org.proteios.io
Class MascotParameterSet

java.lang.Object
  org.proteios.io.MascotParameterSet

public class MascotParameterSet
extends Object

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

Author:

olle

Constructor Summary

MascotParameterSet()

Method Summary

String	getDataFormat() Get data format.
String	getDb()
String	getDecoy() Get decoy.
String	getEnzyme()
String	getErrorTolerant() Get error tolerant.
String	getFixed()
String	getInstrument() Get instrument.
String	getMascotQuery() Get Mascot query.
String	getMassIonType() Get mass ion type.
String	getMassType() Get mass type.
String	getMissedCleavages()
String	getMsMsTol() Get MS-MS mass tolerance.
String	getMsMsTolUnit() Get MS-MS mass tolerance unit.
String	getPeptideCharge() Get peptide charge.
String	getPeptideIsotopeError() Get peptide isotope error.
String	getPepTol() Get peptide mass tolerance.
String	getPepTolUnit() Get peptide mass tolerance unit.
String	getPrecursor() Get precursor.
String	getProteinMass() Get protein mass (kDa).
String	getQuantitation()
String	getReportTop() Get report top.
String	getSearchTitle()
String	getSearchType() Get search type.
String	getSpecies()
String	getVariable()
void	setDataFormat(String dataFormat) Set data format.
void	setDb(String db)
void	setDecoy(String decoy) Set decoy.
void	setEnzyme(String enzyme)
void	setErrorTolerant(String errorTolerant) Set error tolerant.
void	setFixed(String fixed)
void	setInstrument(String instrument) Set instrument.
void	setMascotQuery(String mascotQuery) Set Mascot query.
void	setMassIonType(String massIonType) Set mass ion type.
void	setMassType(String massType) Set mass type.
void	setMissedCleavages(String missedCleavages)
void	setMsMsTol(String msMsTol) Set MS-MS mass tolerance.
void	setMsMsTolUnit(String msMsTolUnit) Set MS-MS mass tolerance unit.
void	setPeptideCharge(String peptideCharge) Set peptide charge.
void	setPeptideIsotopeError(String peptideIsotopeError) Set peptide isotope error.
void	setPepTol(String pepTol) Set peptide mass tolerance.
void	setPepTolUnit(String pepTolUnit) Set peptide mass tolerance unit.
void	setPrecursor(String precursor) Set precursor.
void	setProteinMass(String proteinMass) Set protein mass (kDa).
void	setQuantitation(String quantitation)
void	setReportTop(String reportTop) Set report top.
void	setSearchTitle(String searchTitle)
void	setSearchType(String searchType) Set search type.
void	setSpecies(String species)
void	setVariable(String variable)

Methods inherited from class java.lang.Object

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

Constructor Detail

MascotParameterSet

public MascotParameterSet()

Method Detail

getSearchType

public String getSearchType()

Get search type. Alternatives are "MIS" (MS/MS Ions Search), "SQ" (Sequence Query), "PMF" (Peptide Mass Fingerprint).

Returns:

String search spectrum type.

setSearchType

public void setSearchType(String searchType)

Set search type. Alternatives are "MIS" (MS/MS Ions Search), "SQ" (Sequence Query), "PMF" (Peptide Mass Fingerprint).

Parameters:

searchType - String search type.

getSearchTitle

public String getSearchTitle()

Returns:

String search title.

setSearchTitle

public void setSearchTitle(String searchTitle)

Parameters:

searchTitle - String searchTitle.

getDb

public String getDb()

Returns:

String db.

setDb

public void setDb(String db)

Parameters:

db - String db.

getSpecies

public String getSpecies()

Returns:

String search species.

setSpecies

public void setSpecies(String species)

Parameters:

species - String.

getEnzyme

public String getEnzyme()

Returns:

String enzyme.

setEnzyme

public void setEnzyme(String enzyme)

Parameters:

enzyme - String enzyme.

getMissedCleavages

public String getMissedCleavages()

Returns:

String missed cleavages.

setMissedCleavages

public void setMissedCleavages(String missedCleavages)

Parameters:

missedCleavages - String missed cleavages.

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.

getQuantitation

public String getQuantitation()

Returns:

String quantitation.

setQuantitation

public void setQuantitation(String quantitation)

Parameters:

quantitation - String quantitation.

getProteinMass

public String getProteinMass()

Get protein mass (kDa).

Returns:

String protein mass.

setProteinMass

public void setProteinMass(String proteinMass)

Set protein mass (kDa).

Parameters:

proteinMass - String protein mass.

getPepTol

public String getPepTol()

Get peptide mass tolerance.

Returns:

String peptide mass tolerance.

setPepTol

public void setPepTol(String pepTol)

Set peptide mass tolerance.

Parameters:

pepTol - String peptide mass tolerance.

getPepTolUnit

public String getPepTolUnit()

Get peptide mass tolerance unit.

Returns:

String peptide mass tolerance unit.

setPepTolUnit

public void setPepTolUnit(String pepTolUnit)

Set peptide mass tolerance unit.

Parameters:

pepTolUnit - String peptide mass tolerance unit.

getPeptideIsotopeError

public String getPeptideIsotopeError()

Get peptide isotope error.

Returns:

String peptide isotope error.

setPeptideIsotopeError

public void setPeptideIsotopeError(String peptideIsotopeError)

Set peptide isotope error.

Parameters:

peptideIsotopeError - String peptide isotope error.

getMsMsTol

public String getMsMsTol()

Get MS-MS mass tolerance.

Returns:

String MS-MS mass tolerance.

setMsMsTol

public void setMsMsTol(String msMsTol)

Set MS-MS mass tolerance.

Parameters:

msMsTol - String MS-MS mass tolerance.

getMsMsTolUnit

public String getMsMsTolUnit()

Get MS-MS mass tolerance unit.

Returns:

String MS-MS tolerance mass unit.

setMsMsTolUnit

public void setMsMsTolUnit(String msMsTolUnit)

Set MS-MS mass tolerance unit.

Parameters:

msMsTolUnit - String MS-MS mass tolerance unit.

getPeptideCharge

public String getPeptideCharge()

Get peptide charge.

Returns:

String peptide charge.

setPeptideCharge

public void setPeptideCharge(String peptideCharge)

Set peptide charge.

Parameters:

peptideCharge - String peptide charge.

getMassIonType

public String getMassIonType()

Get mass ion type.

Returns:

String mass ion type.

setMassIonType

public void setMassIonType(String massIonType)

Set mass ion type.

Parameters:

massIonType - String mass ion type.

getMassType

public String getMassType()

Get mass type.

Returns:

String mass type.

setMassType

public void setMassType(String massType)

Set mass type.

Parameters:

massType - String mass type.

getDataFormat

public String getDataFormat()

Get data format.

Returns:

String data format.

setDataFormat

public void setDataFormat(String dataFormat)

Set data format.

Parameters:

dataFormat - String data format.

getPrecursor

public String getPrecursor()

Get precursor.

Returns:

String precursor.

setPrecursor

public void setPrecursor(String precursor)

Set precursor.

Parameters:

precursor - String precursor.

getMascotQuery

public String getMascotQuery()

Get Mascot query.

Returns:

String Mascot query.

setMascotQuery

public void setMascotQuery(String mascotQuery)

Set Mascot query.

Parameters:

mascotQuery - String Mascot query.

getInstrument

public String getInstrument()

Get instrument.

Returns:

String instrument.

setInstrument

public void setInstrument(String instrument)

Set instrument.

Parameters:

instrument - String instrument.

getErrorTolerant

public String getErrorTolerant()

Get error tolerant.

Returns:

String error tolerant.

setErrorTolerant

public void setErrorTolerant(String errorTolerant)

Set error tolerant.

Parameters:

errorTolerant - String errorTolerant.

getDecoy

public String getDecoy()

Get decoy.

Returns:

String decoy.

setDecoy

public void setDecoy(String decoy)

Set decoy.

Parameters:

decoy - String decoy.

getReportTop

public String getReportTop()

Get report top.

Returns:

String report top.

setReportTop

public void setReportTop(String reportTop)

Set report top.