java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
All Implemented Interfaces:
IdentificationAlgorithmParameter, Serializable

public class AndromedaParameters
extends ExperimentObject
implements IdentificationAlgorithmParameter
The Andromeda specific parameters.
Author:
Marc Vaudel, Harald Barsnes
See Also:
Serialized Form
  • Constructor Details

  • Method Details

    • getMaxPeptideMass

      public double getMaxPeptideMass()
      Returns the maximal peptide mass.
      Returns:
      the maximal peptide mass
    • setMaxPeptideMass

      public void setMaxPeptideMass​(Double maxPeptideMass)
      Sets the maximal peptide mass.
      Parameters:
      maxPeptideMass - the maximal peptide mass
    • getMaxCombinations

      public int getMaxCombinations()
      Returns the maximal number of combinations.
      Returns:
      the maximal number of combinations
    • setMaxCombinations

      public void setMaxCombinations​(int maxCombinations)
      Sets the maximal number of combinations.
      Parameters:
      maxCombinations - the maximal number of combinations
    • getTopPeaks

      public int getTopPeaks()
      Returns the top peaks number.
      Returns:
      the top peaks number
    • setTopPeaks

      public void setTopPeaks​(int topPeaks)
      Sets the top peaks number.
      Parameters:
      topPeaks - the top peaks number
    • getTopPeaksWindow

      public int getTopPeaksWindow()
      Returns the top peaks window size.
      Returns:
      the top peaks window size
    • setTopPeaksWindow

      public void setTopPeaksWindow​(int topPeaksWindow)
      Sets the top peaks window size.
      Parameters:
      topPeaksWindow - the top peaks window size
    • isIncludeWater

      public boolean isIncludeWater()
      Returns a boolean indicating whether water losses should be accounted for.
      Returns:
      a boolean indicating whether water losses should be accounted for
    • setIncludeWater

      public void setIncludeWater​(boolean includeWater)
      Sets whether water losses should be accounted for.
      Parameters:
      includeWater - a boolean indicating whether water losses should be accounted for
    • isIncludeAmmonia

      public boolean isIncludeAmmonia()
      Returns a boolean indicating whether ammonia losses should be accounted for.
      Returns:
      a boolean indicating whether ammonia losses should be accounted for
    • setIncludeAmmonia

      public void setIncludeAmmonia​(boolean includeAmmonia)
      Sets whether ammonia losses should be accounted for.
      Parameters:
      includeAmmonia - a boolean indicating whether ammonia losses should be accounted for
    • isDependentLosses

      public boolean isDependentLosses()
      Returns whether neutral losses should be sequence dependent.
      Returns:
      a boolean indicating whether neutral losses should be sequence dependent
    • setDependentLosses

      public void setDependentLosses​(boolean dependentLosses)
      Sets whether neutral losses should be sequence dependent.
      Parameters:
      dependentLosses - a boolean indicating whether neutral losses should be sequence dependent
    • isFragmentAll

      public boolean isFragmentAll()
      Indicates whether the fragment all option should be used.
      Returns:
      a boolean indicating whether the fragment all option should be used
    • setFragmentAll

      public void setFragmentAll​(boolean fragmentAll)
      Sets whether the fragment all option should be used.
      Parameters:
      fragmentAll - a boolean indicating whether the fragment all option should be used
    • isEmpiricalCorrection

      public boolean isEmpiricalCorrection()
      Indicates whether empirical correction should be used.
      Returns:
      a boolean indicating whether empirical correction should be used
    • setEmpiricalCorrection

      public void setEmpiricalCorrection​(boolean empiricalCorrection)
      Sets whether empirical correction should be used.
      Parameters:
      empiricalCorrection - a boolean indicating whether empirical correction should be used
    • isHigherCharge

      public boolean isHigherCharge()
      Indicates whether higher charge should be considered.
      Returns:
      a boolean indicating whether higher charge should be considered
    • setHigherCharge

      public void setHigherCharge​(boolean higherCharge)
      Sets whether higher charge should be considered.
      Parameters:
      higherCharge - a boolean indicating whether higher charge should be considered
    • getFragmentationMethod

      public FragmentationMethod getFragmentationMethod()
      Returns the fragmentation method used.
      Returns:
      the fragmentation method used
    • setFragmentationMethod

      public void setFragmentationMethod​(FragmentationMethod fragmentationMethod)
      Sets the fragmentation method used.
      Parameters:
      fragmentationMethod - the fragmentation method used
    • getMaxNumberOfModifications

      public int getMaxNumberOfModifications()
      Returns the maximal number of modifications.
      Returns:
      the maximal number of modifications
    • setMaxNumberOfModifications

      public void setMaxNumberOfModifications​(int maxNumberOfModifications)
      Sets the maximal number of modifications.
      Parameters:
      maxNumberOfModifications - the maximal number of modifications
    • getMinPeptideLengthNoEnzyme

      public int getMinPeptideLengthNoEnzyme()
      Returns the minimal peptide length to use when searching with no enzyme.
      Returns:
      the minimal peptide length to use when searching with no enzyme
    • setMinPeptideLengthNoEnzyme

      public void setMinPeptideLengthNoEnzyme​(int minPeptideLengthNoEnzyme)
      Sets the minimal peptide length to use when searching with no enzyme.
      Parameters:
      minPeptideLengthNoEnzyme - the minimal peptide length to use when searching with no enzyme
    • getMaxPeptideLengthNoEnzyme

      public int getMaxPeptideLengthNoEnzyme()
      Returns the maximal peptide length to use when searching with no enzyme.
      Returns:
      the maximal peptide length to use when searching with no enzyme
    • setMaxPeptideLengthNoEnzyme

      public void setMaxPeptideLengthNoEnzyme​(int maxPeptideLengthNoEnzyme)
      Sets the maximal peptide length to use when searching with no enzyme.
      Parameters:
      maxPeptideLengthNoEnzyme - the maximal peptide length to use when searching with no enzyme
    • isEqualIL

      public boolean isEqualIL()
      Indicates whether I and L should be considered indistinguishable.
      Returns:
      a boolean indicating whether I and L should be considered indistinguishable
    • setEqualIL

      public void setEqualIL​(boolean equalIL)
      Sets whether I and L should be considered indistinguishable.
      Parameters:
      equalIL - a boolean indicating whether I and L should be considered indistinguishable
    • getDecoyMode

      Returns the decoy mode.
      Returns:
      the decoy mode.
    • setDecoyMode

      public void setDecoyMode​(AndromedaParameters.AndromedaDecoyMode decoyMode)
      Set the decoy mode.
      Parameters:
      decoyMode - the decoy mode
    • getNumberOfCandidates

      public int getNumberOfCandidates()
      Returns the number of candidates.
      Returns:
      the number of candidates
    • setPtmIndex

      public void setPtmIndex​(String modificationName, int ptmIndex)
      Sets the index for a given modification. If another modification was already given with the same index the previous setting will be silently overwritten.
      Parameters:
      modificationName - the name of the modification
      ptmIndex - the index of the modification
    • getModificationName

      public String getModificationName​(int ptmIndex)
      Returns the name of the modification indexed by the given index. Null if not found.
      Parameters:
      ptmIndex - the index of the modification to look for
      Returns:
      the name of the modification indexed by the given index
    • hasModificationIndexes

      public boolean hasModificationIndexes()
      Indicates whether the modification profile has PTM indexes.
      Returns:
      true if an PTM indexes map is set
    • getPtmIndex

      public Integer getPtmIndex​(String modificationName)
      Returns the index of a given modification, null if not found.
      Parameters:
      modificationName - the name of the modification
      Returns:
      the corresponding index
    • getPtmIndexes

      public HashMap<Integer,​String> getPtmIndexes()
      Returns the PTM indexes as a map.
      Returns:
      the PTM indexes
    • setNumberOfCandidates

      public void setNumberOfCandidates​(int numberOfCandidates)
      Sets the number of candidates.
      Parameters:
      numberOfCandidates - the number of candidates
    • getAlgorithm

      public Advocate getAlgorithm()
      Description copied from interface: IdentificationAlgorithmParameter
      Returns the identification algorithm.
      Specified by:
      getAlgorithm in interface IdentificationAlgorithmParameter
      Returns:
      the identification algorithm
    • equals

      public boolean equals​(IdentificationAlgorithmParameter identificationAlgorithmParameter)
      Description copied from interface: IdentificationAlgorithmParameter
      Indicates whether another identificationAlgorithmParameter has the same parameters.
      Specified by:
      equals in interface IdentificationAlgorithmParameter
      Parameters:
      identificationAlgorithmParameter - the other identificationAlgorithmParameter
      Returns:
      true if the algorithm and parameters are the same
    • toString

      public String toString​(boolean html)
      Description copied from interface: IdentificationAlgorithmParameter
      Returns the parameters as a string.
      Specified by:
      toString in interface IdentificationAlgorithmParameter
      Parameters:
      html - use HTML formatting
      Returns:
      the parameters as a string