, including all inherited members.
| BioDnaSequence(const string &) | BioDnaSequence | |
| BioDnaSequence() | BioDnaSequence | |
| BioDnaSequence(const string &seqnam, const string &seq) | BioDnaSequence | |
| BioFeatures() | BioFeatures | [inline] |
| BioGenBankFeatures() | BioGenBankFeatures | [inline] |
| BioGenBankFeatures(const string &de_) | BioGenBankFeatures | |
| BioGenBankSequence() | BioGenBankSequence | |
| BioGenBankSequence(const string &de_) | BioGenBankSequence | |
| BioSequence() | BioSequence | |
| BioSequence(const string &filename) | BioSequence | |
| BioSequence(const string &seqnam, const string &seq) | BioSequence | |
| checkDnaSequence() | BioDnaSequence | |
| checkSequence() | BioSequence | |
| find(const string &words) | BioSequence | |
| findPattern(const string &pat) | BioSequence | |
| get3PrimeClip(int) | BioFeatures | |
| get3PrimeUtr(int) | BioFeatures | |
| get5PrimeClip(int) | BioFeatures | |
| get5PrimeUtr(int) | BioFeatures | |
| get_(int) | BioFeatures | |
| get_10Signal(int) | BioFeatures | |
| get_35Signal(int) | BioFeatures | |
| getAttenuator(int) | BioFeatures | |
| getBase(const long &) | BioDnaSequence | |
| getCAATSignal(int) | BioFeatures | |
| getCds(int) | BioFeatures | |
| getComplementarySequence() | BioDnaSequence | |
| getComplementarySequence(const long &, const long &) | BioDnaSequence | |
| getConflict(int) | BioFeatures | |
| getCRegion(int) | BioFeatures | |
| getDeletedSequence(const long &, const long &) | BioSequence | |
| getDLoop(int) | BioFeatures | |
| getDSegment(int) | BioFeatures | |
| getEnhancer(int) | BioFeatures | |
| getExon(int) | BioFeatures | |
| getGap(int) | BioFeatures | |
| getGCSignal(int) | BioFeatures | |
| getGene(int) | BioFeatures | |
| getIDna(int) | BioFeatures | |
| getInsertedSequence(const long &, const string &) | BioSequence | |
| getIntron(int) | BioFeatures | |
| getJSegment(int) | BioFeatures | |
| getLtr(int) | BioFeatures | |
| getMatPeptide(int) | BioFeatures | |
| getMiscBinding(int) | BioFeatures | |
| getMiscDifference(int) | BioFeatures | |
| getMiscFeature(int) | BioFeatures | |
| getMiscRecomb(int) | BioFeatures | |
| getMiscRna(int) | BioFeatures | |
| getMiscSignal(int) | BioFeatures | |
| getMiscStructure(int) | BioFeatures | |
| getModifiedBase(int) | BioFeatures | |
| getMolecularWeight() | BioDnaSequence | |
| getMRna(int) | BioFeatures | |
| getmRnaSequence() | BioDnaSequence | |
| getmRnaSequence(const long &, const long &) | BioDnaSequence | |
| getMutatedSequence(const long &, const char &) | BioSequence | |
| getMutatedSequence(const long &, const string &) | BioSequence | |
| getMutatedSequence(const char &, const char &) | BioSequence | |
| getMutatedSequence(const string &, const string &) | BioSequence | |
| getMutatedSequence(const long &, const long &, const string &) | BioSequence | |
| getMutatedSequence(string &s1) | BioSequence | |
| getNRegion(int) | BioFeatures | |
| getNumberOf3PrimeClips() | BioFeatures | |
| getNumberOf3PrimeUtrs() | BioFeatures | |
| getNumberOf5PrimeClips() | BioFeatures | |
| getNumberOf5PrimeUtrs() | BioFeatures | |
| getNumberOf_10Signals() | BioFeatures | |
| getNumberOf_35Signals() | BioFeatures | |
| getNumberOf_s() | BioFeatures | |
| getNumberOfAttenuators() | BioFeatures | |
| getNumberOfCAATSignals() | BioFeatures | |
| getNumberOfCdss() | BioFeatures | |
| getNumberOfConflicts() | BioFeatures | |
| getNumberOfCRegions() | BioFeatures | |
| getNumberOfDLoops() | BioFeatures | |
| getNumberOfDSegments() | BioFeatures | |
| getNumberOfEnhancers() | BioFeatures | |
| getNumberOfExons() | BioFeatures | |
| getNumberOfGaps() | BioFeatures | |
| getNumberOfGCSignals() | BioFeatures | |
| getNumberOfGenes() | BioFeatures | |
| getNumberOfIDnas() | BioFeatures | |
| getNumberOfIntrons() | BioFeatures | |
| getNumberOfJSegments() | BioFeatures | |
| getNumberOfLtrs() | BioFeatures | |
| getNumberOfMatPeptides() | BioFeatures | |
| getNumberOfMiscBindings() | BioFeatures | |
| getNumberOfMiscDifferences() | BioFeatures | |
| getNumberOfMiscFeatures() | BioFeatures | |
| getNumberOfMiscRecombs() | BioFeatures | |
| getNumberOfMiscRnas() | BioFeatures | |
| getNumberOfMiscSignals() | BioFeatures | |
| getNumberOfMiscStructures() | BioFeatures | |
| getNumberOfModifiedBases() | BioFeatures | |
| getNumberOfMRnas() | BioFeatures | |
| getNumberOfNRegions() | BioFeatures | |
| getNumberOfOccurrences(const char &ch) | BioSequence | |
| getNumberOfOccurrences(const string &pattern) | BioSequence | |
| getNumberOfOldSequences() | BioFeatures | |
| getNumberOfOperons() | BioFeatures | |
| getNumberOfOriTs() | BioFeatures | |
| getNumberOfPolyASignals() | BioFeatures | |
| getNumberOfPolyASites() | BioFeatures | |
| getNumberOfPrecursorRnas() | BioFeatures | |
| getNumberOfPrimerBinds() | BioFeatures | |
| getNumberOfPrimTranscripts() | BioFeatures | |
| getNumberOfPromoters() | BioFeatures | |
| getNumberOfProteinBinds() | BioFeatures | |
| getNumberOfRbs() | BioFeatures | |
| getNumberOfRepeatRegions() | BioFeatures | |
| getNumberOfRepeatUnits() | BioFeatures | |
| getNumberOfRepOrigins() | BioFeatures | |
| getNumberOfRRnas() | BioFeatures | |
| getNumberOfSatellites() | BioFeatures | |
| getNumberOfSCRnas() | BioFeatures | |
| getNumberOfSigPeptides() | BioFeatures | |
| getNumberOfSNORnas() | BioFeatures | |
| getNumberOfSNRnas() | BioFeatures | |
| getNumberOfSources() | BioFeatures | |
| getNumberOfSRegions() | BioFeatures | |
| getNumberOfSSRs(const string &pat, const int &repeats) | BioSequence | |
| getNumberOfStemLoops() | BioFeatures | |
| getNumberOfSts() | BioFeatures | |
| getNumberOfTATASignals() | BioFeatures | |
| getNumberOfTerminators() | BioFeatures | |
| getNumberOfTransitPeptides() | BioFeatures | |
| getNumberOfTRnas() | BioFeatures | |
| getNumberOfUnsures() | BioFeatures | |
| getNumberOfVariations() | BioFeatures | |
| getNumberOfVRegions() | BioFeatures | |
| getNumberOfVSegments() | BioFeatures | |
| getOldSequence(int) | BioFeatures | |
| getOperon(int) | BioFeatures | |
| getOriT(int) | BioFeatures | |
| getPercentAT() | BioDnaSequence | |
| getPercentGC() | BioDnaSequence | |
| getPolyASignal(int) | BioFeatures | |
| getPolyASite(int) | BioFeatures | |
| getPositionsOfPattern(const string &pat) | BioSequence | |
| getPositionsOfSSRs(const string &pat, const int &repeats) | BioSequence | |
| getPrecursorRna(int) | BioFeatures | |
| getPrimerBind(int) | BioFeatures | |
| getPrimTranscript(int) | BioFeatures | |
| getPromoter(int) | BioFeatures | |
| getProteinBind(int) | BioFeatures | |
| getRbs(int) | BioFeatures | |
| getRepeatRegion(int) | BioFeatures | |
| getRepeatUnit(int) | BioFeatures | |
| getRepOrigin(int) | BioFeatures | |
| getRRna(int) | BioFeatures | |
| getSatellite(int) | BioFeatures | |
| getSCRna(int) | BioFeatures | |
| getSequence() const | BioSequence | |
| getSequenceLength() const | BioSequence | |
| getSequenceName() const | BioSequence | |
| getSequenceSegment(const long &a, const long &b) | BioSequence | |
| getShuffledSequence() | BioSequence | |
| getSigPeptide(int) | BioFeatures | |
| getSNORna(int) | BioFeatures | |
| getSNRna(int) | BioFeatures | |
| getSource(int) | BioFeatures | |
| getSRegion(int) | BioFeatures | |
| getStemLoop(int) | BioFeatures | |
| getSts(int) | BioFeatures | |
| getTATASignal(int) | BioFeatures | |
| getTerminator(int) | BioFeatures | |
| getTm() | BioDnaSequence | |
| getTransitPeptide(int) | BioFeatures | |
| getTranslatedSequence(const int &frameNumber) | BioDnaSequence | |
| getTranslatedSequence(const long &, const long &, const int &frameNumber) | BioDnaSequence | |
| getTRna(int) | BioFeatures | |
| getUnsure(int) | BioFeatures | |
| getVariation(int) | BioFeatures | |
| getVRegion(int) | BioFeatures | |
| getVSegment(int) | BioFeatures | |
| readFasta(ifstream &) | BioSequence | |
| seqname_ | BioSequence | [protected] |
| sequence_ | BioSequence | [protected] |
| setFeatures(vector< string >) | BioFeatures | |
| setSequence(string, vector< string >) | BioGenBankSequence | [protected] |
| BioDnaSequence::setSequence(const string &seqnam, const string &seq) | BioDnaSequence | |
| BioDnaSequence::setSequence(const string &seq) | BioDnaSequence | |
| setSequenceName(const string &seqnam) | BioDnaSequence | |
| showBioFeatures(ostream &=cout, string st=" ") | BioFeatures | |
| showCds(int, ostream &os=cout) | BioFeatures | |
| showFeatureKeys(ostream &=cout) | BioFeatures | |
| showFeatures(ostream &os=cout) | BioGenBankFeatures | |
| showInFasta(ostream &=cout) | BioSequence | |
| showPositionsOfPattern(const string &pat, ostream &os=cout) | BioSequence | |
| showPositionsOfPattern(const string &pat, BioPostScript &ps, const int &xpos=100, const int &ypos=650, const int &w=450, const int &h=20) | BioSequence | |
| showSequence(ostream &=cout) | BioGenBankSequence | |
| showShuffledSequence(ostream &os=cout) | BioSequence | |
| showSSRs(const string &pat, const int &repeats, ostream &os=cout) | BioSequence | |
| showSSRs(const string &pat, const int &repeats, BioPostScript &ps, const int &xpos=100, const int &ypos=650, const int &w=450, const int &h=20) | BioSequence | |
| showTranslatedSequences(ostream &os=cout) | BioDnaSequence | |
| showTranslatedSequences(const long &, const long &, ostream &os=cout) | BioDnaSequence | |
| showTranslatedSequences(BioHtml &) | BioDnaSequence | |
| showTranslatedSequences(BioPostScript &, int startX=75, int startY=200, int len=400) | BioDnaSequence | |
| ~BioDnaSequence() | BioDnaSequence | |
| ~BioFeatures() | BioFeatures | |
1.7.6.1 
