uk.ac.ebi.pride.utilities.data.utils

Class MzTabUtils

java.lang.Object

uk.ac.ebi.pride.utilities.data.utils.MzTabUtils

public class MzTabUtils
extends Object

Author:

Yasset Perez-Riverol, Rui Wang

Field Summary

Fields

Modifier and Type	Field and Description
static String	CUSTOM_CHROM_INF_PARAM
static String	OPTIONAL_CHROM_COLUMN
static String	OPTIONAL_CHROMEND_COLUMN
static String	OPTIONAL_CHROMSTART_COLUMN
static String	OPTIONAL_DECOY_COLUMN
static String	OPTIONAL_ID_COLUMN
static String	OPTIONAL_PREDICTION_COLUMN
static String	OPTIONAL_PROTEIN_NAME_COLUMN
static String	OPTIONAL_PSM_FDRSCORE_COLUMN
static String	OPTIONAL_RANK_COLUMN
static String	OPTIONAL_SEQUENCE_COLUMN
static String	OPTIONAL_STRAND_COLUMN

Constructor Summary

Constructors

Constructor and Description
MzTabUtils()

Method Summary

Methods

Modifier and Type	Method and Description
static void	addOptionalColumnValue(uk.ac.ebi.pride.jmztab.model.MZTabRecord record, uk.ac.ebi.pride.jmztab.model.MZTabColumnFactory columnFactory, String name, String value)
static uk.ac.ebi.pride.jmztab.model.CVParam	convertCvParamToCVParam(CvParam cvParam) This function takes the value of a CVParam and retrieve the corresponding CVParam
static uk.ac.ebi.pride.jmztab.model.CVParam	convertCvParamToCVParam(CvParam cvParam, Double mass) This function takes the value of a CVParam and retrieve the corresponding CVParam
static List<CvParam>	convertParamToCvParam(List<uk.ac.ebi.pride.jmztab.model.Param> params)
static CvParam	convertParamToCvParam(uk.ac.ebi.pride.jmztab.model.Param param)
static List<UserParam>	convertStringListToUserParam(List<String> settingList)
static UserParam	convertStringToUserParam(String value)
static uk.ac.ebi.pride.jmztab.model.CVParam	convertUserParamToCVParam(UserParam param) This function takes the value of a UserParam and returns a corresponding CVParam
static String	getOriginalSpectrumId(SpectraData spectraData, String spectrumID)
static List<uk.ac.ebi.pride.jmztab.utils.convert.SearchEngineScoreParam>	getSearchEngineScoreTerm(Score score) Get the Search Engines Scores for a Proteins or Peptide
static Constants.SpecFileFormat	getSpectraDataFormat(SpectraData spectraData)
static Constants.SpecIdFormat	getSpectraDataIdFormat(SpectraData spectraData)
static String	getSpectrumId(SpectraData spectraData, String spectrumID)
static CvParam	parseQuantitationReagentCvParam(uk.ac.ebi.pride.jmztab.model.Param quantificationReagent) Param for the reagent to retrieve the PRIDE Term for that, is important that most of the fields can be null, for that reason we look through all the the information looking for patterns.
static String	removeNewLineAndTab(String value) If there exists reserved characters in value, remove them all.

Methods inherited from class java.lang.Object

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

Field Detail

OPTIONAL_ID_COLUMN

public static final String OPTIONAL_ID_COLUMN

See Also:

Constant Field Values

OPTIONAL_SEQUENCE_COLUMN

public static final String OPTIONAL_SEQUENCE_COLUMN

See Also:

Constant Field Values

OPTIONAL_DECOY_COLUMN

public static final String OPTIONAL_DECOY_COLUMN

See Also:

Constant Field Values

OPTIONAL_RANK_COLUMN

public static final String OPTIONAL_RANK_COLUMN

See Also:

Constant Field Values

OPTIONAL_PREDICTION_COLUMN

public static final String OPTIONAL_PREDICTION_COLUMN

See Also:

Constant Field Values

OPTIONAL_CHROM_COLUMN

public static final String OPTIONAL_CHROM_COLUMN

See Also:

Constant Field Values

OPTIONAL_CHROMSTART_COLUMN

public static final String OPTIONAL_CHROMSTART_COLUMN

See Also:

Constant Field Values

OPTIONAL_CHROMEND_COLUMN

public static final String OPTIONAL_CHROMEND_COLUMN

See Also:

Constant Field Values

OPTIONAL_STRAND_COLUMN

public static final String OPTIONAL_STRAND_COLUMN

See Also:

Constant Field Values

OPTIONAL_PROTEIN_NAME_COLUMN

public static final String OPTIONAL_PROTEIN_NAME_COLUMN

See Also:

Constant Field Values

OPTIONAL_PSM_FDRSCORE_COLUMN

public static final String OPTIONAL_PSM_FDRSCORE_COLUMN

See Also:

Constant Field Values

CUSTOM_CHROM_INF_PARAM

public static final String CUSTOM_CHROM_INF_PARAM

See Also:

Constant Field Values

Constructor Detail

MzTabUtils

public MzTabUtils()

Method Detail

convertCvParamToCVParam

public static uk.ac.ebi.pride.jmztab.model.CVParam convertCvParamToCVParam(CvParam cvParam)

This function takes the value of a CVParam and retrieve the corresponding CVParam

Parameters:

cvParam - A CvParam

Returns:

CVParam for mzTab

convertCvParamToCVParam

public static uk.ac.ebi.pride.jmztab.model.CVParam convertCvParamToCVParam(CvParam cvParam,
                                                           Double mass)

This function takes the value of a CVParam and retrieve the corresponding CVParam

Parameters:

cvParam - A CvParam

Returns:

CVParam for mzTab

convertParamToCvParam

public static List<CvParam> convertParamToCvParam(List<uk.ac.ebi.pride.jmztab.model.Param> params)

convertStringListToUserParam

public static List<UserParam> convertStringListToUserParam(List<String> settingList)

convertStringToUserParam

public static UserParam convertStringToUserParam(String value)

convertUserParamToCVParam

public static uk.ac.ebi.pride.jmztab.model.CVParam convertUserParamToCVParam(UserParam param)

This function takes the value of a UserParam and returns a corresponding CVParam

Parameters:

param - User Param

Returns:

Return a CVParam

getSearchEngineScoreTerm

public static List<uk.ac.ebi.pride.jmztab.utils.convert.SearchEngineScoreParam> getSearchEngineScoreTerm(Score score)

Get the Search Engines Scores for a Proteins or Peptide

Returns:

List of SearchEngine Score params

addOptionalColumnValue

public static void addOptionalColumnValue(uk.ac.ebi.pride.jmztab.model.MZTabRecord record,
                          uk.ac.ebi.pride.jmztab.model.MZTabColumnFactory columnFactory,
                          String name,
                          String value)

getSpectraDataIdFormat

public static Constants.SpecIdFormat getSpectraDataIdFormat(SpectraData spectraData)

getSpectraDataFormat

public static Constants.SpecFileFormat getSpectraDataFormat(SpectraData spectraData)

getSpectrumId

public static String getSpectrumId(SpectraData spectraData,
                   String spectrumID)

getOriginalSpectrumId

public static String getOriginalSpectrumId(SpectraData spectraData,
                           String spectrumID)

convertParamToCvParam

public static CvParam convertParamToCvParam(uk.ac.ebi.pride.jmztab.model.Param param)

parseQuantitationReagentCvParam

public static CvParam parseQuantitationReagentCvParam(uk.ac.ebi.pride.jmztab.model.Param quantificationReagent)

Param for the reagent to retrieve the PRIDE Term for that, is important that most of the fields can be null, for that reason we look through all the the information looking for patterns. Todo: Looks for an option to properly the information for quantitation.

Parameters:

quantificationReagent - The quantitative Reagent Param

Returns:

Return a CVParam for the mzTab Quant Parameter

removeNewLineAndTab

public static String removeNewLineAndTab(String value)

If there exists reserved characters in value, remove them all.

Parameters:

value - The Value of the MzTab Term

Returns:

Return a value without tab