double score) | Tblastn | |
| addMatch(M8Match *mptr) | Tblastn | [inline] |
| checkContain(ostream &ous, float factor=0.8) const | Tblastn | |
| clear() | Tblastn | [inline] |
| directionalSortMatchByTarget() | Tblastn | |
| empty() | Tblastn | [inline] |
| erase(int b, int e) | Tblastn | [private] |
| eraseMatch(const Range &r) | Tblastn | [private] |
| findFootprint(ostream &SUMM, ostream &DETA, float covcut=0.4) | Tblastn | |
| findSections() | Tblastn | |
| firstQueryRange() const | Tblastn | |
| getIntronProbility(int len) | Tblastn | [static] |
| getMatches() const | Tblastn | [inline] |
| intronProb | Tblastn | [private, static] |
| isFirstQueryMatch(const M8Match *m) const | Tblastn | |
| isLastQueryMatch(const M8Match *m) const | Tblastn | |
| isSortedByTarget() const | Tblastn | [inline] |
| lastQueryRange() const | Tblastn | |
| matches | Tblastn | [private] |
| matchesQS | Tblastn | [mutable, private] |
| numMatches() const | Tblastn | [inline] |
| operator<<(ostream &ous, const Tblastn &b) | Tblastn | [friend] |
| operator=(const Tblastn &tbn) | Tblastn | |
| output(ostream &ous, char delimiter[]="\t") const | Tblastn | |
| outputModel(const M8MatchChain &amodel, int &id, ostream &ouss, ostream &ousd, char delimiter[]="\t") const | Tblastn | |
| outputModel(const Boxchain &amodel, int &id, ostream &ouss, ostream &ousd, char delimiter[]="\t") const | Tblastn | |
| overlapFirstQueryMatch(const M8Match *m, int cutoff=9) const | Tblastn | |
| overlapLastQueryMatch(const M8Match *m, int cutoff=9) const | Tblastn | |
| qcov() const | Tblastn | |
| qcovCutoff | Tblastn | [private, static] |
| qid | Tblastn | [private] |
| qlen | Tblastn | [private] |
| query() const | Tblastn | [inline] |
| queryLength() const | Tblastn | [inline] |
| readConfig(const string &conf) | Tblastn | [static] |
| removeAll(list< string > &rmlist, ostream &ous) | Tblastn | [private] |
| removeAll() | Tblastn | [private] |
| removeJunk(const Protein &qseq, const DNA &tseq, float factor=0.8) | Tblastn | |
| removeNullMatch() | Tblastn | [private] |
| sameQTPair(const Tblastn &tbn) | Tblastn | [inline] |
| setSortedByTarget(bool yes=true) | Tblastn | [inline] |
| show(ostream &ous) const | Tblastn | |
| sortedByQuery | Tblastn | [mutable, private] |
| sortedByTarget | Tblastn | [private] |
| sortMatchByQuery() const | Tblastn | [private] |
| sortMatchByTarget() | Tblastn | |
| target() const | Tblastn | [inline] |
| targetLength() const | Tblastn | [inline] |
| Tblastn() | Tblastn | [inline] |
| Tblastn(const string &query, const string &target, int queryLen, int targetLen) | Tblastn | [inline] |
| Tblastn(const Tblastn &tbn) | Tblastn | |
| tid | Tblastn | [private] |
| tlen | Tblastn | [private] |
| ~Tblastn() | Tblastn | |
