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

Class NovorParameters

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.tool_specific.NovorParameters
All Implemented Interfaces:
IdentificationAlgorithmParameter, Serializable
public class NovorParameters extends ExperimentObject implements IdentificationAlgorithmParameter
Novor specific parameters.
Author:
Harald Barsnes
See Also:

  • Constructor Details

    • NovorParameters

      public NovorParameters()
      Constructor.

  • Method Details

    • 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

    • getFragmentationMethod

      public String getFragmentationMethod()
      Returns the fragmentation method.
      Returns:
      the fragmentation method

    • setFragmentationMethod

      public void setFragmentationMethod(String fragmentationMethod)
      Set the fragmentation method.
      Parameters:
      fragmentationMethod - the fragmentation method to set

    • getMassAnalyzer

      public String getMassAnalyzer()
      Returns the mass analyzer.
      Returns:
      the mass analyzer

    • setMassAnalyzer

      public void setMassAnalyzer(String massAnalyzer)
      Set the mass analyzer.
      Parameters:
      massAnalyzer - the mass analyzer to set

    • getNovorPtmMap

      public HashMap<String,String> getNovorPtmMap()
      Returns the Novor to utilities PTM map. Null if not set.
      Returns:
      the Novor to utilities PTM map, null if not set

    • setNovorPtmMap

      public void setNovorPtmMap(HashMap<String,String> novorPtmMap)
      Set the Novor to utilities PTM map.
      Parameters:
      novorPtmMap - the novorPtmMap to set

    • getUtilitiesPtmName

      public String getUtilitiesPtmName(String novorPtmShortName)
      Returns the utilities PTM name corresponding to the given Novor PTM short name. Null if not found.
      Parameters:
      novorPtmShortName - the Novor PTM short name
      Returns:
      the utilities PTM name