BioDnaSequenceOverlapAlignment Member List

This is the complete list of members for BioDnaSequenceOverlapAlignment, 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]
BioDnaSequenceOverlapAlignment()	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(BioDnaSequence, BioDnaSequence, string, string MatName, int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(BioDnaSequence, string, string, string MatName, int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(BioDnaSequence, BioDnaSequence, string MatName="IDENTITY", int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(BioDnaSequence, string, string MatName="IDENTITY", int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(BioDnaSequence, BioDnaSequence, int MS, int MMS, int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(BioDnaSequence, string, int MS, int MMS, int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(BioGenBank, BioGenBank, string, string MatName, int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(BioGenBank, string, string, string MatName, int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(BioGenBank, BioGenBank, string MatName="IDENTITY", int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(BioGenBank, string, string MatName="IDENTITY", int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(BioGenBank, BioGenBank, int MS, int MMS, int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(BioGenBank, string, int MS, int MMS, int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(BioFasta, BioFasta, string, string MatName, int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(BioFasta, string, string, string MatName, int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(BioFasta, BioFasta, string MatName="IDENTITY", int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(BioFasta, string, string MatName="IDENTITY", int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(BioFasta, BioFasta, int MS, int MMS, int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(BioFasta, string, int MS, int MMS, int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(BioEmbl, BioEmbl, string, string MatName, int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(BioEmbl, string, string, string MatName, int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(BioEmbl, BioEmbl, string MatName="IDENTITY", int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(BioEmbl, string, string MatName="IDENTITY", int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(BioEmbl, BioEmbl, int MS, int MMS, int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(BioEmbl, string, int MS, int MMS, int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(string, string, string, string, int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(string, string, string, int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
BioDnaSequenceOverlapAlignment(string, string, int MS, int MMS, int GP=-11, int extn=-9999, int TH=10)	BioDnaSequenceOverlapAlignment
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]
getAlignedSequence1()	BioDnaSequenceOverlapAlignment
getAlignedSequence2()	BioDnaSequenceOverlapAlignment
getIdentity()	BioDnaSequenceOverlapAlignment
getNumberOfIdentities()	BioDnaSequenceOverlapAlignment
getScore()	BioDnaSequenceOverlapAlignment
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
setThreshold(int)	BioDnaSequenceOverlapAlignment
showAccumulationMatrix(ostream &=cout)	BioDnaSequenceOverlapAlignment
showAlignment(ostream &=cout)	BioDnaSequenceOverlapAlignment
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]