FPGModel Class Reference
#include <FPGModel.h>
Public Member Functions | |
| FPGModel (const string &qid, const string &tid, int fpnum, int ql, int tl, int qb, int qe, int tb, int te, int nx, double ss, double ai, double qc, double so) | |
| bool | cover (const FPGModel &mm) const |
| bool | similar (const FPGModel &mm, float fr=0.15) const |
| double | getSumscore () const |
| double | getNormSumscore () const |
| double | getAvgiden () const |
| FPGModel (const string &qid, const string &tid, int fpnum, int ql, int tl, int qb, int qe, int tb, int te, int nx, double ss, double ai, double qc, double so) | |
| bool | cover (const FPGModel &mm) const |
| bool | similar (const FPGModel &mm, float fr=0.15) const |
| double | getSumscore () const |
| double | getNormSumscore () const |
| double | getAvgiden () const |
Private Attributes | |
| int | qlen |
| int | tlen |
| int | qbegin |
| int | qend |
| int | tbegin |
| int | tend |
| int | numexon |
| double | sumscore |
| double | avgiden |
| double | qcov |
| double | sumoverlap |
Friends | |
| ostream & | operator<< (ostream &ous, const FPGModel &mm) |
| ostream & | operator<< (ostream &ous, const FPGModel &mm) |
Constructor & Destructor Documentation
| FPGModel::FPGModel | ( | const string & | qid, | |
| const string & | tid, | |||
| int | fpnum, | |||
| int | ql, | |||
| int | tl, | |||
| int | qb, | |||
| int | qe, | |||
| int | tb, | |||
| int | te, | |||
| int | nx, | |||
| double | ss, | |||
| double | ai, | |||
| double | qc, | |||
| double | so | |||
| ) | [inline] |
| FPGModel::FPGModel | ( | const string & | qid, | |
| const string & | tid, | |||
| int | fpnum, | |||
| int | ql, | |||
| int | tl, | |||
| int | qb, | |||
| int | qe, | |||
| int | tb, | |||
| int | te, | |||
| int | nx, | |||
| double | ss, | |||
| double | ai, | |||
| double | qc, | |||
| double | so | |||
| ) | [inline] |
Member Function Documentation
| bool FPGModel::cover | ( | const FPGModel & | mm | ) | const |
check that all exons of mm is inside of exons of this object Basic condition: mm inside this, mm score < this score number of exon of this > number of exons of mm
References GModel< T >::direction(), GModel< fpkey >::direction(), GModel< fpkey >::endsContain(), GModel< T >::exons, GModel< fpkey >::exons, getNormSumscore(), GModel< T >::numExons(), and GModel< fpkey >::numExons().
| bool FPGModel::similar | ( | const FPGModel & | mm, | |
| float | fr = 0.15 | |||
| ) | const |
ends similar, identity similar, score similar
References GModel< T >::begin(), GModel< fpkey >::begin(), GModel< T >::direction(), GModel< fpkey >::direction(), GModel< T >::end(), GModel< fpkey >::end(), getAvgiden(), getNormSumscore(), GModel< T >::numExons(), GModel< fpkey >::numExons(), and GModel< fpkey >::overlap().
| double FPGModel::getSumscore | ( | ) | const [inline] |
References sumscore.
| double FPGModel::getNormSumscore | ( | ) | const [inline] |
| bool FPGModel::cover | ( | const FPGModel & | mm | ) | const |
check that all exons of mm is inside of exons of this object Basic condition: mm inside this, mm score < this score number of exon of this > number of exons of mm
| bool FPGModel::similar | ( | const FPGModel & | mm, | |
| float | fr = 0.15 | |||
| ) | const |
ends similar, identity similar, score similar
| double FPGModel::getSumscore | ( | ) | const [inline] |
References sumscore.
| double FPGModel::getNormSumscore | ( | ) | const [inline] |
References sumoverlap, and sumscore.
| double FPGModel::getAvgiden | ( | ) | const [inline] |
References avgiden.
Friends And Related Function Documentation
| ostream& operator<< | ( | ostream & | ous, | |
| const FPGModel & | mm | |||
| ) | [friend] |
| ostream& operator<< | ( | ostream & | ous, | |
| const FPGModel & | mm | |||
| ) | [friend] |
Member Data Documentation
int FPGModel::qlen [private] |
Referenced by operator<<().
int FPGModel::tlen [private] |
Referenced by operator<<().
int FPGModel::qbegin [private] |
Referenced by operator<<().
int FPGModel::qend [private] |
Referenced by operator<<().
int FPGModel::tbegin [private] |
Referenced by operator<<().
int FPGModel::tend [private] |
Referenced by operator<<().
int FPGModel::numexon [private] |
Referenced by operator<<().
double FPGModel::sumscore [private] |
Referenced by getNormSumscore(), getSumscore(), and operator<<().
double FPGModel::avgiden [private] |
Referenced by getAvgiden(), and operator<<().
double FPGModel::qcov [private] |
Referenced by operator<<().
double FPGModel::sumoverlap [private] |
Referenced by getNormSumscore(), and operator<<().
The documentation for this class was generated from the following files:
- bioseq/FPGModel.h
- util/FPGModel.h
- bioseq/FPGModel.cpp
