addCon	addCon
align-class	align-class
bfile2tmat	bfile2tmat
bgModel	bgModel
boundCon	boundCon-class
boundCon-class	boundCon-class
constraintSet-class	constraintSet-class
cosmo	cosmo
cosmo-class	cosmo-class
intInfo	intInfo-class
intInfo-class	intInfo-class
license.cosmo	license.cosmo
makeBoundCon	makeBoundCon
makeConSet	makeConSet
makePalCon	makePalCon
makePosFreqCon	makePosFreqCon
makeShapeCon	makeShapeCon
makeShapeDiffCon	makeShapeDiffCon
makeSubMotifCon	makeSubMotifCon
motifPWM	motifPWM
palCon	palCon-class
palCon-class	palCon-class
plot,constraintSet-method	constraintSet-class
plot,cosmo-method	cosmo-class
plot,intInfo-method	intInfo-class
plot,postProbs-method	postProbs-class
posFreqCon	posFreqCon-class
posFreqCon-class	posFreqCon-class
postProbs-class	postProbs-class
print,align-method	align-class
print,constraintSet-method	constraintSet-class
print,cosmo-method	cosmo-class
readConFile	readConFile
rseq	rseq
shapeCon	shapeCon-class
shapeCon-class	shapeCon-class
shapeDiffCon	shapeDiffCon-class
shapeDiffCon-class	shapeDiffCon-class
show,align-method	align-class
show,constraintSet-method	constraintSet-class
show,cosmo-method	cosmo-class
simScore	simScore
subMotifCon	subMotifCon-class
subMotifCon-class	subMotifCon-class
summary,align-method	align-class
summary,cosmo-method	cosmo-class
transMats	transMats
writeConFile	writeConFile
