public class TagAssumption extends SpectrumIdentificationAssumption implements UrParameter
advocate, aminoAcidScores, identificationCharge, identificationFile, rank, rawScore, score
Constructor and Description |
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TagAssumption()
Constructor for en empty assumption.
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TagAssumption(int advocate,
int rank,
Tag tag,
Charge identificationCharge,
double score)
Constructor.
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Modifier and Type | Method and Description |
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String |
getFamilyName()
This method returns the family name of the parameter.
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int |
getIndex()
This method returns the index of the parameter.
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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.
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Tag |
getTag()
Returns the tag of this assumption.
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Double |
getTheoreticMass()
Returns the theoretic mass of the given assumption.
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double |
getTheoreticMass(boolean includeCTermGap,
boolean includeNTermGap)
Returns the theoretic mass of the tag, eventually without terminal gaps.
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double |
getTheoreticMz(boolean includeCTermGap,
boolean includeNTermGap)
Returns the theoretic mass of the tag, eventually without terminal gaps.
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TagAssumption |
reverse(boolean yIon)
Retunrs a new TagAssumption instance where the tag is a reversed version
of this tag.
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String |
toString() |
getAdvocate, getAminoAcidScores, getDeltaMass, getIdentificationCharge, getIdentificationFile, getIsotopeNumber, getPrecursorMatch, getRank, getRawScore, getScore, getTheoreticMz, setAminoAcidScores, setIdentificationCharge, setRank, setRawScore, setScore
addUrParam, getParameterKey, getUrParam
public TagAssumption()
public TagAssumption(int advocate, int rank, Tag tag, Charge identificationCharge, double score)
advocate
- the advocate supporting this assumptionrank
- the rank of the assumptiontag
- the identified tagidentificationCharge
- the identified chargescore
- the scorepublic Tag getTag()
public Double getTheoreticMass()
SpectrumIdentificationAssumption
getTheoreticMass
in class SpectrumIdentificationAssumption
public double getTheoreticMass(boolean includeCTermGap, boolean includeNTermGap)
includeCTermGap
- if true the C-terminal gap will be added if
presentincludeNTermGap
- if true the N-terminal gap will be added if
presentpublic double getTheoreticMz(boolean includeCTermGap, boolean includeNTermGap)
includeCTermGap
- if true the C-terminal gap will be added if
presentincludeNTermGap
- if true the N-terminal gap will be added if
presentpublic ArrayList<TagAssumption> getPossibleTags(boolean forwardIon, int minCharge, int maxCharge, int maxIsotope)
forwardIon
- indicates whether the tag is based on forward ions (a,
b, or c)minCharge
- the minimal precursor charge to considermaxCharge
- the maximal precursor charge to considermaxIsotope
- the maximal isotope number to considerpublic TagAssumption reverse(boolean yIon)
yIon
- indicates whether the tag is based on y ionspublic String getFamilyName()
UrParameter
getFamilyName
in interface UrParameter
public int getIndex()
UrParameter
getIndex
in interface UrParameter
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