BioInt  1.02.00
BioInt: An integrative biological object-oriented application framework and interpreter
BioProteinSequenceRepeatAlignment Member List
This is the complete list of members for BioProteinSequenceRepeatAlignment, including all inherited members.
aminoAcidSeq_BioProteinSequenceAlignment [protected, static]
BioProteinSequenceAlignment()BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, BioProteinSequence, string mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, BioProteinSequence, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, BioProteinSequence, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, string, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, string, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, BioSwissProt, string mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, BioSwissProt, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, BioSwissProt, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, string, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, string, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(const BioFasta &, const BioFasta &, const string &mat="BLOSUM62", const int &GP=-11, const int &extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioFasta, BioFasta, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioFasta, BioFasta, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioFasta, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioFasta, string, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioFasta, string, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(const string &, const string &, const string &mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(const string &, const string &, const string &, const string &, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(const string &, const string &, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment()BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, BioProteinSequence, string mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, BioProteinSequence, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, BioProteinSequence, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, string, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, string, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, BioSwissProt, string mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, BioSwissProt, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, BioSwissProt, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, string, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, string, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(const BioFasta &, const BioFasta &, const string &mat="BLOSUM62", const int &GP=-11, const int &extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioFasta, BioFasta, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioFasta, BioFasta, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioFasta, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioFasta, string, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioFasta, string, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(const string &, const string &, const string &mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(const string &, const string &, const string &, const string &, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(const string &, const string &, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment()BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, BioProteinSequence, string mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, BioProteinSequence, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, BioProteinSequence, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, string, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, string, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, BioSwissProt, string mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, BioSwissProt, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, BioSwissProt, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, string, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, string, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(const BioFasta &, const BioFasta &, const string &mat="BLOSUM62", const int &GP=-11, const int &extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioFasta, BioFasta, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioFasta, BioFasta, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioFasta, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioFasta, string, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioFasta, string, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(const string &, const string &, const string &mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(const string &, const string &, const string &, const string &, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(const string &, const string &, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment()BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, BioProteinSequence, string mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, BioProteinSequence, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, BioProteinSequence, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, string, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, string, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, BioSwissProt, string mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, BioSwissProt, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, BioSwissProt, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, string, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, string, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(const BioFasta &, const BioFasta &, const string &mat="BLOSUM62", const int &GP=-11, const int &extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioFasta, BioFasta, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioFasta, BioFasta, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioFasta, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioFasta, string, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioFasta, string, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(const string &, const string &, const string &mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(const string &, const string &, const string &, const string &, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(const string &, const string &, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment()BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, BioProteinSequence, string mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, BioProteinSequence, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, BioProteinSequence, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, string, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioProteinSequence, string, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, BioSwissProt, string mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, BioSwissProt, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, BioSwissProt, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, string, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioSwissProt, string, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(const BioFasta &, const BioFasta &, const string &mat="BLOSUM62", const int &GP=-11, const int &extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioFasta, BioFasta, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioFasta, BioFasta, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioFasta, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioFasta, string, string, string, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(BioFasta, string, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(const string &, const string &, const string &mat="BLOSUM62", int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(const string &, const string &, const string &, const string &, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceAlignment(const string &, const string &, int MS, int MMS, int GP=-11, int extn=-9999)BioProteinSequenceAlignment [protected]
BioProteinSequenceRepeatAlignment()BioProteinSequenceRepeatAlignment
BioProteinSequenceRepeatAlignment(BioProteinSequence, BioProteinSequence, string="BLOSUM62", int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)BioProteinSequenceRepeatAlignment
BioProteinSequenceRepeatAlignment(BioProteinSequence, BioProteinSequence, string, string, int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)BioProteinSequenceRepeatAlignment
BioProteinSequenceRepeatAlignment(BioProteinSequence, BioProteinSequence, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=20)BioProteinSequenceRepeatAlignment
BioProteinSequenceRepeatAlignment(BioProteinSequence, string, string="BLOSUM62", int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)BioProteinSequenceRepeatAlignment
BioProteinSequenceRepeatAlignment(BioProteinSequence, string, string, string, int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)BioProteinSequenceRepeatAlignment
BioProteinSequenceRepeatAlignment(BioProteinSequence, string, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=20)BioProteinSequenceRepeatAlignment
BioProteinSequenceRepeatAlignment(BioSwissProt, BioSwissProt, string="BLOSUM62", int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)BioProteinSequenceRepeatAlignment
BioProteinSequenceRepeatAlignment(BioSwissProt, BioSwissProt, string, string, int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)BioProteinSequenceRepeatAlignment
BioProteinSequenceRepeatAlignment(BioSwissProt, BioSwissProt, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=20)BioProteinSequenceRepeatAlignment
BioProteinSequenceRepeatAlignment(BioSwissProt, string, string="BLOSUM62", int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)BioProteinSequenceRepeatAlignment
BioProteinSequenceRepeatAlignment(BioSwissProt, string, string, string, int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)BioProteinSequenceRepeatAlignment
BioProteinSequenceRepeatAlignment(BioSwissProt, string, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=20)BioProteinSequenceRepeatAlignment
BioProteinSequenceRepeatAlignment(BioFasta, BioFasta, string="BLOSUM62", int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)BioProteinSequenceRepeatAlignment
BioProteinSequenceRepeatAlignment(BioFasta, BioFasta, string, string, int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)BioProteinSequenceRepeatAlignment
BioProteinSequenceRepeatAlignment(BioFasta, BioFasta, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=20)BioProteinSequenceRepeatAlignment
BioProteinSequenceRepeatAlignment(BioFasta, string, string="BLOSUM62", int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)BioProteinSequenceRepeatAlignment
BioProteinSequenceRepeatAlignment(BioFasta, string, string, string, int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)BioProteinSequenceRepeatAlignment
BioProteinSequenceRepeatAlignment(BioFasta, string, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=20)BioProteinSequenceRepeatAlignment
BioProteinSequenceRepeatAlignment(string, string, string="BLOSUM62", int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)BioProteinSequenceRepeatAlignment
BioProteinSequenceRepeatAlignment(string, string, string, string, int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)BioProteinSequenceRepeatAlignment
BioProteinSequenceRepeatAlignment(string, string, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=20)BioProteinSequenceRepeatAlignment
conseq_BioProteinSequenceAlignment [protected]
formScoringMatrix()BioProteinSequenceAlignment [protected]
formScoringMatrix()BioProteinSequenceAlignment [protected]
formScoringMatrix()BioProteinSequenceAlignment [protected]
formScoringMatrix()BioProteinSequenceAlignment [protected]
formScoringMatrix()BioProteinSequenceAlignment [protected]
gapExtnBioProteinSequenceAlignment [protected]
gapPenaltyBioProteinSequenceAlignment [protected]
getAccValMov(long, long, int)BioProteinSequenceAlignment [protected]
getAccValMov(long, long, int)BioProteinSequenceAlignment [protected]
getAccValMov(long, long, int)BioProteinSequenceAlignment [protected]
getAccValMov(long, long, int)BioProteinSequenceAlignment [protected]
getAccValMov(long, long, int)BioProteinSequenceAlignment [protected]
getAlignedRepeat(long)BioProteinSequenceRepeatAlignment
getAlignedSequence1()BioProteinSequenceRepeatAlignment
getAlignedSequence2()BioProteinSequenceRepeatAlignment
getIdentity(int)BioProteinSequenceRepeatAlignment
getNumberOfIdentities()BioProteinSequenceRepeatAlignment
getNumberOfRepeats()BioProteinSequenceRepeatAlignment
getNumberOfSimilarities()BioProteinSequenceRepeatAlignment
getRepeat(long)BioProteinSequenceRepeatAlignment
getRepeatEndingPosition(long)BioProteinSequenceRepeatAlignment
getRepeatScore(int)BioProteinSequenceRepeatAlignment
getRepeatStartingPosition(long)BioProteinSequenceRepeatAlignment
getScore()BioProteinSequenceRepeatAlignment
operator<(const BioProteinSequenceRepeatAlignment &, const BioProteinSequenceRepeatAlignment &)BioProteinSequenceRepeatAlignment [friend]
operator==(const BioProteinSequenceRepeatAlignment &, const BioProteinSequenceRepeatAlignment &)BioProteinSequenceRepeatAlignment [friend]
operator>(const BioProteinSequenceRepeatAlignment &, const BioProteinSequenceRepeatAlignment &)BioProteinSequenceRepeatAlignment [friend]
outSeq1_BioProteinSequenceAlignment [protected]
outSeq2_BioProteinSequenceAlignment [protected]
scoringMatrixBioProteinSequenceAlignment [protected]
seq1_BioProteinSequenceAlignment [protected]
seq2_BioProteinSequenceAlignment [protected]
seqName1_BioProteinSequenceAlignment [protected]
seqName2_BioProteinSequenceAlignment [protected]
setGapPenalty(int GP=-11, int extn=-9999)BioProteinSequenceAlignment
setGapPenalty(int GP=-11, int extn=-9999)BioProteinSequenceAlignment
setGapPenalty(int GP=-11, int extn=-9999)BioProteinSequenceAlignment
setGapPenalty(int GP=-11, int extn=-9999)BioProteinSequenceAlignment
setGapPenalty(int GP=-11, int extn=-9999)BioProteinSequenceAlignment
setGaps(int)BioProteinSequenceRepeatAlignment
setMatchMisMatchScore(int MS=1, int MMS=0)BioProteinSequenceAlignment
setMatchMisMatchScore(int MS=1, int MMS=0)BioProteinSequenceAlignment
setMatchMisMatchScore(int MS=1, int MMS=0)BioProteinSequenceAlignment
setMatchMisMatchScore(int MS=1, int MMS=0)BioProteinSequenceAlignment
setMatchMisMatchScore(int MS=1, int MMS=0)BioProteinSequenceAlignment
setRepeatIdentity(int)BioProteinSequenceRepeatAlignment
setSequence1(BioProteinSequence)BioProteinSequenceAlignment
setSequence1(BioSwissProt)BioProteinSequenceAlignment
setSequence1(BioFasta)BioProteinSequenceAlignment
setSequence1(const string &)BioProteinSequenceAlignment
setSequence1(BioProteinSequence)BioProteinSequenceAlignment
setSequence1(BioSwissProt)BioProteinSequenceAlignment
setSequence1(BioFasta)BioProteinSequenceAlignment
setSequence1(const string &)BioProteinSequenceAlignment
setSequence1(BioProteinSequence)BioProteinSequenceAlignment
setSequence1(BioSwissProt)BioProteinSequenceAlignment
setSequence1(BioFasta)BioProteinSequenceAlignment
setSequence1(const string &)BioProteinSequenceAlignment
setSequence1(BioProteinSequence)BioProteinSequenceAlignment
setSequence1(BioSwissProt)BioProteinSequenceAlignment
setSequence1(BioFasta)BioProteinSequenceAlignment
setSequence1(const string &)BioProteinSequenceAlignment
setSequence1(BioProteinSequence)BioProteinSequenceAlignment
setSequence1(BioSwissProt)BioProteinSequenceAlignment
setSequence1(BioFasta)BioProteinSequenceAlignment
setSequence1(const string &)BioProteinSequenceAlignment
setSequence2(BioProteinSequence)BioProteinSequenceAlignment
setSequence2(BioSwissProt)BioProteinSequenceAlignment
setSequence2(BioFasta)BioProteinSequenceAlignment
setSequence2(const string &)BioProteinSequenceAlignment
setSequence2(BioProteinSequence)BioProteinSequenceAlignment
setSequence2(BioSwissProt)BioProteinSequenceAlignment
setSequence2(BioFasta)BioProteinSequenceAlignment
setSequence2(const string &)BioProteinSequenceAlignment
setSequence2(BioProteinSequence)BioProteinSequenceAlignment
setSequence2(BioSwissProt)BioProteinSequenceAlignment
setSequence2(BioFasta)BioProteinSequenceAlignment
setSequence2(const string &)BioProteinSequenceAlignment
setSequence2(BioProteinSequence)BioProteinSequenceAlignment
setSequence2(BioSwissProt)BioProteinSequenceAlignment
setSequence2(BioFasta)BioProteinSequenceAlignment
setSequence2(const string &)BioProteinSequenceAlignment
setSequence2(BioProteinSequence)BioProteinSequenceAlignment
setSequence2(BioSwissProt)BioProteinSequenceAlignment
setSequence2(BioFasta)BioProteinSequenceAlignment
setSequence2(const string &)BioProteinSequenceAlignment
setSubstitutionMatrix(const string &)BioProteinSequenceAlignment
setSubstitutionMatrix(const string &, const string &)BioProteinSequenceAlignment
setSubstitutionMatrix(const string &)BioProteinSequenceAlignment
setSubstitutionMatrix(const string &, const string &)BioProteinSequenceAlignment
setSubstitutionMatrix(const string &)BioProteinSequenceAlignment
setSubstitutionMatrix(const string &, const string &)BioProteinSequenceAlignment
setSubstitutionMatrix(const string &)BioProteinSequenceAlignment
setSubstitutionMatrix(const string &, const string &)BioProteinSequenceAlignment
setSubstitutionMatrix(const string &)BioProteinSequenceAlignment
setSubstitutionMatrix(const string &, const string &)BioProteinSequenceAlignment
setThreshold(int)BioProteinSequenceRepeatAlignment
showAccumulationMatrix(ostream &=cout)BioProteinSequenceRepeatAlignment
showAlignment(ostream &=cout)BioProteinSequenceRepeatAlignment
showAlignment(BioPostScript &ps, float=100, float=650, float=450)BioProteinSequenceRepeatAlignment
showScoringMatrix(ostream &=cout)BioProteinSequenceAlignment
showScoringMatrix(ostream &=cout)BioProteinSequenceAlignment
showScoringMatrix(ostream &=cout)BioProteinSequenceAlignment
showScoringMatrix(ostream &=cout)BioProteinSequenceAlignment
showScoringMatrix(ostream &=cout)BioProteinSequenceAlignment
statusBioProteinSequenceAlignment [protected]
substitutionMatrixBioProteinSequenceAlignment [protected]
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