org.proteios.io
Class OMSSAParameterSet

java.lang.Object
  org.proteios.io.OMSSAParameterSet

public class OMSSAParameterSet
extends Object

This file API should be used to get parameter data from OMSSA input files.

Author:

olle

Constructor Summary

OMSSAParameterSet()

Method Summary

String	getAutoMassAdjust()
String	getConsiderMult() Minimum charge to start using multiply charged products
String	getCutHi() Peak high intensity cutoff (fraction of most intense)
String	getCutInc()
String	getCutLo() Peak low intensity cutoff (fraction of most intense)
String	getCutoff()
String	getDb()
String	getDoubleNum()
String	getDoubleWin()
String	getEnzyme()
String	getExactMass()
String	getFixed()
String	getHitListLen()
String	getIonsToSearch1()
String	getIonsToSearch2()
String	getMaxCharge() Upper bound of precursor charge
String	getMaxMods()
String	getMaxNoEnzyme()
String	getMaxProductCharge()
String	getMaxProductions()
String	getMinCharge() Lower bound of precursor charge
String	getMinHit()
String	getMinNoEnzyme()
String	getMinSpectra()
String	getMissedCleave()
String	getMsCalcCharge()
String	getMsCalcPlusOne()
String	getMsMsTol() Product mass tolerance (Da).
String	getNMethionineAttribute()
String	getNoCorrelationScore()
String	getPepTol() Precursor mass tolerance (Da).
String	getPlusOne() Fraction of product peaks below precursor to determine +1 precursor
String	getPrecursorCull()
String	getPrecursorSearchType()
String	getProbFollowingIon()
String	getProductSearchType()
String	getPseudoCount()
String	getReplaceThresh()
String	getResearchThresh()
String	getScale()
String	getSearchB1()
String	getSearchCTermProduct()
String	getSearchSpectrumType()
String	getSettingId()
String	getSingleNum()
String	getSingleWin()
String	getSpecies()
String	getSubsetThresh()
String	getTopHitNum() Number of top intensity peaks in first pass
String	getVariable()
String	getZDep()
void	setAutoMassAdjust(String autoMassAdjust)
void	setConsiderMult(String considerMult) Minimum charge to start using multiply charged products
void	setCutHi(String cutHi) Peak high intensity cutoff (fraction of most intense)
void	setCutInc(String cutInc)
void	setCutLo(String cutLo) Peak low intensity cutoff (fraction of most intense)
void	setCutoff(String cutoff)
void	setDb(String db)
void	setDoubleNum(String doubleNum)
void	setDoubleWin(String doubleWin)
void	setEnzyme(String enzyme)
void	setExactMass(String exactMass)
void	setFixed(String fixed)
void	setHitListLen(String hitListLen)
void	setIonsToSearch1(String ionsToSearch1)
void	setIonsToSearch2(String ionsToSearch2)
void	setMaxCharge(String maxCharge) Upper bound of precursor charge
void	setMaxMods(String maxMods)
void	setMaxNoEnzyme(String maxNoEnzyme)
void	setMaxProductCharge(String maxProductCharge)
void	setMaxProductions(String maxProductions)
void	setMinCharge(String minCharge) Lower bound of precursor charge
void	setMinHit(String minHit)
void	setMinNoEnzyme(String minNoEnzyme)
void	setMinSpectra(String minSpectra)
void	setMissedCleave(String missedCleave)
void	setMsCalcCharge(String msCalcCharge)
void	setMsCalcPlusOne(String msCalcPlusOne)
void	setMsMsTol(String msMsTol) Product mass tolerance (Da).
void	setNMethionineAttribute(String nMethionineAttribute)
void	setNoCorrelationScore(String noCorrelationScore)
void	setPepTol(String pepTol) Precursor mass tolerance (Da).
void	setPlusOne(String plusOne) Fraction of product peaks below precursor to determine +1 precursor
void	setPrecursorCull(String precursorCull)
void	setPrecursorSearchType(String precursorSearchType)
void	setProbFollowingIon(String probFollowingIon)
void	setProductSearchType(String productSearchType)
void	setPseudoCount(String pseudoCount)
void	setReplaceThresh(String replaceThresh)
void	setResearchThresh(String researchThresh)
void	setScale(String scale)
void	setSearchB1(String searchB1)
void	setSearchCTermProduct(String searchCTermProduct)
void	setSearchSpectrumType(String searchSpectrumType)
void	setSettingId(String settingId)
void	setSingleNum(String singleNum)
void	setSingleWin(String singleWin)
void	setSpecies(String species)
void	setSubsetThresh(String subsetThresh)
void	setTopHitNum(String topHitNum) Number of top intensity peaks in first pass
void	setVariable(String variable)
void	setZDep(String zDep)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

OMSSAParameterSet

public OMSSAParameterSet()

Method Detail

getSpecies

public String getSpecies()

Returns:

String search species.

setSpecies

public void setSpecies(String species)

Parameters:

species - String.

getSearchSpectrumType

public String getSearchSpectrumType()

Returns:

String search spectrum type (iontrap or etd).

setSearchSpectrumType

public void setSearchSpectrumType(String searchSpectrumType)

Parameters:

searchSpectrumType - String search spectrum type (iontrap or etd).

getPrecursorSearchType

public String getPrecursorSearchType()

Returns:

String precursor search type.

setPrecursorSearchType

public void setPrecursorSearchType(String precursorSearchType)

Parameters:

precursorSearchType - String precursor search type.

getProductSearchType

public String getProductSearchType()

Returns:

String product search type.

setProductSearchType

public void setProductSearchType(String productSearchType)

Parameters:

productSearchType - String product search type.

getIonsToSearch1

public String getIonsToSearch1()

Returns:

String ions to search 1.

setIonsToSearch1

public void setIonsToSearch1(String ionsToSearch1)

Parameters:

ionsToSearch1 - String ions to search 1.

getIonsToSearch2

public String getIonsToSearch2()

Returns:

String ions to search 2.

setIonsToSearch2

public void setIonsToSearch2(String ionsToSearch2)

Parameters:

ionsToSearch2 - String ions to search 2.

getPepTol

public String getPepTol()

Precursor mass tolerance (Da).

Returns:

String peptide tolerance.

setPepTol

public void setPepTol(String pepTol)

Precursor mass tolerance (Da).

Parameters:

pepTol - String peptide tolerance.

getMsMsTol

public String getMsMsTol()

Product mass tolerance (Da).

Returns:

String ms-ms tolerance.

setMsMsTol

public void setMsMsTol(String msMsTol)

Product mass tolerance (Da).

Parameters:

msMsTol - String ms-ms tolerance.

getZDep

public String getZDep()

Returns:

String z-dep.

setZDep

public void setZDep(String zDep)

Parameters:

zDep - String z-dep.

getCutoff

public String getCutoff()

Returns:

String cutoff.

setCutoff

public void setCutoff(String cutoff)

Parameters:

cutoff - String cutoff.

getCutLo

public String getCutLo()

Peak low intensity cutoff (fraction of most intense)

Returns:

String cut low.

setCutLo

public void setCutLo(String cutLo)

Peak low intensity cutoff (fraction of most intense)

Parameters:

cutLo - String cut low.

getCutHi

public String getCutHi()

Peak high intensity cutoff (fraction of most intense)

Returns:

String cut high.

setCutHi

public void setCutHi(String cutHi)

Peak high intensity cutoff (fraction of most intense)

Parameters:

cutHi - String cutHi.

getCutInc

public String getCutInc()

Returns:

String cut inc.

setCutInc

public void setCutInc(String cutInc)

Parameters:

cutInc - String cut inc.

getSingleWin

public String getSingleWin()

Returns:

String single window.

setSingleWin

public void setSingleWin(String singleWin)

Parameters:

singleWin - String single window.

getDoubleWin

public String getDoubleWin()

Returns:

String double window.

setDoubleWin

public void setDoubleWin(String doubleWin)

Parameters:

doubleWin - String double window.

getSingleNum

public String getSingleNum()

Returns:

String single number.

setSingleNum

public void setSingleNum(String singleNum)

Parameters:

singleNum - String single number.

getDoubleNum

public String getDoubleNum()

Returns:

String double number.

setDoubleNum

public void setDoubleNum(String doubleNum)

Parameters:

doubleNum - String double number.

getFixed

public String getFixed()

Returns:

String fixed.

setFixed

public void setFixed(String fixed)

Parameters:

fixed - String fixed.

getVariable

public String getVariable()

Returns:

String variable.

setVariable

public void setVariable(String variable)

Parameters:

variable - String variable.

getEnzyme

public String getEnzyme()

Returns:

String enzyme.

setEnzyme

public void setEnzyme(String enzyme)

Parameters:

enzyme - String enzyme.

getMissedCleave

public String getMissedCleave()

Returns:

String missed cleavages.

setMissedCleave

public void setMissedCleave(String missedCleave)

Parameters:

missedCleave - String missed cleavages.

getHitListLen

public String getHitListLen()

Returns:

String hit list length.

setHitListLen

public void setHitListLen(String hitListLen)

Parameters:

hitListLen - String hit list length.

getDb

public String getDb()

Returns:

String db.

setDb

public void setDb(String db)

Parameters:

db - String db.

getTopHitNum

public String getTopHitNum()

Number of top intensity peaks in first pass

Returns:

String top hit number.

setTopHitNum

public void setTopHitNum(String topHitNum)

Number of top intensity peaks in first pass

Parameters:

topHitNum - String top hit number.

getMinHit

public String getMinHit()

Returns:

String minHit.

setMinHit

public void setMinHit(String minHit)

Parameters:

minHit - String minHit.

getMinSpectra

public String getMinSpectra()

Returns:

String minSpectra.

setMinSpectra

public void setMinSpectra(String minSpectra)

Parameters:

minSpectra - String minSpectra.

getScale

public String getScale()

Returns:

String scale.

setScale

public void setScale(String scale)

Parameters:

scale - String scale.

getMaxMods

public String getMaxMods()

Returns:

String max modifications.

setMaxMods

public void setMaxMods(String maxMods)

Parameters:

maxMods - String max modifications.

getMsCalcPlusOne

public String getMsCalcPlusOne()

Returns:

String msCalcPlusOne.

setMsCalcPlusOne

public void setMsCalcPlusOne(String msCalcPlusOne)

Parameters:

msCalcPlusOne - String msCalcPlusOne.

getMsCalcCharge

public String getMsCalcCharge()

Returns:

String msCalcCharge.

setMsCalcCharge

public void setMsCalcCharge(String msCalcCharge)

Parameters:

msCalcCharge - String msCalcCharge.

getMinCharge

public String getMinCharge()

Lower bound of precursor charge

Returns:

String min charge.

setMinCharge

public void setMinCharge(String minCharge)

Lower bound of precursor charge

Parameters:

minCharge - String min charge.

getMaxCharge

public String getMaxCharge()

Upper bound of precursor charge

Returns:

String max charge.

setMaxCharge

public void setMaxCharge(String maxCharge)

Upper bound of precursor charge

Parameters:

maxCharge - String max charge.

getConsiderMult

public String getConsiderMult()

Minimum charge to start using multiply charged products

Returns:

String considerMult.

setConsiderMult

public void setConsiderMult(String considerMult)

Minimum charge to start using multiply charged products

Parameters:

considerMult - String considerMult.

getPlusOne

public String getPlusOne()

Fraction of product peaks below precursor to determine +1 precursor

Returns:

String plusOne.

setPlusOne

public void setPlusOne(String plusOne)

Fraction of product peaks below precursor to determine +1 precursor

Parameters:

plusOne - String plusOne.

getMaxProductCharge

public String getMaxProductCharge()

Returns:

String max product charge.

setMaxProductCharge

public void setMaxProductCharge(String maxProductCharge)

Parameters:

maxProductCharge - String max product charge.

getPseudoCount

public String getPseudoCount()

Returns:

String pseudo count.

setPseudoCount

public void setPseudoCount(String pseudoCount)

Parameters:

pseudoCount - String pseudo count.

getSearchB1

public String getSearchB1()

Returns:

String search b1.

setSearchB1

public void setSearchB1(String searchB1)

Parameters:

searchB1 - String search b1.

getSearchCTermProduct

public String getSearchCTermProduct()

Returns:

String search C term product.

setSearchCTermProduct

public void setSearchCTermProduct(String searchCTermProduct)

Parameters:

searchCTermProduct - String search C term product.

getMaxProductions

public String getMaxProductions()

Returns:

String max productions.

setMaxProductions

public void setMaxProductions(String maxProductions)

Parameters:

maxProductions - String max productions.

getMinNoEnzyme

public String getMinNoEnzyme()

Returns:

String min number of enzymes.

setMinNoEnzyme

public void setMinNoEnzyme(String minNoEnzyme)

Parameters:

minNoEnzyme - String min number of enzymes.

getMaxNoEnzyme

public String getMaxNoEnzyme()

Returns:

String max number of enzymes.

setMaxNoEnzyme

public void setMaxNoEnzyme(String maxNoEnzyme)

Parameters:

maxNoEnzyme - String max number of enzymes.

getExactMass

public String getExactMass()

Returns:

String exact mass.

setExactMass

public void setExactMass(String exactMass)

Parameters:

exactMass - String exact mass.

getSettingId

public String getSettingId()

Returns:

String setting id.

setSettingId

public void setSettingId(String settingId)

Parameters:

settingId - String setting id.

getResearchThresh

public String getResearchThresh()

Returns:

String research threshold.

setResearchThresh

public void setResearchThresh(String researchThresh)

Parameters:

researchThresh - String research threshold.

getSubsetThresh

public String getSubsetThresh()

Returns:

String subset threshold.

setSubsetThresh

public void setSubsetThresh(String subsetThresh)

Parameters:

subsetThresh - String subset threshold.

getReplaceThresh

public String getReplaceThresh()

Returns:

String replace threshold.

setReplaceThresh

public void setReplaceThresh(String replaceThresh)

Parameters:

replaceThresh - String replace threshold.

getPrecursorCull

public String getPrecursorCull()

Returns:

String precursor cull.

setPrecursorCull

public void setPrecursorCull(String precursorCull)

Parameters:

precursorCull - String precursor cull.

getNoCorrelationScore

public String getNoCorrelationScore()

Returns:

String noCorrelationScore.

setNoCorrelationScore

public void setNoCorrelationScore(String noCorrelationScore)

Parameters:

noCorrelationScore - String noCorrelationScore.

getProbFollowingIon

public String getProbFollowingIon()

Returns:

String probFollowingIon.

setProbFollowingIon

public void setProbFollowingIon(String probFollowingIon)

Parameters:

probFollowingIon - String probFollowingIon.

getNMethionineAttribute

public String getNMethionineAttribute()

Returns:

String nMethionine.

setNMethionineAttribute

public void setNMethionineAttribute(String nMethionineAttribute)

Parameters:

nMethionineAttribute - String nMethionineAttribute.

getAutoMassAdjust

public String getAutoMassAdjust()

Returns:

String auto mass adjustment.

setAutoMassAdjust

public void setAutoMassAdjust(String autoMassAdjust)

Parameters:

autoMassAdjust - String auto mass adjustment.