MSGFplus-package	MSGFplus-package
chargeRange	chargeRange
chargeRange,msgfPar-method	chargeRange
chargeRange<-	chargeRange
chargeRange<-,msgfPar,msgfParChargeRange-method	chargeRange
chargeRange<-,msgfPar,numeric-method	chargeRange
db	db
db,msgfPar-method	db
db<-	db
db<-,msgfPar,character-method	db
enzyme	enzyme
enzyme,msgfPar-method	enzyme
enzyme<-	enzyme
enzyme<-,msgfPar,character-method	enzyme
enzyme<-,msgfPar,msgfParEnzyme-method	enzyme
enzyme<-,msgfPar,numeric-method	enzyme
finished	msgfAsync-class
finished,msgfAsync-method	msgfAsync-class
fragmentation	fragmentation
fragmentation,msgfPar-method	fragmentation
fragmentation<-	fragmentation
fragmentation<-,msgfPar,character-method	fragmentation
fragmentation<-,msgfPar,msgfParFragmentation-method	fragmentation
fragmentation<-,msgfPar,numeric-method	fragmentation
getMSGFpar	getMSGFpar
getMSGFpar,msgfPar-method	msgfPar-class
getMSGFpar,msgfParChargeRange-method	msgfParChargeRange-class
getMSGFpar,msgfParEnzyme-method	msgfParEnzyme-class
getMSGFpar,msgfParFragmentation-method	msgfParFragmentation-class
getMSGFpar,msgfParInstrument-method	msgfParInstrument-class
getMSGFpar,msgfParIsotopeError-method	msgfParIsotopeError-class
getMSGFpar,msgfParLengthRange-method	msgfParLengthRange-class
getMSGFpar,msgfParMatches-method	msgfParMatches-class
getMSGFpar,msgfParModification-method	msgfParModification-class
getMSGFpar,msgfParModificationList-method	msgfParModificationList-class
getMSGFpar,msgfParNtt-method	msgfParNtt-class
getMSGFpar,msgfParProtocol-method	msgfParProtocol-class
getMSGFpar,msgfParTda-method	msgfParTda-class
getMSGFpar,msgfParTolerance-method	msgfParTolerance-class
import	msgfAsync-class
import,msgfAsync-method	msgfAsync-class
instrument	instrument
instrument,msgfPar-method	instrument
instrument<-	instrument
instrument<-,msgfPar,character-method	instrument
instrument<-,msgfPar,msgfParInstrument-method	instrument
instrument<-,msgfPar,numeric-method	instrument
isotopeError	isotopeError
isotopeError,msgfPar-method	isotopeError
isotopeError<-	isotopeError
isotopeError<-,msgfPar,msgfParIsotopeError-method	isotopeError
isotopeError<-,msgfPar,numeric-method	isotopeError
length,msgfPar-method	msgfPar-class
length,msgfParChargeRange-method	msgfParChargeRange-class
length,msgfParEnzyme-method	msgfParEnzyme-class
length,msgfParFragmentation-method	msgfParFragmentation-class
length,msgfParInstrument-method	msgfParInstrument-class
length,msgfParIsotopeError-method	msgfParIsotopeError-class
length,msgfParLengthRange-method	msgfParLengthRange-class
length,msgfParMatches-method	msgfParMatches-class
length,msgfParModificationList-method	msgfParModificationList-class
length,msgfParNtt-method	msgfParNtt-class
length,msgfParProtocol-method	msgfParProtocol-class
length,msgfParTda-method	msgfParTda-class
length,msgfParTolerance-method	msgfParTolerance-class
lengthRange	lengthRange
lengthRange,msgfPar-method	lengthRange
lengthRange<-	lengthRange
lengthRange<-,msgfPar,msgfParLengthRange-method	lengthRange
lengthRange<-,msgfPar,numeric-method	lengthRange
matches	matches
matches,msgfPar-method	matches
matches<-	matches
matches<-,msgfPar,msgfParMatches-method	matches
matches<-,msgfPar,numeric-method	matches
mods	mods
mods,msgfPar-method	mods
mods<-	mods
mods<-,msgfPar,msgfParModificationList-method	mods
msgfAsync-class	msgfAsync-class
msgfPar	msgfPar
msgfPar-class	msgfPar-class
msgfParChargeRange	msgfParChargeRange-class
msgfParChargeRange-class	msgfParChargeRange-class
msgfParEnzyme	msgfParEnzyme-class
msgfParEnzyme-class	msgfParEnzyme-class
msgfParFragmentation	msgfParFragmentation-class
msgfParFragmentation-class	msgfParFragmentation-class
msgfParFromID	msgfParFromID
msgfParInstrument	msgfParInstrument-class
msgfParInstrument-class	msgfParInstrument-class
msgfParIsotopeError	msgfParIsotopeError-class
msgfParIsotopeError-class	msgfParIsotopeError-class
msgfParLengthRange	msgfParLengthRange-class
msgfParLengthRange-class	msgfParLengthRange-class
msgfParMatches	msgfParMatches-class
msgfParMatches-class	msgfParMatches-class
msgfParModification	msgfParModification-class
msgfParModification-class	msgfParModification-class
msgfParModificationList	msgfParModificationList-class
msgfParModificationList-class	msgfParModificationList-class
msgfParNtt	msgfParNtt-class
msgfParNtt-class	msgfParNtt-class
msgfParProtocol	msgfParProtocol-class
msgfParProtocol-class	msgfParProtocol-class
msgfParTda	msgfParTda-class
msgfParTda-class	msgfParTda-class
msgfParTolerance	msgfParTolerance-class
msgfParTolerance-class	msgfParTolerance-class
nMod	mods
nMod,msgfPar-method	mods
nMod<-	mods
nMod<-,msgfPar,numeric-method	mods
ntt	ntt
ntt,msgfPar-method	ntt
ntt<-	ntt
ntt<-,msgfPar,msgfParNtt-method	ntt
ntt<-,msgfPar,numeric-method	ntt
protocol	protocol
protocol,msgfPar-method	protocol
protocol<-	protocol
protocol<-,msgfPar,character-method	protocol
protocol<-,msgfPar,msgfParProtocol-method	protocol
protocol<-,msgfPar,numeric-method	protocol
runMSGF	runMSGF
runMSGF,msgfPar-method	msgfPar-class
running	msgfAsync-class
running,msgfAsync-method	msgfAsync-class
show,msgfPar-method	msgfPar-class
show,msgfParChargeRange-method	msgfParChargeRange-class
show,msgfParEnzyme-method	msgfParEnzyme-class
show,msgfParFragmentation-method	msgfParFragmentation-class
show,msgfParInstrument-method	msgfParInstrument-class
show,msgfParIsotopeError-method	msgfParIsotopeError-class
show,msgfParLengthRange-method	msgfParLengthRange-class
show,msgfParMatches-method	msgfParMatches-class
show,msgfParModification-method	msgfParModification-class
show,msgfParModificationList-method	msgfParModificationList-class
show,msgfParNtt-method	msgfParNtt-class
show,msgfParProtocol-method	msgfParProtocol-class
show,msgfParTda-method	msgfParTda-class
show,msgfParTolerance-method	msgfParTolerance-class
tda	tda
tda,msgfPar-method	tda
tda<-	tda
tda<-,msgfPar,logical-method	tda
tda<-,msgfPar,msgfParTda-method	tda
tolerance	tolerance
tolerance,msgfPar-method	tolerance
tolerance<-	tolerance
tolerance<-,msgfPar,character-method	tolerance
tolerance<-,msgfPar,msgfParTolerance-method	tolerance
toleranceRange	tolerance
toleranceRange,msgfPar-method	tolerance
toleranceRange<-	tolerance
toleranceRange<-,msgfPar,numeric-method	tolerance
toleranceUnit	tolerance
toleranceUnit,msgfPar-method	tolerance
toleranceUnit<-	tolerance
toleranceUnit<-,msgfPar,character-method	tolerance
[[,msgfParModificationList,numeric,missing-method	msgfParModificationList-class
[[<-,msgfParModificationList,numeric,missing,msgfParModification-method	msgfParModificationList-class
