com.compomics.util.experiment.identification
Class PeptideAssumption

java.lang.Object
  extended by com.compomics.util.experiment.personalization.ExperimentObject
      extended by com.compomics.util.experiment.identification.PeptideAssumption
All Implemented Interfaces:
Serializable, Cloneable

public class PeptideAssumption
extends ExperimentObject

This object will models the assumption made by an advocate.

Author:
Marc Vaudel, Harald Barsnes
See Also:
Serialized Form

Constructor Summary
PeptideAssumption(Peptide aPeptide, int rank, int advocate, Charge identificationCharge, double score)
          Constructor for a peptide assumption.
PeptideAssumption(Peptide aPeptide, int rank, int advocate, Charge identificationCharge, double score, String identificationFile)
          Constructor for a peptide assumption.
 
Method Summary
 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
addUrParam, getParameterKey, getUrParam
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

PeptideAssumption

public PeptideAssumption(Peptide aPeptide,
                         int rank,
                         int advocate,
                         Charge identificationCharge,
                         double score,
                         String identificationFile)
Constructor for a peptide assumption.

Parameters:
aPeptide - the theoretic peptide
rank - the identification rank
advocate - the advocate used
identificationCharge - the charge used by the search engine for identification
score - 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 file

PeptideAssumption

public PeptideAssumption(Peptide aPeptide,
                         int rank,
                         int advocate,
                         Charge identificationCharge,
                         double score)
Constructor for a peptide assumption.

Parameters:
aPeptide - the theoretic peptide
rank - the identification rank
advocate - the advocate used
identificationCharge - the charge used by the search engine for identification
score - the score (whether the score is ascending or descending can be known from the SearchEngine class)
Method Detail

getRank

public int getRank()
Get the identification rank.

Returns:
the identification rank

getPeptide

public Peptide getPeptide()
Get the theoretic peptide.

Returns:
the peptide

getAdvocate

public int getAdvocate()
Get the used advocate.

Returns:
the advocate index

getDeltaMass

public double getDeltaMass(double measuredMZ,
                           boolean ppm,
                           boolean subtractIsotope)
Returns the precursor mass error (in ppm or Da). Note that the value is returns as (experimental mass - theoretical mass) and that negative values thus can occur. The isotopic error can subtracted and retrieved by the function getIsotopeNumber().

Parameters:
measuredMZ - the precursor m/z
ppm - if true the error is returns in ppm, false returns the error in Da
subtractIsotope - if true the isotope number will be subtracted from the theoretic mass
Returns:
the precursor mass error (in ppm or Da)

getDeltaMass

public double getDeltaMass(double measuredMZ,
                           boolean ppm)
Returns the precursor mass error (in ppm or Da). Note that the value is returns as (experimental mass - theoretical mass) and that negative values thus can occur. The isotopic error is subtracted and can be retrieved by the function getIsotopeNumber().

Parameters:
measuredMZ - the precursor m/z
ppm - if true the error is returns in ppm, false returns the error in Da
Returns:
the precursor mass error (in ppm or Da)

getTheoreticMz

public double getTheoreticMz()
Returns the theoretic m/z expected for this assumption.

Returns:
the theoretic m/z expected for this assumption

getIsotopeNumber

public int getIsotopeNumber(double measuredMZ)
Returns the precursor isotope number according to the number of protons.

Parameters:
measuredMZ -
Returns:
the precursor isotope number according to the number of protons

getEValue

public double getEValue()
Deprecated. use getScore instead

Returns the e-value assigned by the advocate.

Returns:
the e-value

getScore

public double getScore()
Returns the score assigned by the advocate.

Returns:
the score

getFile

public String getFile()
Returns the file.

Returns:
the identification file

getIdentificationCharge

public Charge getIdentificationCharge()
Returns the charge used for identification.

Returns:
the charge used for identification

setRank

public void setRank(int aRank)
Set the rank of the PeptideAssumption.

Parameters:
aRank - the rank of the PeptideAssumptio

getPrecursorMatch

public IonMatch getPrecursorMatch(Peak precursorPeak)
Returns the ion match.

Parameters:
precursorPeak -
Returns:
the ion match


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