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java.lang.Objectcom.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.identification.PeptideAssumption
public class PeptideAssumption
This object will models the assumption made by an advocate.
Constructor Summary | |
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PeptideAssumption(Peptide aPeptide,
int rank,
int advocate,
Charge identificationCharge,
double score)
Constructor for a peptide assumption. |
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PeptideAssumption(Peptide aPeptide,
int rank,
int advocate,
Charge identificationCharge,
double score,
String identificationFile)
Constructor for a peptide assumption. |
Method Summary | |
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int |
getAdvocate()
Get the used advocate. |
double |
getDeltaMass(double measuredMZ,
boolean ppm)
Returns the precursor mass error (in ppm or Da). |
double |
getDeltaMass(double measuredMZ,
boolean ppm,
boolean subtractIsotope)
Returns the precursor mass error (in ppm or Da). |
double |
getEValue()
Deprecated. use getScore instead |
String |
getFile()
Returns the file. |
Charge |
getIdentificationCharge()
Returns the charge used for identification. |
int |
getIsotopeNumber(double measuredMZ)
Returns the precursor isotope number according to the number of protons. |
Peptide |
getPeptide()
Get the theoretic peptide. |
IonMatch |
getPrecursorMatch(Peak precursorPeak)
Returns the ion match. |
int |
getRank()
Get the identification rank. |
double |
getScore()
Returns the score assigned by the advocate. |
double |
getTheoreticMz()
Returns the theoretic m/z expected for this assumption. |
void |
setRank(int aRank)
Set the rank of the PeptideAssumption. |
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject |
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addUrParam, getParameterKey, getUrParam |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public PeptideAssumption(Peptide aPeptide, int rank, int advocate, Charge identificationCharge, double score, String identificationFile)
aPeptide
- the theoretic peptiderank
- the identification rankadvocate
- the advocate usedidentificationCharge
- the charge used by the search engine for
identificationscore
- the score, typically a search engine e-value (whether the
score is ascending or descending can be known from the SearchEngine
class)identificationFile
- the identification filepublic PeptideAssumption(Peptide aPeptide, int rank, int advocate, Charge identificationCharge, double score)
aPeptide
- the theoretic peptiderank
- the identification rankadvocate
- the advocate usedidentificationCharge
- the charge used by the search engine for
identificationscore
- the score (whether the score is ascending or descending can
be known from the SearchEngine class)Method Detail |
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public int getRank()
public Peptide getPeptide()
public int getAdvocate()
public double getDeltaMass(double measuredMZ, boolean ppm, boolean subtractIsotope)
measuredMZ
- the precursor m/zppm
- if true the error is returns in ppm, false returns the error
in DasubtractIsotope
- if true the isotope number will be subtracted from
the theoretic mass
public double getDeltaMass(double measuredMZ, boolean ppm)
measuredMZ
- the precursor m/zppm
- if true the error is returns in ppm, false returns the error
in Da
public double getTheoreticMz()
public int getIsotopeNumber(double measuredMZ)
measuredMZ
-
public double getEValue()
public double getScore()
public String getFile()
public Charge getIdentificationCharge()
public void setRank(int aRank)
aRank
- the rank of the PeptideAssumptiopublic IonMatch getPrecursorMatch(Peak precursorPeak)
precursorPeak
-
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