Package eu.isas.peptideshaker.parameters

Class PeptideShakerParameters

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
eu.isas.peptideshaker.parameters.PeptideShakerParameters
All Implemented Interfaces:
com.compomics.util.experiment.personalization.UrParameter, Serializable
public class PeptideShakerParameters extends com.compomics.util.experiment.personalization.ExperimentObject implements com.compomics.util.experiment.personalization.UrParameter
This class stores parameters for a PeptideShaker project.
Author:
Marc Vaudel, Harald Barsnes
See Also:

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final long
    KEY
    The key of the object when stored in settings table of a psdb file.

    Fields inherited from class com.compomics.util.experiment.personalization.ExperimentObject

    NO_KEY

  • Constructor Summary

    Constructors
    Constructor
    Description
    PeptideShakerParameters()
    Empty default constructor.
    PeptideShakerParameters(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences, ProjectDetails projectDetails, com.compomics.util.gui.filtering.FilterParameters filterPreferences, DisplayParameters displayPreferences, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.parameters.peptide_shaker.ProjectType projectType, com.compomics.util.experiment.identification.features.IdentificationFeaturesCache identificationFeaturesCache)
    Constructor for a PeptideShaker Settings class.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    cleanProviders()
    Cleans the SequenceProvider and ProteinDetailsProvider, please use only temporary or if you know what you do
    DisplayParameters
    getDisplayParameters()
    Returns the GUI display parameters.
    com.compomics.util.gui.filtering.FilterParameters
    getFilterParameters()
    Returns the GUI display parameters.
    com.compomics.util.experiment.biology.genes.GeneMaps
    getGeneMaps()
    Returns the gene maps.
    com.compomics.util.experiment.identification.features.IdentificationFeaturesCache
    getIdentificationFeaturesCache()
    Returns the identification features cache used by the identification features generator before saving the file.
    com.compomics.util.parameters.identification.IdentificationParameters
    getIdentificationParameters()
    Returns the identification parameters.
    com.compomics.util.experiment.identification.peptide_shaker.Metrics
    getMetrics()
    Returns the metrics saved when loading the files.
    long
    getParameterKey()
     
    ProjectDetails
    getProjectDetails()
    Returns the project details.
    com.compomics.util.parameters.peptide_shaker.ProjectType
    getProjectType()
    Returns the project type.
    com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider
    getProteinDetailsProvider()
    Returns the protein details provider.
    com.compomics.util.experiment.io.biology.protein.SequenceProvider
    getSequenceProvider()
    Returns the sequence provider saved when loading the files.
    com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
    getSpectrumCountingPreferences()
    Returns the spectrum counting preferences of the project.
    void
    setProteinDetailsProvider(com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider)
    Setter for the protein details provider
    void
    setSequenceProvider(com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider)
    Setter for the sequence provider

    Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject

    addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams

    Methods inherited from class java.lang.Object

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

  • Field Details

    • KEY

      public static final long KEY
      The key of the object when stored in settings table of a psdb file.

  • Constructor Details

    • PeptideShakerParameters

      public PeptideShakerParameters()
      Empty default constructor.

    • PeptideShakerParameters

      public PeptideShakerParameters(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences, ProjectDetails projectDetails, com.compomics.util.gui.filtering.FilterParameters filterPreferences, DisplayParameters displayPreferences, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.parameters.peptide_shaker.ProjectType projectType, com.compomics.util.experiment.identification.features.IdentificationFeaturesCache identificationFeaturesCache)
      Constructor for a PeptideShaker Settings class.
      Parameters:
      identificationParameters - the parameters used for identification
      spectrumCountingPreferences - the spectrum counting preferences
      projectDetails - the project details
      filterPreferences - the filter preferences
      displayPreferences - the display preferences
      metrics - the metrics saved when loading the files
      sequenceProvider - the sequence provider
      proteinDetailsProvider - the protein details provider
      geneMaps - the gene maps
      projectType - the project type
      identificationFeaturesCache - the identification features cache

  • Method Details

    • getIdentificationParameters

      public com.compomics.util.parameters.identification.IdentificationParameters getIdentificationParameters()
      Returns the identification parameters.
      Returns:
      the identification parameters

    • getSpectrumCountingPreferences

      public com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters getSpectrumCountingPreferences()
      Returns the spectrum counting preferences of the project.
      Returns:
      the spectrum counting preferences of the project

    • getProjectDetails

      public ProjectDetails getProjectDetails()
      Returns the project details.
      Returns:
      the project details

    • getFilterParameters

      public com.compomics.util.gui.filtering.FilterParameters getFilterParameters()
      Returns the GUI display parameters.
      Returns:
      the GUI display parameters

    • getDisplayParameters

      public DisplayParameters getDisplayParameters()
      Returns the GUI display parameters.
      Returns:
      the GUI display parameters

    • getMetrics

      public com.compomics.util.experiment.identification.peptide_shaker.Metrics getMetrics()
      Returns the metrics saved when loading the files.
      Returns:
      the metrics saved when loading the files

    • getSequenceProvider

      public com.compomics.util.experiment.io.biology.protein.SequenceProvider getSequenceProvider()
      Returns the sequence provider saved when loading the files.
      Returns:
      the sequence provider saved when loading the files

    • getProteinDetailsProvider

      public com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider getProteinDetailsProvider()
      Returns the protein details provider.
      Returns:
      the protein details provider

    • getGeneMaps

      public com.compomics.util.experiment.biology.genes.GeneMaps getGeneMaps()
      Returns the gene maps.
      Returns:
      the gene maps

    • getIdentificationFeaturesCache

      public com.compomics.util.experiment.identification.features.IdentificationFeaturesCache getIdentificationFeaturesCache()
      Returns the identification features cache used by the identification features generator before saving the file.
      Returns:
      the identification features cache

    • getParameterKey

      public long getParameterKey()
      Specified by:
      getParameterKey in interface com.compomics.util.experiment.personalization.UrParameter

    • getProjectType

      public com.compomics.util.parameters.peptide_shaker.ProjectType getProjectType()
      Returns the project type.
      Returns:
      the project type

    • cleanProviders

      public void cleanProviders()
      Cleans the SequenceProvider and ProteinDetailsProvider, please use only temporary or if you know what you do

    • setSequenceProvider

      public void setSequenceProvider(com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider)
      Setter for the sequence provider
      Parameters:
      sequenceProvider - the sequence provider instance

    • setProteinDetailsProvider

      public void setProteinDetailsProvider(com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider)
      Setter for the protein details provider
      Parameters:
      proteinDetailsProvider - the protein details provider instance