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
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Field Summary
Fields inherited from class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
advocate, aminoAcidScores, identificationCharge, identificationFile, rank, rawScore, score
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Constructor Summary
Constructors Constructor Description TagAssumption()
Constructor for en empty assumption.TagAssumption(int advocate, int rank, Tag tag, int identificationCharge, double score)
Constructor. -
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)
Retunrs 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, getDeltaMass, 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
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Constructor Details
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TagAssumption
public TagAssumption()Constructor for en empty assumption. -
TagAssumption
Constructor. Note: if PsmScores.scoreRoundingDecimal is not null the scored will be floored accordingly.- Parameters:
advocate
- the advocate supporting this assumptionrank
- the rank of the assumptiontag
- the identified tagidentificationCharge
- the identified chargescore
- the score
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Method Details
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getTag
Returns the tag of this assumption.- Returns:
- the tag of this assumption
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setTag
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getTheoreticMass
public double getTheoreticMass()Description copied from class:SpectrumIdentificationAssumption
Returns the theoretic mass of the given assumption.- Specified by:
getTheoreticMass
in classSpectrumIdentificationAssumption
- Returns:
- the theoretic mass of the given assumption
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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 presentincludeNTermGap
- if true the N-terminal gap will be added if present- Returns:
- the theoretic mass of the tag
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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 presentincludeNTermGap
- if true the N-terminal gap will be added if present- Returns:
- the theoretic mass of the tag
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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 considermaxCharge
- the maximal precursor charge to considermaxIsotope
- 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
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reverse
Retunrs 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
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toString
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