|
|
| Block (DistanceType, const vector< string > &, string) |
| |
|
void | initDistributions () |
| |
|
bool | initThresholds () |
| |
|
void | setIntronProfile (const vector< string > &) |
| |
|
int | size () const |
| |
|
const Column & | operator[] (int columnNr) const |
| |
|
Double | scoreFromScratch (bool complement, int dna_offset, int block_offset, int len) const |
| |
|
Double | scoreFromScratch (bool complement, int dna_offset, int block_offset) const |
| |
|
Double | scoreFromScratch (bool complement, int dna_offset) const |
| |
|
Double | checkedSuffixScore (bool complement, int dna_offset, int block_offset) const |
| |
|
void | bestPartialLogScore (bool complement, int dna_offset, PartScoreType &) const |
| |
|
Block | reverse (DistanceType dist) |
| |
|
Double | getPrefixThresh (bool complement, int i) const |
| |
|
Double | getSuffixThresh (bool complement, int i) const |
| |
|
Double | getPartialThresh (bool complement, int from, int to) const |
| |
|
Double | getPartialThresh (bool complement, int from) const |
| |
|
Double | getThreshold () const |
| |
|
bool | hasIP () const |
| |
|
double | getIntronFreq (int i, int frame) const |
| |
|
bool | isAnchor () |
| |
|
Dist | getOwnDist (int from, int to, bool complement=false) const |
| |
|
Dist | getOwnDist (int from=0) const |
| |
|
Dist | getBackDist (int from, int to, bool complement=false) const |
| |
|
Dist | getBackDist (int from=0) const |
| |
|
double | ownNormalize (double logscore, int from, int to, bool complement=false) const |
| |
|
double | backNormalize (double logscore, int from, int to, bool complement=false) const |
| |
|
double | getSensThresh (double stddev, int from, int to) const |
| |
|
double | getSensThresh (double stddev, int from=0) const |
| |
|
double | getSpecThresh (double stddev, int from, int to) const |
| |
|
double | getSpecThresh (double stddev, int from=0) const |
| |
|
const vector< Dist > & | getAllOwnDists () const |
| |
