BioDnaSequenceAlignment Member List

This is the complete list of members for BioDnaSequenceAlignment, including all inherited members.

BioDnaSequenceAlignment()	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, BioDnaSequence, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, string, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, BioDnaSequence, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, string, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, BioDnaSequence, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, string, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, BioGenBank, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, string, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, BioGenBank, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, string, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, BioGenBank, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, string, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, BioFasta, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, string, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, BioFasta, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, string, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, BioFasta, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, string, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, BioEmbl, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, string, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, BioEmbl, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, string, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, BioEmbl, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, string, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(string, string, string, string, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(string, string, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(string, string, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment()	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, BioDnaSequence, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, string, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, BioDnaSequence, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, string, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, BioDnaSequence, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, string, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, BioGenBank, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, string, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, BioGenBank, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, string, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, BioGenBank, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, string, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, BioFasta, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, string, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, BioFasta, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, string, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, BioFasta, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, string, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, BioEmbl, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, string, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, BioEmbl, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, string, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, BioEmbl, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, string, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(string, string, string, string, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(string, string, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(string, string, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment()	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, BioDnaSequence, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, string, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, BioDnaSequence, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, string, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, BioDnaSequence, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, string, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, BioGenBank, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, string, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, BioGenBank, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, string, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, BioGenBank, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, string, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, BioFasta, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, string, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, BioFasta, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, string, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, BioFasta, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, string, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, BioEmbl, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, string, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, BioEmbl, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, string, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, BioEmbl, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, string, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(string, string, string, string, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(string, string, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(string, string, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment()	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, BioDnaSequence, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, string, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, BioDnaSequence, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, string, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, BioDnaSequence, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, string, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, BioGenBank, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, string, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, BioGenBank, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, string, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, BioGenBank, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, string, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, BioFasta, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, string, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, BioFasta, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, string, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, BioFasta, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, string, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, BioEmbl, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, string, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, BioEmbl, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, string, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, BioEmbl, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, string, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(string, string, string, string, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(string, string, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(string, string, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment()	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, BioDnaSequence, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, string, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, BioDnaSequence, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, string, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, BioDnaSequence, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioDnaSequence, string, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, BioGenBank, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, string, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, BioGenBank, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, string, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, BioGenBank, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioGenBank, string, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, BioFasta, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, string, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, BioFasta, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, string, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, BioFasta, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioFasta, string, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, BioEmbl, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, string, string, string MatName, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, BioEmbl, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, string, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, BioEmbl, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(BioEmbl, string, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(string, string, string, string, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(string, string, string mat="IDENTITY", int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
BioDnaSequenceAlignment(string, string, int MS, int MMS, int GP=-11, int extn=-9999)	BioDnaSequenceAlignment	[protected]
formScoringMatrix()	BioDnaSequenceAlignment	[protected]
formScoringMatrix()	BioDnaSequenceAlignment	[protected]
formScoringMatrix()	BioDnaSequenceAlignment	[protected]
formScoringMatrix()	BioDnaSequenceAlignment	[protected]
formScoringMatrix()	BioDnaSequenceAlignment	[protected]
gapExtn	BioDnaSequenceAlignment	[protected]
gapPenalty	BioDnaSequenceAlignment	[protected]
getAccValMov(long, long, int)	BioDnaSequenceAlignment	[protected]
getAccValMov(long, long, int)	BioDnaSequenceAlignment	[protected]
getAccValMov(long, long, int)	BioDnaSequenceAlignment	[protected]
getAccValMov(long, long, int)	BioDnaSequenceAlignment	[protected]
getAccValMov(long, long, int)	BioDnaSequenceAlignment	[protected]
nucleicAcidSeq	BioDnaSequenceAlignment	[protected, static]
outSeq1_	BioDnaSequenceAlignment	[protected]
outSeq2_	BioDnaSequenceAlignment	[protected]
seq1_	BioDnaSequenceAlignment	[protected]
seq2_	BioDnaSequenceAlignment	[protected]
seqName1_	BioDnaSequenceAlignment	[protected]
seqName2_	BioDnaSequenceAlignment	[protected]
setGapPenalty(int GP=-11, int extn=-9999)	BioDnaSequenceAlignment
setGapPenalty(int GP=-11, int extn=-9999)	BioDnaSequenceAlignment
setGapPenalty(int GP=-11, int extn=-9999)	BioDnaSequenceAlignment
setGapPenalty(int GP=-11, int extn=-9999)	BioDnaSequenceAlignment
setGapPenalty(int GP=-11, int extn=-9999)	BioDnaSequenceAlignment
setMatchMisMatchScore(int MS=1, int MMS=0)	BioDnaSequenceAlignment
setMatchMisMatchScore(int MS=1, int MMS=0)	BioDnaSequenceAlignment
setMatchMisMatchScore(int MS=1, int MMS=0)	BioDnaSequenceAlignment
setMatchMisMatchScore(int MS=1, int MMS=0)	BioDnaSequenceAlignment
setMatchMisMatchScore(int MS=1, int MMS=0)	BioDnaSequenceAlignment
setSequence1(BioDnaSequence)	BioDnaSequenceAlignment
setSequence1(BioGenBank)	BioDnaSequenceAlignment
setSequence1(BioFasta)	BioDnaSequenceAlignment
setSequence1(BioEmbl)	BioDnaSequenceAlignment
setSequence1(string)	BioDnaSequenceAlignment
setSequence1(BioDnaSequence)	BioDnaSequenceAlignment
setSequence1(BioGenBank)	BioDnaSequenceAlignment
setSequence1(BioFasta)	BioDnaSequenceAlignment
setSequence1(BioEmbl)	BioDnaSequenceAlignment
setSequence1(string)	BioDnaSequenceAlignment
setSequence1(BioDnaSequence)	BioDnaSequenceAlignment
setSequence1(BioGenBank)	BioDnaSequenceAlignment
setSequence1(BioFasta)	BioDnaSequenceAlignment
setSequence1(BioEmbl)	BioDnaSequenceAlignment
setSequence1(string)	BioDnaSequenceAlignment
setSequence1(BioDnaSequence)	BioDnaSequenceAlignment
setSequence1(BioGenBank)	BioDnaSequenceAlignment
setSequence1(BioFasta)	BioDnaSequenceAlignment
setSequence1(BioEmbl)	BioDnaSequenceAlignment
setSequence1(string)	BioDnaSequenceAlignment
setSequence1(BioDnaSequence)	BioDnaSequenceAlignment
setSequence1(BioGenBank)	BioDnaSequenceAlignment
setSequence1(BioFasta)	BioDnaSequenceAlignment
setSequence1(BioEmbl)	BioDnaSequenceAlignment
setSequence1(string)	BioDnaSequenceAlignment
setSequence2(BioDnaSequence)	BioDnaSequenceAlignment
setSequence2(BioGenBank)	BioDnaSequenceAlignment
setSequence2(BioFasta)	BioDnaSequenceAlignment
setSequence2(BioEmbl)	BioDnaSequenceAlignment
setSequence2(string)	BioDnaSequenceAlignment
setSequence2(BioDnaSequence)	BioDnaSequenceAlignment
setSequence2(BioGenBank)	BioDnaSequenceAlignment
setSequence2(BioFasta)	BioDnaSequenceAlignment
setSequence2(BioEmbl)	BioDnaSequenceAlignment
setSequence2(string)	BioDnaSequenceAlignment
setSequence2(BioDnaSequence)	BioDnaSequenceAlignment
setSequence2(BioGenBank)	BioDnaSequenceAlignment
setSequence2(BioFasta)	BioDnaSequenceAlignment
setSequence2(BioEmbl)	BioDnaSequenceAlignment
setSequence2(string)	BioDnaSequenceAlignment
setSequence2(BioDnaSequence)	BioDnaSequenceAlignment
setSequence2(BioGenBank)	BioDnaSequenceAlignment
setSequence2(BioFasta)	BioDnaSequenceAlignment
setSequence2(BioEmbl)	BioDnaSequenceAlignment
setSequence2(string)	BioDnaSequenceAlignment
setSequence2(BioDnaSequence)	BioDnaSequenceAlignment
setSequence2(BioGenBank)	BioDnaSequenceAlignment
setSequence2(BioFasta)	BioDnaSequenceAlignment
setSequence2(BioEmbl)	BioDnaSequenceAlignment
setSequence2(string)	BioDnaSequenceAlignment
setSubstitutionMatrix(string)	BioDnaSequenceAlignment
setSubstitutionMatrix(string, string)	BioDnaSequenceAlignment
setSubstitutionMatrix(string)	BioDnaSequenceAlignment
setSubstitutionMatrix(string, string)	BioDnaSequenceAlignment
setSubstitutionMatrix(string)	BioDnaSequenceAlignment
setSubstitutionMatrix(string, string)	BioDnaSequenceAlignment
setSubstitutionMatrix(string)	BioDnaSequenceAlignment
setSubstitutionMatrix(string, string)	BioDnaSequenceAlignment
setSubstitutionMatrix(string)	BioDnaSequenceAlignment
setSubstitutionMatrix(string, string)	BioDnaSequenceAlignment
showScoringMatrix(ostream &=cout)	BioDnaSequenceAlignment
showScoringMatrix(ostream &=cout)	BioDnaSequenceAlignment
showScoringMatrix(ostream &=cout)	BioDnaSequenceAlignment
showScoringMatrix(ostream &=cout)	BioDnaSequenceAlignment
showScoringMatrix(ostream &=cout)	BioDnaSequenceAlignment
status	BioDnaSequenceAlignment	[protected]
substitutionMatrix	BioDnaSequenceAlignment	[protected]
tempMatrix	BioDnaSequenceAlignment	[protected]