|
|
| Transcript (const Transcript &other) |
| |
|
Transcript & | operator= (const Transcript &other) |
| |
|
virtual Transcript * | clone () |
| |
|
Transcript * | cloneGeneSequence () |
| |
|
void | addStatePostProbs (float p) |
| |
|
void | setStatePostProbs (float p) |
| |
|
void | addSampleCount (int k) |
| |
|
void | setSampleCount (int k) |
| |
|
virtual long | geneBegin () const |
| |
|
virtual long | geneEnd () const |
| |
|
virtual bool | isCoding () const |
| |
|
bool | operator< (const Transcript &other) const |
| |
|
bool | operator== (const Transcript &other) const |
| |
|
void | normPostProb (float n) |
| |
|
void | updatePostProb (Transcript *other) |
| |
|
virtual list< State * > | getExInHeads () const |
| |
|
virtual list< State * > | getExInInHeads () const |
| |
|
double | meanStateProb () |
| |
|
char * | getExonicSequence (AnnoSequence *annoseq=NULL, bool noOffset=false) const |
| |
|
virtual void | shiftCoordinates (long d) |
| |
|
virtual bool | almostIdenticalTo (Transcript *other) |
| |
|
virtual void | printCodingSeq (AnnoSequence *annoseq) const |
| |
|
virtual void | printProteinSeq (AnnoSequence *annoseq) const |
| |
|
virtual void | printBlockSequences (AnnoSequence *annoseq) const |
| |
|
virtual void | printGFF () const |
| |
|
virtual void | printEvidence () const |
| |
|
void | setStateHasScore (bool has) |
| |
|
virtual double | supportingFraction (HintGroup *group) |
| |
|
|
static void | destroyGeneSequence (Transcript *head) |
| |
|
static Transcript * | getGenesOnStrand (Transcript *genes, Strand strand) |
| |
|
static void | filterTranscriptsByMaxTracks (list< Transcript * > &gl, int maxTracks) |
| |
|
|
State * | exons |
| |
|
State * | introns |
| |
|
long | transstart |
| |
|
long | transend |
| |
|
Transcript * | next |
| |
|
string | id |
| |
|
string | seqname |
| |
|
string | source |
| |
|
Strand | strand |
| |
|
Boolean | complete |
| |
|
string | geneid |
| |
|
float | apostprob |
| |
|
bool | hasProbs |
| |
|
bool | throwaway |
| |
|
bool | viterbi |
| |
|
|
static bool | gff3 = false |
| |
|
static bool | print_tss =false |
| |
|
static bool | print_tts =false |
| |
The documentation for this class was generated from the following files:
