BioInt  1.02.00
BioInt: An integrative biological object-oriented application framework and interpreter
BioDnaMultiPatternAlignment Member List
This is the complete list of members for BioDnaMultiPatternAlignment, 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
 All Classes Files Functions Variables Typedefs Enumerations Enumerator Friends Defines