OMSSAParameterSet (${name} ${version} Class documentation)

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

Constructors
Constructor and Description

OMSSAParameterSet()

Constructors
Constructor and Description
`OMSSAParameterSet()`

Method Summary

Methods
Modifier and Type	Method and Description
`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.

Class OMSSAParameterSet

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

OMSSAParameterSet

Method Detail

getSpecies

setSpecies

getSearchSpectrumType

setSearchSpectrumType

getPrecursorSearchType

setPrecursorSearchType

getProductSearchType

setProductSearchType

getIonsToSearch1

setIonsToSearch1

getIonsToSearch2

setIonsToSearch2

getPepTol

setPepTol

getMsMsTol

setMsMsTol

getZDep

setZDep

getCutoff

setCutoff

getCutLo

setCutLo

getCutHi

setCutHi

getCutInc

setCutInc

getSingleWin

setSingleWin

getDoubleWin

setDoubleWin

getSingleNum

setSingleNum

getDoubleNum

setDoubleNum

getFixed

setFixed

getVariable

setVariable

getEnzyme

setEnzyme

getMissedCleave

setMissedCleave

getHitListLen

setHitListLen

getDb

setDb

getTopHitNum

setTopHitNum

getMinHit

setMinHit

getMinSpectra

setMinSpectra

getScale

setScale

getMaxMods

setMaxMods

getMsCalcPlusOne

setMsCalcPlusOne

getMsCalcCharge

setMsCalcCharge

getMinCharge

setMinCharge

getMaxCharge

setMaxCharge

getConsiderMult

setConsiderMult

getPlusOne

setPlusOne

getMaxProductCharge

setMaxProductCharge

getPseudoCount

setPseudoCount

getSearchB1