eu.isas.peptideshaker.export

Class PeptideShakerMethods

java.lang.Object

eu.isas.peptideshaker.export.PeptideShakerMethods

public class PeptideShakerMethods
extends Object

This class generates the text needed to for the identification section of the methods section of a paper.

Author:

Harald Barsnes, Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
PeptideShakerMethods()

Method Summary

Modifier and Type	Method and Description
static String	getDatabaseText(com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters, com.compomics.util.experiment.io.biology.protein.FastaSummary fastaSummary) Returns the database usage details.
static String	getDecoyType() Returns the decoy sequences creation details.
static String	getGeneAnnotation() Returns the gene annotation method usage details.
static String	getIdentificationSettings(com.compomics.util.parameters.identification.search.SearchParameters searchParameters) Returns the identification settings details.
static String	getPeptideShaker() Returns the PeptideShaker usage details.
static String	getProteomeXchange() Returns the ProteomeXchange upload details.
static String	getPtmScoring(com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters ptmScoringPreferences) Returns the PTM scoring methods used.
static String	getSearchEnginesText(ProjectDetails projectDetails) Returns the search engines usage details.
static String	getSearchGUIText() Returns the SearchGUI usage details.
static String	getSpectrumCounting(com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences) Returns the spectrum counting method usage details.
static String	getValidation(com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters idMatchValidationPreferences) Returns the validation thresholds used.

Methods inherited from class java.lang.Object

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

Constructor Detail

PeptideShakerMethods

public PeptideShakerMethods()

Method Detail

getSearchEnginesText

public static String getSearchEnginesText(ProjectDetails projectDetails)

Returns the search engines usage details.

Parameters:

projectDetails - the PeptideShaker project details

Returns:

the search engines usage details

getSearchGUIText

public static String getSearchGUIText()

Returns the SearchGUI usage details.

Returns:

the SearchGUI usage details

getDatabaseText

public static String getDatabaseText(com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters,
                                     com.compomics.util.experiment.io.biology.protein.FastaSummary fastaSummary)

Returns the database usage details.

Parameters:

fastaParameters - the FASTA parameters

fastaSummary - the FASTA summary

Returns:

the database usage details

getDecoyType

public static String getDecoyType()

Returns the decoy sequences creation details.

Returns:

the decoy sequences creation details

getIdentificationSettings

public static String getIdentificationSettings(com.compomics.util.parameters.identification.search.SearchParameters searchParameters)

Returns the identification settings details.

Parameters:

searchParameters - the search parameters

Returns:

the identification settings details

getPeptideShaker

public static String getPeptideShaker()

Returns the PeptideShaker usage details.

Returns:

the PeptideShaker usage details

getValidation

public static String getValidation(com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters idMatchValidationPreferences)

Returns the validation thresholds used.

Parameters:

idMatchValidationPreferences - the match validation preferences

Returns:

the validation thresholds used

getPtmScoring

public static String getPtmScoring(com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters ptmScoringPreferences)

Returns the PTM scoring methods used.

Parameters:

ptmScoringPreferences - the PTM localization scoring preferences

Returns:

the PTM scoring methods used

getGeneAnnotation

public static String getGeneAnnotation()

Returns the gene annotation method usage details.

Returns:

the gene annotation method usage details

getSpectrumCounting

public static String getSpectrumCounting(com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences)

Returns the spectrum counting method usage details.

Parameters:

spectrumCountingPreferences - the spectrum counting preferences used

Returns:

the spectrum counting method usage details

getProteomeXchange

public static String getProteomeXchange()

Returns the ProteomeXchange upload details.

Returns:

the ProteomeXchange upload details