, including all inherited members.
| addPattern(string, int ReapIden=100, int GP=-50, int extn=-9999, int TH=20) | BioProteinMultiPatternAlignment | |
| BioProteinMultiPatternAlignment() | BioProteinMultiPatternAlignment | |
| BioProteinMultiPatternAlignment(BioProteinSequence, string, string="BLOSUM62", int ReapIden=100, int GP=-50, int extn=-9999, int TH=20) | BioProteinMultiPatternAlignment | |
| BioProteinMultiPatternAlignment(BioProteinSequence, string, string, string, int ReapIden=100, int GP=-50, int extn=-9999, int TH=20) | BioProteinMultiPatternAlignment | |
| BioProteinMultiPatternAlignment(BioProteinSequence, string, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=20) | BioProteinMultiPatternAlignment | |
| BioProteinMultiPatternAlignment(BioFasta, string, string="BLOSUM62", int ReapIden=100, int GP=-50, int extn=-9999, int TH=20) | BioProteinMultiPatternAlignment | |
| BioProteinMultiPatternAlignment(BioFasta, string, string, string, int ReapIden=100, int GP=-50, int extn=-9999, int TH=20) | BioProteinMultiPatternAlignment | |
| BioProteinMultiPatternAlignment(BioFasta, string, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=20) | BioProteinMultiPatternAlignment | |
| BioProteinMultiPatternAlignment(string, string, string="BLOSUM62", int ReapIden=100, int GP=-50, int extn=-9999, int TH=20) | BioProteinMultiPatternAlignment | |
| BioProteinMultiPatternAlignment(string, string, string, string, int ReapIden=100, int GP=-50, int extn=-9999, int TH=20) | BioProteinMultiPatternAlignment | |
| BioProteinMultiPatternAlignment(string, string, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=20) | BioProteinMultiPatternAlignment | |
| getAlignedRepeat(int) | BioProteinMultiPatternAlignment | |
| getNumberOfRepeats() | BioProteinMultiPatternAlignment | |
| getRepeat(int) | BioProteinMultiPatternAlignment | |
| getRepeatEndingPosition(int) | BioProteinMultiPatternAlignment | |
| getRepeatStartingPosition(int) | BioProteinMultiPatternAlignment | |
| getScore(int) | BioProteinMultiPatternAlignment | |
| operator<(const BioProteinMultiPatternAlignment &, const BioProteinMultiPatternAlignment &) | BioProteinMultiPatternAlignment | [friend] |
| operator==(const BioProteinMultiPatternAlignment &, const BioProteinMultiPatternAlignment &) | BioProteinMultiPatternAlignment | [friend] |
| operator>(const BioProteinMultiPatternAlignment &, const BioProteinMultiPatternAlignment &) | BioProteinMultiPatternAlignment | [friend] |
| setGapPenalty(int GP=-11, int extn=-9999, int index=-1) | BioProteinMultiPatternAlignment | |
| setGaps(int cou, int index=-1) | BioProteinMultiPatternAlignment | |
| setMatchMisMatchScore(int MS=1, int MMS=0) | BioProteinMultiPatternAlignment | |
| setOffsetRange(int st, int ed, int index=-1) | BioProteinMultiPatternAlignment | |
| setOrder(string) | BioProteinMultiPatternAlignment | |
| setRepeatIdentity(int identity, int index=-1) | BioProteinMultiPatternAlignment | |
| setSequence(BioProteinSequence) | BioProteinMultiPatternAlignment | |
| setSequence(BioFasta) | BioProteinMultiPatternAlignment | |
| setSequence(string) | BioProteinMultiPatternAlignment | |
| setSubstitutionMatrix(string) | BioProteinMultiPatternAlignment | |
| setSubstitutionMatrix(string, string) | BioProteinMultiPatternAlignment | |
| setThreshold(int, int index=-1) | BioProteinMultiPatternAlignment | |
| showAlignment(ostream &=cout) | BioProteinMultiPatternAlignment | |
| showAlignment(BioPostScript &ps, float=100, float=650, float=450) | BioProteinMultiPatternAlignment | |
| ~BioProteinMultiPatternAlignment() | BioProteinMultiPatternAlignment | |
1.7.6.1 
