Class SearchParameters

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.search.SearchParameters
All Implemented Interfaces:
MarshallableParameter, Serializable

public class SearchParameters
extends ExperimentObject
implements MarshallableParameter
This class groups the parameters used for identification.
Author:
Marc Vaudel, Harald Barsnes
See Also:
Serialized Form
  • Field Details

  • Constructor Details

  • Method Details

    • setDefaultAdvancedSettings

      public void setDefaultAdvancedSettings()
      Set the advanced settings to the default values.
    • setDefaultAdvancedSettings

      public void setDefaultAdvancedSettings​(SearchParameters searchParameters)
      Set the advanced settings to the values in the given search parameters object or to the default values of the advanced settings are not set for a given advocate.
      Parameters:
      searchParameters - the search parameter to extract the advanced settings from
    • getRefMass

      public double getRefMass()
      Returns the reference mass used to convert ppm to Da.
      Returns:
      the reference mass used to convert ppm to Da
    • setRefMass

      public void setRefMass​(double refMass)
      Sets the reference mass used to convert ppm to Da.
      Parameters:
      refMass - the reference mass used to convert ppm to Da
    • getModificationParameters

      public ModificationParameters getModificationParameters()
      Returns the modification settings.
      Returns:
      the modification settings
    • setModificationParameters

      public void setModificationParameters​(ModificationParameters modificationParameters)
      Sets the modification settings.
      Parameters:
      modificationParameters - the modification settings
    • getFragmentIonAccuracy

      public double getFragmentIonAccuracy()
      Returns the MS2 ion m/z tolerance.
      Returns:
      the MS2 ion m/z tolerance
    • getFragmentIonAccuracyInDaltons

      public double getFragmentIonAccuracyInDaltons()
      Returns the absolute fragment ion tolerance in Dalton. If the tolerance is in ppm, the internal reference mass is used.
      Returns:
      the absolute fragment ion tolerance in Dalton
    • getFragmentIonAccuracyInDaltons

      public double getFragmentIonAccuracyInDaltons​(double refMass)
      Returns the absolute fragment ion tolerance in Dalton. If the tolerance is in ppm, the given reference mass is used.
      Parameters:
      refMass - the reference mass to use for the conversion of tolerances in ppm.
      Returns:
      the absolute fragment ion tolerance in Dalton
    • setFragmentIonAccuracy

      public void setFragmentIonAccuracy​(double fragmentIonMZTolerance)
      Sets the fragment ion m/z tolerance.
      Parameters:
      fragmentIonMZTolerance - the fragment ion m/z tolerance
    • getDigestionParameters

      public DigestionParameters getDigestionParameters()
      Returns the digestion preferences.
      Returns:
      the digestion preferences
    • setDigestionParameters

      public void setDigestionParameters​(DigestionParameters digestionParameters)
      Sets the digestion preferences.
      Parameters:
      digestionParameters - the digestion preferences
    • getForwardIons

      public ArrayList<Integer> getForwardIons()
      Returns the forward ions searched as list of integers as indexed in the FragmentIon class.
      Returns:
      the forward ions searched
    • setForwardIons

      public void setForwardIons​(ArrayList<Integer> forwardIons)
      Sets the forward ions searched as list of integers as indexed in the FragmentIon class.
      Parameters:
      forwardIons - the forward ions searched
    • getRewindIons

      public ArrayList<Integer> getRewindIons()
      Returns the rewind ions searched as list of integers as indexed in the FragmentIon class.
      Returns:
      the rewind ions searched
    • setRewindIons

      public void setRewindIons​(ArrayList<Integer> rewindIons)
      Sets the rewind ions searched as list of integers as indexed in the FragmentIon class.
      Parameters:
      rewindIons - the rewind ions searched
    • getIons

      public static String[] getIons()
      Getter for the list of ion symbols used.
      Returns:
      the list of ion symbols used
    • getPrecursorAccuracy

      public double getPrecursorAccuracy()
      Returns the precursor tolerance.
      Returns:
      the precursor tolerance
    • setPrecursorAccuracy

      public void setPrecursorAccuracy​(double precursorTolerance)
      Sets the precursor tolerance.
      Parameters:
      precursorTolerance - the precursor tolerance
    • getPrecursorAccuracyType

      public SearchParameters.MassAccuracyType getPrecursorAccuracyType()
      Returns the precursor accuracy type.
      Returns:
      the precursor accuracy type
    • setPrecursorAccuracyType

      public void setPrecursorAccuracyType​(SearchParameters.MassAccuracyType precursorAccuracyType)
      Sets the precursor accuracy type.
      Parameters:
      precursorAccuracyType - the precursor accuracy type
    • getFragmentAccuracyType

      public SearchParameters.MassAccuracyType getFragmentAccuracyType()
      Returns the fragment accuracy type.
      Returns:
      the fragment accuracy type
    • setFragmentAccuracyType

      public void setFragmentAccuracyType​(SearchParameters.MassAccuracyType fragmentAccuracyType)
      Sets the fragment accuracy type.
      Parameters:
      fragmentAccuracyType - the fragment accuracy type
    • isPrecursorAccuracyTypePpm

      public Boolean isPrecursorAccuracyTypePpm()
      Returns true if the current precursor accuracy type is ppm.
      Returns:
      true if the current precursor accuracy type is ppm
    • getMaxChargeSearched

      public int getMaxChargeSearched()
      Returns the maximal charge searched.
      Returns:
      the maximal charge searched
    • setMaxChargeSearched

      public void setMaxChargeSearched​(int maxChargeSearched)
      Sets the maximal charge searched.
      Parameters:
      maxChargeSearched - the maximal charge searched
    • getMinChargeSearched

      public int getMinChargeSearched()
      Returns the minimal charge searched.
      Returns:
      the minimal charge searched
    • setMinChargeSearched

      public void setMinChargeSearched​(int minChargeSearched)
      Sets the minimal charge searched.
      Parameters:
      minChargeSearched - the minimal charge searched
    • getAlgorithmSpecificParameters

      public HashMap<Integer,​IdentificationAlgorithmParameter> getAlgorithmSpecificParameters()
      Returns the algorithm specific parameters in a map: algorithm as indexed in the Advocate class > parameters. null if not set.
      Returns:
      the algorithm specific parameters in a map
    • getIdentificationAlgorithmParameter

      public IdentificationAlgorithmParameter getIdentificationAlgorithmParameter​(int algorithmID)
      Returns the algorithm specific parameters, null if not found.
      Parameters:
      algorithmID - the index of the search engine as indexed in the Advocate class
      Returns:
      the algorithm specific parameters
    • setIdentificationAlgorithmParameter

      public void setIdentificationAlgorithmParameter​(int algorithmID, IdentificationAlgorithmParameter identificationAlgorithmParameter)
      Adds identification algorithm specific parameters.
      Parameters:
      algorithmID - the algorithm id as indexed in the Advocate class
      identificationAlgorithmParameter - the specific parameters
    • getAlgorithms

      public Set<Integer> getAlgorithms()
      Returns the algorithms for which specific parameters are stored. Warning: this does not mean that the algorithm was actually used.
      Returns:
      the algorithms for which specific parameters are stored in a set of indexes as listed in the Advocate class
    • getMinIsotopicCorrection

      public int getMinIsotopicCorrection()
      Returns the minimal isotopic correction.
      Returns:
      the minimal isotopic correction
    • setMinIsotopicCorrection

      public void setMinIsotopicCorrection​(int minIsotopicCorrection)
      Sets the minimal isotopic correction.
      Parameters:
      minIsotopicCorrection - the minimal isotopic correction
    • getMaxIsotopicCorrection

      public int getMaxIsotopicCorrection()
      Returns the maximal isotopic correction.
      Returns:
      the maximal isotopic correction
    • setMaxIsotopicCorrection

      public void setMaxIsotopicCorrection​(int maxIsotopicCorrection)
      Sets the maximal isotopic correction.
      Parameters:
      maxIsotopicCorrection - the maximal isotopic correction
    • getIdentificationParameters

      public static SearchParameters getIdentificationParameters​(File searchParametersFile) throws IOException, ClassNotFoundException
      Loads the identification parameters from a file. If the file is an identification parameters file, the search parameters are extracted.
      Parameters:
      searchParametersFile - the search parameter file
      Returns:
      the search parameters
      Throws:
      IOException - if an IOException occurs
      ClassNotFoundException - if a ClassNotFoundException occurs
    • saveIdentificationParameters

      public static void saveIdentificationParameters​(SearchParameters searchParameters, File searchParametersFile) throws IOException
      Saves the identification parameters to a serialized file.
      Parameters:
      searchParameters - the identification parameters
      searchParametersFile - the file
      Throws:
      IOException - if an IOException occurs
    • saveIdentificationParametersAsTextFile

      public void saveIdentificationParametersAsTextFile​(File file) throws IOException
      Saves the identification parameters as a human readable text file.
      Parameters:
      file - the file
      Throws:
      IOException - if an IOException occurs
    • toString

      public String toString()
      Overrides:
      toString in class Object
    • getShortDescription

      public String getShortDescription()
      Returns a short description of the parameters.
      Returns:
      a short description of the parameters
    • toString

      public String toString​(boolean html)
      Returns the search parameters as a string.
      Parameters:
      html - use HTML formatting
      Returns:
      the search parameters as a string
    • equals

      public boolean equals​(SearchParameters otherSearchParameters)
      Returns true if the search parameter objects have identical settings.
      Parameters:
      otherSearchParameters - the parameters to compare to
      Returns:
      true if the search parameter objects have identical settings
    • setFlanking

      public void setFlanking​(boolean flanking)
      Set whether the flanking amino acids of a mapped peptide are to be reported.
      Parameters:
      flanking - whether the flanking amino acids of a mapped peptide are to be reported
    • getFlanking

      public boolean getFlanking()
      Return whether the flanking amino acids of a mapped peptide are to be reported.
      Returns:
      true if whether the flanking amino acids of a mapped peptide are to be reported
    • 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