All Implemented Interfaces:
Filter, Serializable

public class ProteinFilter
extends MatchFilter
Protein filter.
Author:
Marc Vaudel
See Also:
Serialized Form
  • Constructor Details

    • ProteinFilter

      public ProteinFilter()
      Constructor.
    • ProteinFilter

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

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

      public ProteinFilter​(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 matchKey, 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
      matchKey - 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.
    • 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