Package eu.isas.peptideshaker.utils

Class PsdbParent

java.lang.Object
eu.isas.peptideshaker.preferences.UserPreferencesParent
eu.isas.peptideshaker.utils.PsdbParent
All Implemented Interfaces:
AutoCloseable
Direct Known Subclasses:
FollowUpCLI, MzidCLI, PeptideShakerCLI, ReportCLI
public class PsdbParent extends UserPreferencesParent implements AutoCloseable
Implementing this abstract class allows interacting with a psdb files.
Author:
Marc Vaudel, Harald Barsnes

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    protected File
    dbFolder
    The folder where the database is stored.
    protected DisplayParameters
    displayParameters
    The display parameters.
    protected com.compomics.util.gui.filtering.FilterParameters
    filterParameters
    The filter parameters.
    protected com.compomics.util.experiment.biology.genes.GeneMaps
    geneMaps
    The gene maps.
    protected com.compomics.util.experiment.identification.Identification
    identification
    The identification.
    protected com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
    identificationFeaturesGenerator
    The identification features generator.
    protected com.compomics.util.parameters.identification.IdentificationParameters
    identificationParameters
    The identification parameters.
    protected com.compomics.util.experiment.identification.peptide_shaker.Metrics
    metrics
    The metrics stored during processing.
    protected com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
    msFileHandler
    The mass spectrometry file handler.
    protected ProjectDetails
    projectDetails
    The project details.
    com.compomics.util.experiment.ProjectParameters
    projectParameters
    All parameters of a project.
    protected com.compomics.util.parameters.peptide_shaker.ProjectType
    projectType
    The project type.
    protected com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider
    proteinDetailsProvider
    The protein details provider.
    protected File
    psdbFile
    The currently loaded psdb file.
    protected com.compomics.util.experiment.io.biology.protein.SequenceProvider
    sequenceProvider
    The sequence provider.
    protected com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
    spectrumCountingParameters
    The spectrum counting preferences.

    Fields inherited from class eu.isas.peptideshaker.preferences.UserPreferencesParent

    userPreferences

  • Constructor Summary

    Constructors
    Constructor
    Description
    PsdbParent()
    Empty constructor for instantiation purposes.
    PsdbParent​(File dbFolder)
    Constructor.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    close()
     
    File
    getDbFolder()
    Returns the folder where the database is stored.
    DisplayParameters
    getDisplayParameters()
    Returns the display preferences.
    String
    getExtendedProjectReport​(String waitingHandlerReport)
    Returns an extended HTML project report.
    com.compomics.util.gui.filtering.FilterParameters
    getFilterParameters()
    Returns the filter preferences.
    com.compomics.util.experiment.biology.genes.GeneMaps
    getGeneMaps()
    Returns the gene maps.
    com.compomics.util.experiment.identification.Identification
    getIdentification()
    Returns the identification object.
    com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator
    getIdentificationFeaturesGenerator()
    Returns the identification features generator object.
    com.compomics.util.parameters.identification.IdentificationParameters
    getIdentificationParameters()
    Returns the identification parameters.
    com.compomics.util.experiment.identification.peptide_shaker.Metrics
    getMetrics()
    Returns the metrics object.
    ProjectDetails
    getProjectDetails()
    Returns the project details.
    com.compomics.util.experiment.ProjectParameters
    getProjectParameters()
    Returns the project parameters.
    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.
    File
    getPsdbFile()
    Returns the psdb file.
    boolean
    getPsdbImportFromZip()
    Returns the psdb import from zip.
    com.compomics.util.experiment.io.biology.protein.SequenceProvider
    getSequenceProvider()
    Returns the sequence provider.
    com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
    getSpectrumCountingParameters()
    Returns the spectrum counting preferences.
    com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
    getSpectrumProvider()
    Returns the spectrum provider.
    UserParameters
    getUserParameters()
    Returns the user preferences.
    com.compomics.util.experiment.io.biology.protein.FastaSummary
    loadFastaFile​(com.compomics.util.waiting.WaitingHandler waitingHandler)
    Loads the FASTA file.
    void
    loadPsdbFile​(File dbFolder, com.compomics.util.waiting.WaitingHandler waitingHandler, boolean openFromZip)
    Loads the information from a psdb file.
    void
    loadPsdbFromZipFile​(File zipFile, File dbFolder, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Loads the information from a psdb file.
    void
    loadSpectrumFile​(File spectrumFile, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Adds a spectrum file to the spectrum provider.
    boolean
    loadSpectrumFile​(String spectrumFileName, ArrayList<File> spectrumFiles, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Loads the spectrum file.
    boolean
    loadSpectrumFiles​(com.compomics.util.waiting.WaitingHandler waitingHandler)
    Loads the spectra in the spectrum factory.
    boolean
    loadSpectrumFiles​(File folder, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Loads the spectrum files.
    void
    resetIdentificationFeaturesGenerator()
    Resets the feature generator.
    void
    saveProject​(com.compomics.util.waiting.WaitingHandler waitingHandler, boolean emptyCache)
    Saves the project in the psdb file.
    void
    setDbFolder​(File dbFolder)
    Sets the folder where the database is stored.
    void
    setDefaultParameters()
    Sets the default preferences.
    void
    setDisplayParameters​(DisplayParameters displayPreferences)
    Sets the display preferences.
    void
    setFilterParameters​(com.compomics.util.gui.filtering.FilterParameters filterPreferences)
    Sets the filter preferences.
    void
    setGeneMaps​(com.compomics.util.experiment.biology.genes.GeneMaps geneMaps)
    Sets the gene maps.
    void
    setIdentification​(com.compomics.util.experiment.identification.Identification identification)
    Sets the identification object.
    void
    setIdentificationFeaturesGenerator​(com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator)
    Sets the identification feature generator.
    void
    setIdentificationParameters​(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters)
    Sets new identification parameters.
    void
    setMetrics​(com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics)
    Sets the metrics.
    void
    setMsFileHandler​(com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler msFileHandler)
    Sets the mass spectrometry file handler.
    void
    setProject​(com.compomics.util.experiment.ProjectParameters projectParameters)
    Sets the project parameters.
    void
    setProjectDetails​(ProjectDetails projectDetails)
    Sets the project details.
    void
    setProjectType​(com.compomics.util.parameters.peptide_shaker.ProjectType projectType)
    Sets the project type.
    void
    setProteinDetailsProvider​(com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider)
    Sets the protein details provider.
    void
    setPsdbFile​(File psdbFile)
    Sets the psdb file.
    void
    setPsdbImportFromZip​(boolean importFromZip)
    Sets that the psdb file is imported from a zip file.
    void
    setSequenceProvider​(com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider)
    Sets the sequence provider.
    void
    setSpectrumCountingParameters​(com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences)
    Sets the spectrum counting preferences.

    Methods inherited from class eu.isas.peptideshaker.preferences.UserPreferencesParent

    loadUserParameters, saveUserParameters

    Methods inherited from class java.lang.Object

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

  • Field Details

    • identification

      protected com.compomics.util.experiment.identification.Identification identification
      The identification.

    • identificationFeaturesGenerator

      protected com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator
      The identification features generator.

    • identificationParameters

      protected com.compomics.util.parameters.identification.IdentificationParameters identificationParameters
      The identification parameters.

    • spectrumCountingParameters

      protected com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingParameters
      The spectrum counting preferences.

    • projectDetails

      protected ProjectDetails projectDetails
      The project details.

    • metrics

      protected com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics
      The metrics stored during processing.

    • sequenceProvider

      protected com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider
      The sequence provider.

    • proteinDetailsProvider

      protected com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider
      The protein details provider.

    • msFileHandler

      protected com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler msFileHandler
      The mass spectrometry file handler.

    • geneMaps

      protected com.compomics.util.experiment.biology.genes.GeneMaps geneMaps
      The gene maps.

    • filterParameters

      protected com.compomics.util.gui.filtering.FilterParameters filterParameters
      The filter parameters.

    • displayParameters

      protected DisplayParameters displayParameters
      The display parameters.

    • dbFolder

      protected File dbFolder
      The folder where the database is stored.

    • psdbFile

      protected File psdbFile
      The currently loaded psdb file.

    • projectParameters

      public com.compomics.util.experiment.ProjectParameters projectParameters
      All parameters of a project.

    • projectType

      protected com.compomics.util.parameters.peptide_shaker.ProjectType projectType
      The project type.

  • Constructor Details

    • PsdbParent

      public PsdbParent()
      Empty constructor for instantiation purposes.

    • PsdbParent

      public PsdbParent​(File dbFolder)
      Constructor.
      Parameters:
      dbFolder - the folder where the database is stored.

  • Method Details

    • loadPsdbFromZipFile

      public void loadPsdbFromZipFile​(File zipFile, File dbFolder, com.compomics.util.waiting.WaitingHandler waitingHandler) throws IOException
      Loads the information from a psdb file.
      Parameters:
      zipFile - the zip file containing the psdb file
      dbFolder - the folder where to extract the project
      waitingHandler - a waiting handler displaying feedback to the user. Ignored if null
      Throws:
      IOException - thrown if an error occurred while reading the file

    • loadPsdbFile

      public void loadPsdbFile​(File dbFolder, com.compomics.util.waiting.WaitingHandler waitingHandler, boolean openFromZip) throws IOException
      Loads the information from a psdb file.
      Parameters:
      dbFolder - the folder where to untar the project
      waitingHandler - a waiting handler displaying feedback to the user. Ignored if null
      openFromZip - flag determining if pdsb file was opened from a zip file
      Throws:
      IOException - thrown of IOException occurs exception thrown whenever an error occurred while reading or writing a file

    • saveProject

      public void saveProject​(com.compomics.util.waiting.WaitingHandler waitingHandler, boolean emptyCache) throws IOException
      Saves the project in the psdb file.
      Parameters:
      waitingHandler - waiting handler displaying feedback to the user. can be null.
      emptyCache - if true the cache will be emptied
      Throws:
      IOException - thrown of IOException occurs exception thrown whenever an error occurred while writing the file

    • loadSpectrumFiles

      public boolean loadSpectrumFiles​(com.compomics.util.waiting.WaitingHandler waitingHandler) throws IOException
      Loads the spectra in the spectrum factory.
      Parameters:
      waitingHandler - a waiting handler displaying progress to the user. Can be null.
      Returns:
      a boolean indicating whether the loading was successful
      Throws:
      IOException - thrown of IOException occurs exception thrown whenever an error occurred loading the spectrum files

    • loadSpectrumFiles

      public boolean loadSpectrumFiles​(File folder, com.compomics.util.waiting.WaitingHandler waitingHandler) throws IOException
      Loads the spectrum files.
      Parameters:
      folder - The folder to look into. Can be null.
      waitingHandler - The waiting handler displaying progress to the user. Can be null.
      Returns:
      a boolean indicating whether the loading was successful
      Throws:
      IOException - Exception thrown whenever an error occurred while reading or writing a file.

    • loadSpectrumFile

      public boolean loadSpectrumFile​(String spectrumFileName, ArrayList<File> spectrumFiles, com.compomics.util.waiting.WaitingHandler waitingHandler) throws IOException
      Loads the spectrum file.
      Parameters:
      spectrumFileName - The name of the spectrum file.
      spectrumFiles - The list to add the detected spectrum files to.
      waitingHandler - The waiting handler displaying progress to the user. Can be null.
      Returns:
      A boolean indicating whether the loading was successful.
      Throws:
      IOException - Exception thrown whenever an error occurred while reading or writing a file

    • loadSpectrumFile

      public void loadSpectrumFile​(File spectrumFile, com.compomics.util.waiting.WaitingHandler waitingHandler) throws IOException
      Adds a spectrum file to the spectrum provider.
      Parameters:
      spectrumFile - The spectrum file to add.
      waitingHandler - The waiting handler.
      Throws:
      IOException - Exception thrown whenever an error occurred while reading or writing a file

    • loadFastaFile

      public com.compomics.util.experiment.io.biology.protein.FastaSummary loadFastaFile​(com.compomics.util.waiting.WaitingHandler waitingHandler) throws IOException
      Loads the FASTA file.
      Parameters:
      waitingHandler - a waiting handler displaying progress to the user. Can be null
      Returns:
      the FASTA summary
      Throws:
      IOException - exception thrown if an error occurred while reading or writing the file

    • getIdentification

      public com.compomics.util.experiment.identification.Identification getIdentification()
      Returns the identification object.
      Returns:
      the identification object

    • getIdentificationFeaturesGenerator

      public com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator getIdentificationFeaturesGenerator()
      Returns the identification features generator object.
      Returns:
      the identification features generator object

    • getSpectrumCountingParameters

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

    • getProjectDetails

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

    • getMetrics

      public com.compomics.util.experiment.identification.peptide_shaker.Metrics getMetrics()
      Returns the metrics object.
      Returns:
      the metrics object

    • getGeneMaps

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

    • getFilterParameters

      public com.compomics.util.gui.filtering.FilterParameters getFilterParameters()
      Returns the filter preferences.
      Returns:
      the filter preferences

    • getDisplayParameters

      public DisplayParameters getDisplayParameters()
      Returns the display preferences.
      Returns:
      the display preferences

    • getPsdbFile

      public File getPsdbFile()
      Returns the psdb file.
      Returns:
      the psdb file

    • getPsdbImportFromZip

      public boolean getPsdbImportFromZip()
      Returns the psdb import from zip.
      Returns:
      the psdb import from zip

    • setIdentificationFeaturesGenerator

      public void setIdentificationFeaturesGenerator​(com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator)
      Sets the identification feature generator.
      Parameters:
      identificationFeaturesGenerator - the identification feature generator

    • setSpectrumCountingParameters

      public void setSpectrumCountingParameters​(com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences)
      Sets the spectrum counting preferences.
      Parameters:
      spectrumCountingPreferences - the spectrum counting preferences

    • setProjectDetails

      public void setProjectDetails​(ProjectDetails projectDetails)
      Sets the project details.
      Parameters:
      projectDetails - the project details

    • setMetrics

      public void setMetrics​(com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics)
      Sets the metrics.
      Parameters:
      metrics - the metrics

    • setGeneMaps

      public void setGeneMaps​(com.compomics.util.experiment.biology.genes.GeneMaps geneMaps)
      Sets the gene maps.
      Parameters:
      geneMaps - the gene maps

    • getProjectParameters

      public com.compomics.util.experiment.ProjectParameters getProjectParameters()
      Returns the project parameters.
      Returns:
      the project parameters

    • setProject

      public void setProject​(com.compomics.util.experiment.ProjectParameters projectParameters)
      Sets the project parameters.
      Parameters:
      projectParameters - the project parameters

    • setFilterParameters

      public void setFilterParameters​(com.compomics.util.gui.filtering.FilterParameters filterPreferences)
      Sets the filter preferences.
      Parameters:
      filterPreferences - the filter preferences

    • setDisplayParameters

      public void setDisplayParameters​(DisplayParameters displayPreferences)
      Sets the display preferences.
      Parameters:
      displayPreferences - the display preferences

    • setPsdbFile

      public void setPsdbFile​(File psdbFile)
      Sets the psdb file.
      Parameters:
      psdbFile - the psdb file

    • setPsdbImportFromZip

      public void setPsdbImportFromZip​(boolean importFromZip)
      Sets that the psdb file is imported from a zip file.
      Parameters:
      importFromZip - if the psdb was extracted from a zip file

    • getUserParameters

      public UserParameters getUserParameters()
      Returns the user preferences.
      Returns:
      the user preferences

    • setIdentification

      public void setIdentification​(com.compomics.util.experiment.identification.Identification identification)
      Sets the identification object.
      Parameters:
      identification - the identification object

    • setDefaultParameters

      public void setDefaultParameters()
      Sets the default preferences.

    • resetIdentificationFeaturesGenerator

      public void resetIdentificationFeaturesGenerator()
      Resets the feature generator.

    • getIdentificationParameters

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

    • setIdentificationParameters

      public void setIdentificationParameters​(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters)
      Sets new identification parameters.
      Parameters:
      identificationParameters - the new identification parameters

    • getDbFolder

      public File getDbFolder()
      Returns the folder where the database is stored.
      Returns:
      the folder where the database is stored

    • setDbFolder

      public void setDbFolder​(File dbFolder)
      Sets the folder where the database is stored.
      Parameters:
      dbFolder - the folder where the database is stored

    • getSequenceProvider

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

    • getSpectrumProvider

      public com.compomics.util.experiment.mass_spectrometry.SpectrumProvider getSpectrumProvider()
      Returns the spectrum provider.
      Returns:
      the spectrum provider

    • setMsFileHandler

      public void setMsFileHandler​(com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler msFileHandler)
      Sets the mass spectrometry file handler.
      Parameters:
      msFileHandler - The mass spectrometry file handler.

    • setSequenceProvider

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

    • getProteinDetailsProvider

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

    • setProteinDetailsProvider

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

    • getProjectType

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

    • setProjectType

      public void setProjectType​(com.compomics.util.parameters.peptide_shaker.ProjectType projectType)
      Sets the project type.
      Parameters:
      projectType - the project type

    • getExtendedProjectReport

      public String getExtendedProjectReport​(String waitingHandlerReport)
      Returns an extended HTML project report.
      Parameters:
      waitingHandlerReport - the progress report, if null the report from the project details will be used
      Returns:
      an extended HTML project report

    • close

      public void close()
      Specified by:
      close in interface AutoCloseable