, including all inherited members.
| addPattern(string, int ReapIden=100, int GP=-50, int extn=-9999, int TH=10) | BioDnaMultiPatternAlignment | |
| BioDnaMultiPatternAlignment() | BioDnaMultiPatternAlignment | |
| BioDnaMultiPatternAlignment(BioDnaSequence, string, string, string MatName, int ReapIden=100, int GP=-50, int extn=-9999, int TH=10) | BioDnaMultiPatternAlignment | |
| BioDnaMultiPatternAlignment(BioDnaSequence, string, string MatName="IDENTITY", int ReapIden=100, int GP=-50, int extn=-9999, int TH=10) | BioDnaMultiPatternAlignment | |
| BioDnaMultiPatternAlignment(BioDnaSequence, string, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=10) | BioDnaMultiPatternAlignment | |
| BioDnaMultiPatternAlignment(BioFasta, string, string, string MatName, int ReapIden=100, int GP=-50, int extn=-9999, int TH=10) | BioDnaMultiPatternAlignment | |
| BioDnaMultiPatternAlignment(BioFasta, string, string MatName="IDENTITY", int ReapIden=100, int GP=-50, int extn=-9999, int TH=10) | BioDnaMultiPatternAlignment | |
| BioDnaMultiPatternAlignment(BioFasta, string, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=10) | BioDnaMultiPatternAlignment | |
| BioDnaMultiPatternAlignment(string, string, string, string, int ReapIden=100, int GP=-50, int extn=-9999, int TH=10) | BioDnaMultiPatternAlignment | |
| BioDnaMultiPatternAlignment(string, string, string matName="IDENTITY", int ReapIden=100, int GP=-50, int extn=-9999, int TH=10) | BioDnaMultiPatternAlignment | |
| BioDnaMultiPatternAlignment(string, string, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=10) | BioDnaMultiPatternAlignment | |
| getAlignedRepeat(int) | BioDnaMultiPatternAlignment | |
| getNumberOfRepeats() | BioDnaMultiPatternAlignment | |
| getRepeat(int) | BioDnaMultiPatternAlignment | |
| getRepeatEndingPosition(int) | BioDnaMultiPatternAlignment | |
| getRepeatStartingPosition(int) | BioDnaMultiPatternAlignment | |
| getScore(int) | BioDnaMultiPatternAlignment | |
| operator<(const BioDnaMultiPatternAlignment &, const BioDnaMultiPatternAlignment &) | BioDnaMultiPatternAlignment | [friend] |
| operator==(const BioDnaMultiPatternAlignment &, const BioDnaMultiPatternAlignment &) | BioDnaMultiPatternAlignment | [friend] |
| operator>(const BioDnaMultiPatternAlignment &, const BioDnaMultiPatternAlignment &) | BioDnaMultiPatternAlignment | [friend] |
| setGapPenalty(int GP=-11, int extn=-9999, int index=-1) | BioDnaMultiPatternAlignment | |
| setGaps(int cou, int index=-1) | BioDnaMultiPatternAlignment | |
| setMatchMisMatchScore(int MS=1, int MMS=0) | BioDnaMultiPatternAlignment | |
| setOffsetRange(int st, int ed, int index=-1) | BioDnaMultiPatternAlignment | |
| setOrder(string) | BioDnaMultiPatternAlignment | |
| setRepeatIdentity(int identity, int index=-1) | BioDnaMultiPatternAlignment | |
| setSequence(BioDnaSequence) | BioDnaMultiPatternAlignment | |
| setSequence(BioFasta) | BioDnaMultiPatternAlignment | |
| setSequence(string) | BioDnaMultiPatternAlignment | |
| setSubstitutionMatrix(string) | BioDnaMultiPatternAlignment | |
| setSubstitutionMatrix(string, string) | BioDnaMultiPatternAlignment | |
| setThreshold(int, int index=-1) | BioDnaMultiPatternAlignment | |
| showAlignment(ostream &=cout) | BioDnaMultiPatternAlignment | |
| showAlignment(BioPostScript &ps, float=100, float=650, float=450) | BioDnaMultiPatternAlignment | |
| ~BioDnaMultiPatternAlignment() | BioDnaMultiPatternAlignment | |
1.7.6.1 
