Package com.compomics.util.experiment.identification.spectrum_assumptions

Class TagAssumption

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.identification.SpectrumIdentificationAssumption

com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption

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

Field Summary

Fields inherited from class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption

advocate, aminoAcidScores, identificationCharge, identificationFile, rank, rawScore, score

Fields inherited from class com.compomics.util.experiment.personalization.ExperimentObject

NO_KEY

Constructor Summary

Constructors

Constructor	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.

Method Summary

Modifier and Type	Method	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()

Methods inherited from class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption

getAdvocate, getAminoAcidScores, getDeltaMz, getIdentificationCharge, getIdentificationFile, getIsotopeNumber, getPrecursorMatch, getRank, getRawScore, getScore, getTheoreticMz, setAdvocate, setAminoAcidScores, setIdentificationCharge, setIdentificationFile, setRank, setRawScore, setScore

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject

addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

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