All Implemented Interfaces:
Filter, Serializable

public class AssumptionFilter
extends MatchFilter
Peptide Assumption filter.
Author:
Marc Vaudel
See Also:
Serialized Form
  • Constructor Details

    • AssumptionFilter

      public AssumptionFilter()
      Constructor.
    • AssumptionFilter

      public AssumptionFilter​(String name)
      Constructor.
      Parameters:
      name - the name of the filter
    • AssumptionFilter

      public AssumptionFilter​(String name, String description)
      Constructor.
      Parameters:
      name - the name of the filter
      description - the description of the filter
    • AssumptionFilter

      public AssumptionFilter​(String name, String description, String condition, String reportPassed, String reportFailed)
      Constructor.
      Parameters:
      name - the name of the filter
      description - the description of the filter
      condition - a description of the condition to be met to pass the filter
      reportPassed - a report for when the filter is passed
      reportFailed - a report for when the filter is not passed
  • Method Details

    • getNew

      protected MatchFilter getNew()
      Description copied from class: MatchFilter
      Returns a new empty filter.
      Specified by:
      getNew in class MatchFilter
      Returns:
      a new empty filter
    • isValidated

      public boolean isValidated​(String itemName, FilterItemComparator filterItemComparator, Object value, long spectrumMatchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
      Description copied from class: MatchFilter
      Indicates whether the match designated by the match key validates the given item using the given comparator and value threshold.
      Specified by:
      isValidated in class MatchFilter
      Parameters:
      itemName - the name of the item to filter on
      filterItemComparator - the comparator to use
      value - the value to use as a threshold
      spectrumMatchKey - the key of the match of interest
      identification - the identification objects where to get identification matches from
      geneMaps - the gene maps
      identificationFeaturesGenerator - the identification feature generator where to get identification features
      identificationParameters - the identification parameters used
      sequenceProvider - the protein sequence provider
      proteinDetailsProvider - the protein details provider
      spectrumProvider - the spectrum provider
      Returns:
      a boolean indicating whether the match designated by the protein key validates the given item using the given comparator and value threshold.
    • isValidated

      public boolean isValidated​(long spectrumMatchKey, String spectrumFile, String spectrumTitle, PeptideAssumption peptideAssumption, Identification identification, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters)
      Tests whether a match is validated by this filter.
      Parameters:
      spectrumMatchKey - the key of the match
      spectrumFile - the file of the spectrum
      spectrumTitle - the title of the spectrum
      peptideAssumption - the peptide assumption
      identification - the identification where to get the information from
      sequenceProvider - the sequence provider
      spectrumProvider - the spectrum provider
      identificationFeaturesGenerator - the identification features generator providing identification features
      identificationParameters - the identification parameters
      Returns:
      a boolean indicating whether a match is validated by a given filter
    • isValidated

      public boolean isValidated​(String itemName, FilterItemComparator filterItemComparator, Object value, long spectrumMatchKey, String spectrumFile, String spectrumTitle, PeptideAssumption peptideAssumption, Identification identification, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters)
      Indicates whether the match designated by the match key validates the given item using the given comparator and value threshold.
      Parameters:
      itemName - the name of the item to filter on
      filterItemComparator - the comparator to use
      value - the value to use as a threshold
      spectrumMatchKey - the key of the match of interest
      spectrumFile - the file of the spectrum
      spectrumTitle - the title of the spectrum
      peptideAssumption - the assumption to validate
      identification - the identification objects where to get identification matches from
      sequenceProvider - the sequence provider
      spectrumProvider - the spectrum provider
      identificationFeaturesGenerator - the identification feature generator where to get identification features
      identificationParameters - the identification parameters used
      Returns:
      a boolean indicating whether the match designated by the protein key validates the given item using the given comparator and value threshold.
    • getPossibleFilterItems

      public FilterItem[] getPossibleFilterItems()
      Description copied from class: MatchFilter
      Returns the filter items accepted by this filter.
      Specified by:
      getPossibleFilterItems in class MatchFilter
      Returns:
      the filter items accepted by this filter
    • getFilterItem

      public FilterItem getFilterItem​(String itemName)
      Description copied from class: MatchFilter
      Returns the filter item corresponding to the given name.
      Specified by:
      getFilterItem in class MatchFilter
      Parameters:
      itemName - the name of the filter item
      Returns:
      the filter item corresponding to the given name