Package com.compomics.util.parameters.identification.tool_specific

Class AndromedaParameters

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:

  • Constructor Details

    • AndromedaParameters

      public AndromedaParameters()
      Constructor.

  • 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

      public AndromedaParameters.AndromedaDecoyMode 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