Package eu.isas.reporter.io

Class ProjectImporter

java.lang.Object
eu.isas.reporter.io.ProjectImporter
public class ProjectImporter extends Object
Imports a project from a psdb file.
Author:
Marc Vaudel, Harald Barsnes

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final double
    DEFAULT_REPORTER_ION_TOLERANCE_ITRAQ
    The default reporter ion tolerance for TMT data.
    static final double
    DEFAULT_REPORTER_ION_TOLERANCE_TMT
    The default reporter ion tolerance for TMT data.

  • Constructor Summary

    Constructors
    Constructor
    Description
    ProjectImporter()
    Constructor.
    ProjectImporter(Dialog owner)
    Constructor.

  • Method Summary

    Modifier and Type
    Method
    Description
    static ClusteringSettings
    getDefaultClusterMetrics(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.identification.Identification identification)
    Returns the cluster metrics for a given project.
    static com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
    getDefaultReporterIonQuantification(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters)
    Returns the default reporter ion quantification based on the identification parameters.
    static ReporterSettings
    getDefaultReporterSettings(com.compomics.util.experiment.quantification.reporterion.ReporterMethod reporterMethod, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters)
    Returns the default reporter settings as inferred from the identification parameters.
    static ReporterSettings
    getDefaultReporterSettings(com.compomics.util.experiment.quantification.reporterion.ReporterMethod reporterMethod, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, ReporterSettings reporterSettings)
    Returns the default reporter settings as inferred from the identification parameters.
    DisplayPreferences
    getDisplayPreferences()
    Returns the display preferences.
    com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
    getReporterIonQuantification()
    Returns the reporter ion quantification object loaded from the file.
    ReporterSettings
    getReporterSettings()
    Returns the reporter settings loaded from the file.
    com.compomics.util.experiment.mass_spectrometry.SpectrumProvider
    getSpectrumProvider()
    Returns the spectrum provider.
    void
    importPeptideShakerProject(eu.isas.peptideshaker.utils.PsdbParent psdbParent, ArrayList<File> mgfFiles, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Imports the identification results from a PeptideShaker file.
    void
    importReporterProject(eu.isas.peptideshaker.utils.PsdbParent psdbParent, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Loads the Reporter project.

    Methods inherited from class java.lang.Object

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

  • Field Details

    • DEFAULT_REPORTER_ION_TOLERANCE_TMT

      public static final double DEFAULT_REPORTER_ION_TOLERANCE_TMT
      The default reporter ion tolerance for TMT data.
      See Also:

    • DEFAULT_REPORTER_ION_TOLERANCE_ITRAQ

      public static final double DEFAULT_REPORTER_ION_TOLERANCE_ITRAQ
      The default reporter ion tolerance for TMT data.
      See Also:

  • Constructor Details

    • ProjectImporter

      public ProjectImporter(Dialog owner)
      Constructor.
      Parameters:
      owner - the dialog owner if operated from the GUI

    • ProjectImporter

      public ProjectImporter()
      Constructor.

  • Method Details

    • importPeptideShakerProject

      public void importPeptideShakerProject(eu.isas.peptideshaker.utils.PsdbParent psdbParent, ArrayList<File> mgfFiles, com.compomics.util.waiting.WaitingHandler waitingHandler) throws IOException, ClassNotFoundException, SQLException, InterruptedException, org.apache.commons.compress.archivers.ArchiveException
      Imports the identification results from a PeptideShaker file.
      Parameters:
      psdbParent - the psdb parent object where the psdb file is loaded
      mgfFiles - the arraylist to add the detected mgf files to
      waitingHandler - a waiting handler to display the progress to the user and allow interrupting the process
      Throws:
      IOException - thrown of IOException occurs exception thrown whenever an error occurred while reading or writing a file
      SQLException - thrown of SQLException occurs exception thrown whenever an error occurred while interacting with the database
      ClassNotFoundException - exception thrown whenever an error occurred while deserializing an object
      InterruptedException - exception thrown whenever a threading error occurred while saving the project
      org.apache.commons.compress.archivers.ArchiveException - exception thrown whenever an error occurs while untaring the file

    • importReporterProject

      public void importReporterProject(eu.isas.peptideshaker.utils.PsdbParent psdbParent, com.compomics.util.waiting.WaitingHandler waitingHandler) throws SQLException, IOException, ClassNotFoundException, InterruptedException
      Loads the Reporter project.
      Parameters:
      psdbParent - the psdb parent object where the psdb file is loaded
      waitingHandler - a waiting handler to display the progress to the user and allow interrupting the process
      Throws:
      SQLException - exception thrown whenever an error occurs while interacting with the database
      IOException - exception thrown whenever an error occurs while reading or writing a file
      ClassNotFoundException - exception thrown whenever an error occurred while deserializing a file from the database
      InterruptedException - exception thrown if a threading error occurs while interacting with the database

    • getDefaultReporterSettings

      public static ReporterSettings getDefaultReporterSettings(com.compomics.util.experiment.quantification.reporterion.ReporterMethod reporterMethod, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters)
      Returns the default reporter settings as inferred from the identification parameters.
      Parameters:
      reporterMethod - the quantification method selected
      identificationParameters - the identification parameters
      Returns:
      the default reporter settings

    • getDefaultReporterSettings

      public static ReporterSettings getDefaultReporterSettings(com.compomics.util.experiment.quantification.reporterion.ReporterMethod reporterMethod, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, ReporterSettings reporterSettings)
      Returns the default reporter settings as inferred from the identification parameters.
      Parameters:
      reporterMethod - the quantification method selected
      identificationParameters - the identification parameters
      reporterSettings - the reporter settings
      Returns:
      the default reporter settings

    • getDefaultReporterIonQuantification

      public static com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification getDefaultReporterIonQuantification(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters)
      Returns the default reporter ion quantification based on the identification parameters.
      Parameters:
      identificationParameters - the identification parameters
      Returns:
      the default reporter ion quantification

    • getDefaultClusterMetrics

      public static ClusteringSettings getDefaultClusterMetrics(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.identification.Identification identification)
      Returns the cluster metrics for a given project.
      Parameters:
      identificationParameters - the identification parameters
      identification - the identification
      Returns:
      the cluster metrics for a given project

    • getReporterSettings

      public ReporterSettings getReporterSettings()
      Returns the reporter settings loaded from the file.
      Returns:
      the reporter settings loaded from the file

    • getReporterIonQuantification

      public com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification getReporterIonQuantification()
      Returns the reporter ion quantification object loaded from the file.
      Returns:
      the reporter ion quantification object loaded from the file

    • getDisplayPreferences

      public DisplayPreferences getDisplayPreferences()
      Returns the display preferences.
      Returns:
      the display preferences

    • getSpectrumProvider

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