public class TagAssumption extends SpectrumIdentificationAssumption
advocate, aminoAcidScores, identificationCharge, identificationFile, rank, rawScore, score
NO_KEY
Constructor and Description |
---|
TagAssumption()
Constructor for en empty assumption.
|
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.
|
Modifier and Type | Method and Description |
---|---|
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.
|
Tag |
getTag()
Returns the tag of this assumption.
|
double |
getTheoreticMass()
Returns the theoretic mass of the given assumption.
|
double |
getTheoreticMass(boolean includeCTermGap,
boolean includeNTermGap)
Returns the theoretic mass of the tag, eventually without terminal gaps.
|
double |
getTheoreticMz(boolean includeCTermGap,
boolean includeNTermGap)
Returns the theoretic mass of the tag, eventually without terminal gaps.
|
TagAssumption |
reverse(boolean yIon)
Returns a new TagAssumption instance where the tag is a reversed version
of this tag.
|
void |
setTag(Tag tag) |
String |
toString() |
getAdvocate, getAminoAcidScores, getDeltaMass, getIdentificationCharge, getIdentificationFile, getIsotopeNumber, getPrecursorMatch, getRank, getRawScore, getScore, getTheoreticMz, setAdvocate, setAminoAcidScores, setIdentificationCharge, setIdentificationFile, setRank, setRawScore, setScore
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
public TagAssumption()
public TagAssumption(int advocate, int rank, Tag tag, int identificationCharge, double rawScore, double score)
advocate
- the advocate supporting this assumptionrank
- the rank of the assumptiontag
- the identified tagidentificationCharge
- the identified chargerawScore
- the raw score, i.e. the untransformed score given by the
search enginescore
- the (potentially transformed) score, typically a search
engine e-value (whether the score is ascending or descending can be known
from the SearchEngine class)public Tag getTag()
public void setTag(Tag tag)
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 ionsCopyright © 2021. All rights reserved.