All Implemented Interfaces:
Serializable

public class TagAssumption
extends SpectrumIdentificationAssumption
This class represent a tag assumption made by an identification algorithm based on a sequence tag.
Author:
Marc Vaudel
See Also:
Serialized Form
  • Constructor Details

    • TagAssumption

      public TagAssumption()
      Constructor for en empty assumption.
    • TagAssumption

      public TagAssumption​(int advocate, int rank, Tag tag, int identificationCharge, double rawScore, double score)
      Constructor.Note: if PsmScores.scoreRoundingDecimal is not null the scored will be floored accordingly.
      Parameters:
      advocate - the advocate supporting this assumption
      rank - the rank of the assumption
      tag - the identified tag
      identificationCharge - the identified charge
      rawScore - the raw score, i.e. the untransformed score given by the search engine
      score - the (potentially transformed) score, typically a search engine e-value (whether the score is ascending or descending can be known from the SearchEngine class)
  • Method Details

    • getTag

      public Tag getTag()
      Returns the tag of this assumption.
      Returns:
      the tag of this assumption
    • setTag

      public void setTag​(Tag tag)
    • getTheoreticMass

      public double getTheoreticMass()
      Description copied from class: SpectrumIdentificationAssumption
      Returns the theoretic mass of the given assumption.
      Specified by:
      getTheoreticMass in class SpectrumIdentificationAssumption
      Returns:
      the theoretic mass of the given assumption
    • getTheoreticMass

      public double getTheoreticMass​(boolean includeCTermGap, boolean includeNTermGap)
      Returns the theoretic mass of the tag, eventually without terminal gaps.
      Parameters:
      includeCTermGap - if true the C-terminal gap will be added if present
      includeNTermGap - if true the N-terminal gap will be added if present
      Returns:
      the theoretic mass of the tag
    • getTheoreticMz

      public double getTheoreticMz​(boolean includeCTermGap, boolean includeNTermGap)
      Returns the theoretic mass of the tag, eventually without terminal gaps.
      Parameters:
      includeCTermGap - if true the C-terminal gap will be added if present
      includeNTermGap - if true the N-terminal gap will be added if present
      Returns:
      the theoretic mass of the tag
    • getPossibleTags

      public ArrayList<TagAssumption> getPossibleTags​(boolean forwardIon, int minCharge, int maxCharge, int maxIsotope)
      Computes the possible tag assumptions which can be obtained from this one by accounting for other charges and isotopes.
      Parameters:
      forwardIon - indicates whether the tag is based on forward ions (a, b, or c)
      minCharge - the minimal precursor charge to consider
      maxCharge - the maximal precursor charge to consider
      maxIsotope - the maximal isotope number to consider
      Returns:
      the possible tag assumptions which can be obtained from this one by accounting for other charges and isotopes
    • reverse

      public TagAssumption reverse​(boolean yIon)
      Returns a new TagAssumption instance where the tag is a reversed version of this tag.
      Parameters:
      yIon - indicates whether the tag is based on y ions
      Returns:
      a new TagAssumption instance where the tag is a reversed version of this tag
    • toString

      public String toString()
      Overrides:
      toString in class Object