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

add(Alignment a1, Alignment a2)	jaligner.Alignment	static
Alignment()	jaligner.Alignment
calculateScore()	jaligner.Alignment
checkScore()	jaligner.Alignment
copy(Alignment alignment)	jaligner.Alignment	static
GAP	jaligner.Alignment	static
getExtend()	jaligner.Alignment
getGaps()	jaligner.Alignment
getGaps1()	jaligner.Alignment
getGaps2()	jaligner.Alignment
getIdentity()	jaligner.Alignment
getLength()	jaligner.Alignment
getLongestPerfectMatch()	jaligner.Alignment
getLongestUngappedAlignment(int maxMismatches)	jaligner.Alignment
getMarkupLine()	jaligner.Alignment
getMatrix()	jaligner.Alignment
getName1()	jaligner.Alignment
getName2()	jaligner.Alignment
getNumberOfMatches()	jaligner.Alignment
getNumberOfMatches2()	jaligner.Alignment
getOpen()	jaligner.Alignment
getOriginalSequence1()	jaligner.Alignment
getOriginalSequence2()	jaligner.Alignment
getPercentIdentity()	jaligner.Alignment
getScore()	jaligner.Alignment
getScoreWithNoTerminalGaps()	jaligner.Alignment
getSequence1()	jaligner.Alignment
getSequence2()	jaligner.Alignment
getSimilarity()	jaligner.Alignment
getStart1()	jaligner.Alignment
getStart2()	jaligner.Alignment
getSummary()	jaligner.Alignment
setExtend(float extend)	jaligner.Alignment
setGaps(int gaps)	jaligner.Alignment
setIdentity(int identity)	jaligner.Alignment
setMarkupLine(char[] markupLine)	jaligner.Alignment
setMatrix(Matrix matrix)	jaligner.Alignment
setName1(String name1)	jaligner.Alignment
setName2(String name2)	jaligner.Alignment
setOpen(float open)	jaligner.Alignment
setOriginalSequence1(Sequence originalSequence1)	jaligner.Alignment
setOriginalSequence2(Sequence originalSequence2)	jaligner.Alignment
setScore(float score)	jaligner.Alignment
setSequence1(char[] sequence1)	jaligner.Alignment
setSequence2(char[] sequence2)	jaligner.Alignment
setSimilarity(int similarity)	jaligner.Alignment
setStart1(int start1)	jaligner.Alignment
setStart2(int start2)	jaligner.Alignment
toString()	jaligner.Alignment