Alignment Member List

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

addGap(int seq, int i)	Alignment	[private]
addGapInSeq0(int i)	Alignment
addGapInSeq1(int j)	Alignment
Alignment(AlignmentParams *params)	Alignment
Alignment(const Alignment &orig)	Alignment
alignmentFinalized	Alignment	[private]
end	Alignment	[private]
finalize()	Alignment
gap_sequences	Alignment	[private]
gapExtensions	Alignment	[private]
gapOpen	Alignment	[private]
gaps	Alignment	[private]
getAlignmentParams() const	Alignment
getEnd(int seq)	Alignment
getGapExtensions() const	Alignment
getGapOpen() const	Alignment
getGaps(int seq)	Alignment	[inline]
getGapSequences()	Alignment
getMatches() const	Alignment
getMismatches() const	Alignment
getPruningFile() const	Alignment
getRawScore() const	Alignment
getStart(int seq)	Alignment
isFinalized()	Alignment
matches	Alignment	[private]
mismatches	Alignment	[private]
params	Alignment	[private]
pruningFile	Alignment	[private]
rawScore	Alignment	[private]
setEnd(int seq, int pos)	Alignment
setGapExtensions(int gapExtensions)	Alignment
setGapOpen(int gapOpen)	Alignment
setMatches(int matches)	Alignment
setMismatches(int mismatches)	Alignment
setPruningFile(string pruningFile)	Alignment
setRawScore(int rawScore)	Alignment
setStart(int seq, int pos)	Alignment
start	Alignment	[private]
~Alignment()	Alignment	[virtual]