BioDnaSequenceRepeatAlignment Member List

This is the complete list of members for BioDnaSequenceRepeatAlignment, 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]
BioDnaSequenceRepeatAlignment()	BioDnaSequenceRepeatAlignment
BioDnaSequenceRepeatAlignment(BioDnaSequence, BioDnaSequence, string, string MatName, int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)	BioDnaSequenceRepeatAlignment
BioDnaSequenceRepeatAlignment(BioDnaSequence, string, string, string MatName, int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)	BioDnaSequenceRepeatAlignment
BioDnaSequenceRepeatAlignment(BioDnaSequence, BioDnaSequence, string MatName="IDENTITY", int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)	BioDnaSequenceRepeatAlignment
BioDnaSequenceRepeatAlignment(BioDnaSequence, string, string MatName="IDENTITY", int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)	BioDnaSequenceRepeatAlignment
BioDnaSequenceRepeatAlignment(BioDnaSequence, BioDnaSequence, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=10)	BioDnaSequenceRepeatAlignment
BioDnaSequenceRepeatAlignment(BioDnaSequence, string, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=10)	BioDnaSequenceRepeatAlignment
BioDnaSequenceRepeatAlignment(BioFasta, BioFasta, string, string MatName, int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)	BioDnaSequenceRepeatAlignment
BioDnaSequenceRepeatAlignment(BioFasta, string, string, string MatName, int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)	BioDnaSequenceRepeatAlignment
BioDnaSequenceRepeatAlignment(BioFasta, BioFasta, string MatName="IDENTITY", int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)	BioDnaSequenceRepeatAlignment
BioDnaSequenceRepeatAlignment(BioFasta, string, string MatName="IDENTITY", int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)	BioDnaSequenceRepeatAlignment
BioDnaSequenceRepeatAlignment(BioFasta, BioFasta, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=10)	BioDnaSequenceRepeatAlignment
BioDnaSequenceRepeatAlignment(BioFasta, string, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=10)	BioDnaSequenceRepeatAlignment
BioDnaSequenceRepeatAlignment(string, string, string, string, int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)	BioDnaSequenceRepeatAlignment
BioDnaSequenceRepeatAlignment(string, string, string matName="IDENTITY", int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)	BioDnaSequenceRepeatAlignment
BioDnaSequenceRepeatAlignment(string, string, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=10)	BioDnaSequenceRepeatAlignment
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]
getAlignedRepeat(long)	BioDnaSequenceRepeatAlignment
getAlignedSequence1()	BioDnaSequenceRepeatAlignment
getAlignedSequence2()	BioDnaSequenceRepeatAlignment
getIdentity(int)	BioDnaSequenceRepeatAlignment
getNumberOfIdentities()	BioDnaSequenceRepeatAlignment
getNumberOfRepeats()	BioDnaSequenceRepeatAlignment
getRepeat(long)	BioDnaSequenceRepeatAlignment
getRepeatEndingPosition(long)	BioDnaSequenceRepeatAlignment
getRepeatScore(int)	BioDnaSequenceRepeatAlignment
getRepeatStartingPosition(long)	BioDnaSequenceRepeatAlignment
getScore()	BioDnaSequenceRepeatAlignment
nucleicAcidSeq	BioDnaSequenceAlignment	[protected, static]
operator<(const BioDnaSequenceRepeatAlignment &, const BioDnaSequenceRepeatAlignment &)	BioDnaSequenceRepeatAlignment	[friend]
operator==(const BioDnaSequenceRepeatAlignment &, const BioDnaSequenceRepeatAlignment &)	BioDnaSequenceRepeatAlignment	[friend]
operator>(const BioDnaSequenceRepeatAlignment &, const BioDnaSequenceRepeatAlignment &)	BioDnaSequenceRepeatAlignment	[friend]
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
setGaps(int)	BioDnaSequenceRepeatAlignment
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
setRepeatIdentity(int)	BioDnaSequenceRepeatAlignment
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
setThreshold(int)	BioDnaSequenceRepeatAlignment
showAccumulationMatrix(ostream &=cout)	BioDnaSequenceRepeatAlignment
showAlignment(ostream &=cout)	BioDnaSequenceRepeatAlignment
showAlignment(BioPostScript &ps, float=100, float=650, float=450)	BioDnaSequenceRepeatAlignment
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]