Package eu.isas.reporter.settings

Class NormalizationSettings

java.lang.Object
eu.isas.reporter.settings.NormalizationSettings
All Implemented Interfaces:
Serializable
public class NormalizationSettings extends Object implements Serializable
Settings used for the normalization.
Author:
Marc Vaudel, Harald Barsnes
See Also:

  • Constructor Details

    • NormalizationSettings

      public NormalizationSettings()
      Constructor.

  • Method Details

    • clone

      public NormalizationSettings clone() throws CloneNotSupportedException
      Overrides:
      clone in class Object
      Throws:
      CloneNotSupportedException

    • isSameAs

      public boolean isSameAs(NormalizationSettings anotherSetting)
      Indicates whether another setting is the same as this one.
      Parameters:
      anotherSetting - another setting
      Returns:
      a boolean indicating whether another setting is the same as this one

    • getPsmNormalization

      public NormalizationType getPsmNormalization()
      Returns the type of normalization used to normalize the PSMs.
      Returns:
      the type of normalization used to normalize the PSMs

    • setPsmNormalization

      public void setPsmNormalization(NormalizationType psmNormalization)
      Sets the type of normalization used to normalize the PSMs.
      Parameters:
      psmNormalization - the type of normalization used to normalize the PSMs

    • getPeptideNormalization

      public NormalizationType getPeptideNormalization()
      Returns the type of normalization used to normalize the peptides.
      Returns:
      the type of normalization used to normalize the peptides

    • setPeptideNormalization

      public void setPeptideNormalization(NormalizationType peptideNormalization)
      Sets the type of normalization used to normalize the peptides.
      Parameters:
      peptideNormalization - the type of normalization used to normalize the peptides

    • getProteinNormalization

      public NormalizationType getProteinNormalization()
      Returns the type of normalization used to normalize the proteins.
      Returns:
      the type of normalization used to normalize the proteins

    • setProteinNormalization

      public void setProteinNormalization(NormalizationType proteinNormalization)
      Sets the type of normalization used to normalize the proteins.
      Parameters:
      proteinNormalization - the type of normalization used to normalize the proteins

    • getStableProteinsFastaFile

      public File getStableProteinsFastaFile()
      Returns the FASTA file containing the stable proteins.
      Returns:
      the FASTA file containing the stable proteins

    • setStableProteinsFastaFile

      public void setStableProteinsFastaFile(File stableProteinsFastaFile)
      Sets the FASTA file containing the stable proteins.
      Parameters:
      stableProteinsFastaFile - the FASTA file containing the stable proteins

    • getContaminantsFastaFile

      public File getContaminantsFastaFile()
      Returns the FASTA file containing the contaminant proteins.
      Returns:
      the FASTA file containing the contaminant proteins

    • setContaminantsFastaFile

      public void setContaminantsFastaFile(File contaminantsFastaFile)
      Sets the FASTA file containing the contaminant proteins.
      Parameters:
      contaminantsFastaFile - the FASTA file containing the contaminant proteins

    • getStableProteins

      public Collection<String> getStableProteins(com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters, com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters peptideVariantsPreferences, com.compomics.util.waiting.WaitingHandler waitingHandler) throws IOException
      Returns the accessions of the stable proteins as a set taken from the stableProteinsFastaFile. Null if no file is set.
      Parameters:
      searchParameters - the search parameters
      fastaParameters - the FASTA parameters
      peptideVariantsPreferences - the peptide variants parameters
      waitingHandler - the waiting handler
      Returns:
      the accessions of the stable proteins as a collection
      Throws:
      IOException - exception thrown whenever an error occurred while accessing the file.

    • getContaminants

      public Collection<String> getContaminants(com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters, com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters peptideVariantsPreferences, com.compomics.util.waiting.WaitingHandler waitingHandler) throws IOException
      Returns the accessions of the contaminants as a set taken from the contaminantsFastaFile. Null if no file is set.
      Parameters:
      searchParameters - the search parameters
      fastaParameters - the FASTA parameters
      peptideVariantsPreferences - the peptide variants parameters
      waitingHandler - the waiting handler
      Returns:
      the accessions of the stable proteins as a collection
      Throws:
      IOException - exception thrown whenever an error occurred while accessing the file.

    • getDefaultContaminantFile

      public static File getDefaultContaminantFile()
      Returns the default contaminants file.
      Returns:
      the default contaminants file