Package com.compomics.util.parameters.identification

Class IdentificationParameters

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.IdentificationParameters
All Implemented Interfaces:
MarshallableParameter, Serializable
public class IdentificationParameters extends ExperimentObject implements MarshallableParameter
Generic class grouping the parameters used for protein identification.
Author:
Marc Vaudel, Harald Barsnes
See Also:

  • Field Details

  • Constructor Details

    • IdentificationParameters

      public IdentificationParameters()
      Creates empty identification parameters.

    • IdentificationParameters

      public IdentificationParameters(SearchParameters searchParameters)
      Creates default identification parameters from the given search parameters.
      Parameters:
      searchParameters - the search parameters

    • IdentificationParameters

      public IdentificationParameters(String name, String description, SearchParameters searchParameters, AnnotationParameters annotationParameters, SequenceMatchingParameters sequenceMatchingParameters, PeptideVariantsParameters peptideVariantsParameters, GeneParameters geneParameters, PsmScoringParameters psmScoringParameters, PeptideAssumptionFilter peptideAssumptionFilter, ModificationLocalizationParameters ModificationLocalizationParameters, ProteinInferenceParameters proteinInferenceParameters, IdMatchValidationParameters idValidationParameters, FractionParameters fractionParameters, FastaParameters fastaParameters)
      Constructor.
      Parameters:
      name - the name of the parameters
      description - the description
      searchParameters - the search parameters
      annotationParameters - the annotation parameters
      sequenceMatchingParameters - the sequence matching parameters
      peptideVariantsParameters - the peptide variant parameters
      geneParameters - the gene parameters
      psmScoringParameters - the PSM scoring parameters
      peptideAssumptionFilter - the peptide assumption filters
      ModificationLocalizationParameters - the PTM localization scoring parameters
      proteinInferenceParameters - the protein inference parameters
      idValidationParameters - the matches validation parameters
      fractionParameters - the fraction parameters
      fastaParameters - the FASTA parameters

  • Method Details

    • getSearchParameters

      public SearchParameters getSearchParameters()
      Returns the parameters used for the spectrum matching.
      Returns:
      the parameters used for the spectrum matching

    • setSearchParameters

      public void setSearchParameters(SearchParameters searchParameters)
      Sets the parameters used for the spectrum matching.
      Parameters:
      searchParameters - the parameters used for the spectrum matching

    • getPpmTolerance

      public static double getPpmTolerance(double daltonTolerance, double refMass)
      Returns the relative tolerance in ppm corresponding to the absolute tolerance in Dalton at the given reference mass.
      Parameters:
      daltonTolerance - the absolute tolerance in Dalton
      refMass - the reference mass in Dalton
      Returns:
      the relative tolerance in ppm

    • getDaTolerance

      public static double getDaTolerance(double ppmTolerance, double refMass)
      Returns the absolute tolerance in Dalton corresponding to the relative tolerance in ppm at the given reference mass.
      Parameters:
      ppmTolerance - the absolute tolerance in ppm
      refMass - the reference mass in Dalton
      Returns:
      the relative tolerance in ppm

    • getAnnotationParameters

      public AnnotationParameters getAnnotationParameters()
      Returns the annotation parameters used for identification.
      Returns:
      the annotation parameters used for identification

    • setAnnotationParameters

      public void setAnnotationParameters(AnnotationParameters annotationParameters)
      Sets the annotation parameters used for identification.
      Parameters:
      annotationParameters - the annotation parameters used for identification

    • getPeptideAssumptionFilter

      public PeptideAssumptionFilter getPeptideAssumptionFilter()
      Returns the filter used when importing PSMs.
      Returns:
      the filter used when importing PSMs

    • setPeptideAssumptionFilter

      public void setPeptideAssumptionFilter(PeptideAssumptionFilter peptideAssumptionFilter)
      Sets the filter used when importing PSMs.
      Parameters:
      peptideAssumptionFilter - the filter used when importing PSMs

    • getPsmScoringParameters

      public PsmScoringParameters getPsmScoringParameters()
      Returns the scoring parameters used when scoring PSMs.
      Returns:
      the scoring parameters used when scoring PSMs

    • setPsmScoringParameters

      public void setPsmScoringParameters(PsmScoringParameters psmScoringParameters)
      Sets the scoring preferences used when scoring PSMs.
      Parameters:
      psmScoringParameters - the scoring preferences used when scoring PSMs

    • getModificationLocalizationParameters

      public ModificationLocalizationParameters getModificationLocalizationParameters()
      Returns the modification localization scoring parameters.
      Returns:
      the modification localization scoring parameters

    • setModificationLocalizationParameters

      public void setModificationLocalizationParameters(ModificationLocalizationParameters modificationLocalizationParameters)
      Sets the modification localization parameters.
      Parameters:
      modificationLocalizationParameters - the modification localization parameters

    • getSequenceMatchingParameters

      public SequenceMatchingParameters getSequenceMatchingParameters()
      Returns the sequence matching parameters.
      Returns:
      the sequence matching parameters

    • setSequenceMatchingParameters

      public void setSequenceMatchingParameters(SequenceMatchingParameters sequenceMatchingParameters)
      Sets the sequence matching preferences.
      Parameters:
      sequenceMatchingParameters - the sequence matching preferences

    • getPeptideVariantsParameters

      public PeptideVariantsParameters getPeptideVariantsParameters()
      Returns the peptide variant parameters.
      Returns:
      the peptide variant parameters

    • setPeptideVariantsParameters

      public void setPeptideVariantsParameters(PeptideVariantsParameters peptideVariantsParameters)
      Sets the peptide variant parameters.
      Parameters:
      peptideVariantsParameters - the peptide variant parameters

    • getIdValidationParameters

      public IdMatchValidationParameters getIdValidationParameters()
      Returns the identification matches validation parameters.
      Returns:
      the identification matches validation parameters

    • setIdValidationParameters

      public void setIdValidationParameters(IdMatchValidationParameters idValidationParameters)
      Sets the identification matches validation parameters.
      Parameters:
      idValidationParameters - the identification matches validation parameters

    • getProteinInferenceParameters

      public ProteinInferenceParameters getProteinInferenceParameters()
      Returns the protein inference parameters.
      Returns:
      the protein inference parameters

    • setProteinInferenceParameters

      public void setProteinInferenceParameters(ProteinInferenceParameters proteinInferenceParameters)
      Sets the protein inference parameters.
      Parameters:
      proteinInferenceParameters - the protein inference parameters

    • getGeneParameters

      public GeneParameters getGeneParameters()
      Returns the gene parameters.
      Returns:
      the gene parameters

    • setGeneParameters

      public void setGeneParameters(GeneParameters geneParameters)
      Sets the gene parameters.
      Parameters:
      geneParameters - the gene parameters

    • getFractionParameters

      public FractionParameters getFractionParameters()
      Returns the fraction parameters.
      Returns:
      the fraction parameters

    • setFractionParameters

      public void setFractionParameters(FractionParameters fractionParameters)
      Sets the fraction parameters.
      Parameters:
      fractionParameters - the fraction parameters

    • getFastaParameters

      public FastaParameters getFastaParameters()
      Returns the FASTA processing parameters.
      Returns:
      the FASTA processing parameters

    • setFastaParameters

      public void setFastaParameters(FastaParameters fastaParameters)
      Sets the ASTA processing parameters.
      Parameters:
      fastaParameters - the FASTA processing parameters

    • getIdentificationParameters

      public static IdentificationParameters getIdentificationParameters(File identificationParametersFile) throws IOException
      Loads the identification parameters from a file. If the given file is a search parameters file, default identification parameters are inferred.
      Parameters:
      identificationParametersFile - the file
      Returns:
      the parameters
      Throws:
      IOException - if an error occurs while reading the file

    • supportedVersion

      public static boolean supportedVersion(File identificationParametersFile) throws IOException
      Returns a boolean indicating whether the version of the parameters file is supported.
      Parameters:
      identificationParametersFile - the parameters file
      Returns:
      a boolean indicating whether the version of the parameters file is supported
      Throws:
      IOException - if an error occurs while reading the file

    • saveIdentificationParameters

      public static void saveIdentificationParameters(IdentificationParameters identificationParameters, File identificationParametersFile) throws IOException
      Saves the identification parameters to a file.
      Parameters:
      identificationParameters - the identification parameters
      identificationParametersFile - the file
      Throws:
      IOException - if an error occurred while writing the file

    • getName

      public String getName()
      Returns the name of the parameters.
      Returns:
      the name of the parameters

    • setName

      public void setName(String name)
      Sets the name of the parameters.
      Parameters:
      name - the name of the parameters

    • getDescription

      public String getDescription()
      Returns the description of the parameters.
      Returns:
      the description of the parameters

    • getDefaultDescription

      public boolean getDefaultDescription()
      Indicates whether the description is automatically generated.
      Returns:
      a boolean indicating whether the description is automatically generated

    • setDescription

      public void setDescription(String description, boolean automaticallyGenerated)
      Sets the description of the parameters.
      Parameters:
      description - the description of the parameters
      automaticallyGenerated - boolean indicating whether the description is automatically generated

    • setParametersFromSearch

      public void setParametersFromSearch(SearchParameters searchParameters)
      Sets identification parameters based on given search parameters.
      Parameters:
      searchParameters - the parameters used for the search

    • setType

      public void setType()
      Description copied from interface: MarshallableParameter
      Sets the parameters type. The type must be set before writing a file but not in the constructor.
      Specified by:
      setType in interface MarshallableParameter

    • getType

      public MarshallableParameter.Type getType()
      Description copied from interface: MarshallableParameter
      Returns the type of marshalled parameter from an unmarshalled object. The type must be written in the file but not set in the constructor. Null if not a MarshallableParameter.
      Specified by:
      getType in interface MarshallableParameter
      Returns:
      the type of marshalled parameter from an unmarshalled object

    • equals

      public boolean equals(IdentificationParameters otherIdentificationParameters)
      Returns true if the identification parameter objects have identical settings.
      Parameters:
      otherIdentificationParameters - the parameters to compare to
      Returns:
      true if the identification parameter objects have identical settings