, including all inherited members.
| anchor | group | [protected] |
| anchorIndex(const int dividx) | gconst | [static] |
| anchorPartial() const | gdiagnosis | |
| avgzval() const | gdiagnosis | [inline] |
| calzval() | gdiagnosis | |
| checkAndRemove(int i, int b, int e, ostream &ou) | group | [protected] |
| coverageDefect(double zcut) const | gdiagnosis | |
| csvIdentity | gconst | [static] |
| csvStd | gconst | [static] |
| csvStdHighVar | gconst | [static] |
| divCnt | group | [protected] |
| divisions | gconst | [static] |
| divm | group | [protected] |
| dostat() | group | [protected] |
| dump(ostream &ou) | group | |
| dumpAllSMratio(ostream &ou) | group | |
| dumpAsTable(ostream &ou) | group | |
| dumpKey(ostream &ou) | group | |
| dumpStat(ostream &ou) | group | |
| dumpWithZval(ostream &ou) const | gdiagnosis | |
| fixScoreAndTest(double szcut, gdiagnosis &d) const | gdiagnosis | |
| gdiagnosis() | gdiagnosis | |
| gdiagnosis(double cut) | gdiagnosis | |
| gdiagnosis(const gdiagnosis &gd) | gdiagnosis | |
| getAnchor() const | group | [inline] |
| getAvgZval() const | gdiagnosis | [inline] |
| getDivCnt() const | group | [inline] |
| getdividx(const string &div) | gconst | [inline, static] |
| getdividx(const char *div) | gconst | [static] |
| getIdenSMratio() const | group | [inline] |
| getMinTcov(int &div) const | group | |
| getMlenSMratio() const | group | [inline] |
| getQcovSMratio() const | group | [inline] |
| getScoreSMratio() const | group | [inline] |
| getspace() | gdiagnosis | [private] |
| getTcovSMratio() const | group | [inline] |
| getzcut() const | gdiagnosis | [inline] |
| goodQuality(double zcut) const | gdiagnosis | |
| group() | group | |
| group(const group &g) | group | |
| group(int &q, istream &in) | group | |
| gstat class | group | [friend] |
| guid | gdiagnosis | [private, static] |
| hgrm | gdiagnosis | [private] |
| highVarDiv | gconst | [static] |
| highVarDivPresent() const | group | [protected] |
| isConserved() const | group | |
| lastTest() const | gdiagnosis | |
| max(int f) const | group | |
| maxidentity() const | group | [inline] |
| maxmatchlen() const | group | [inline] |
| maxngidentity() const | group | [inline] |
| maxnogaplen() const | group | [inline] |
| maxqcov() const | group | [inline] |
| maxscore() const | group | [inline] |
| maxsimilarity() const | group | [inline] |
| maxtcov() const | group | [inline] |
| mintcov() const | group | |
| next(int &q, istream &in) | gdiagnosis | |
| nextAnchor() | group | |
| norm | gdiagnosis | [private] |
| operator<<(ostream &ou, const gdiagnosis &g) | gdiagnosis | [friend] |
| group::operator<<(ostream &o, const group &g) | group | [friend] |
| operator=(const gdiagnosis &g) | gdiagnosis | |
| group::operator=(const group &g) | group | |
| passed(const double zcut) const | gdiagnosis | |
| passedall(const double zcut) const | gdiagnosis | [inline] |
| passedAvg(const double zcut) const | gdiagnosis | |
| passedIdentity(const double zcut) const | gdiagnosis | |
| passedLength(const double zcut) const | gdiagnosis | |
| passedQcov(const double zcut) const | gdiagnosis | |
| pivotdiv | gconst | [static] |
| pivotdividx | gconst | [static] |
| qcovpass() | gdiagnosis | [inline] |
| qualitypass() | gdiagnosis | |
| query | group | [protected] |
| queryDiv | gconst | [static] |
| readconf(const string &gdf) | gconst | [static] |
| readGuid(istream &in) | gdiagnosis | [static] |
| rmbranch(int i, ostream &ou) | group | |
| rmbranch(int i) | group | |
| rmlow(double lowercut=-3, double avgzc=3) | gdiagnosis | |
| scorepass() | gdiagnosis | [inline] |
| searchOrder | gconst | [static] |
| setAnchorOrder(const int a[]) | gconst | [static] |
| setzcut(double c) | gdiagnosis | [inline] |
| showAnchorOrder(ostream &ou) | gconst | [static] |
| stat | group | [protected] |
| targetPartial(int i) const | gdiagnosis | |
| trimAndTest(ostream &ou, double zcut) | gdiagnosis | |
| trimByIden() | gdiagnosis | |
| zcut | gdiagnosis | [private] |
| zval | gdiagnosis | [private] |
| ~group() | group | [inline] |
