Package 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 Details

    • PeptideShakerMethods

      public PeptideShakerMethods()

  • Method Details

    • 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