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 eValue, String identificationFile)
          Constructor for a peptide assumption.
 
Method Summary
 int getAdvocate()
          Get the used advocate.
 int getC13(double measuredMZ)
          Returns the distance in Da between the experimental mass and theoretic mass, image of the error between the precursor mass and the peptide monoisotopic mass (typically for the C13 option).
 double getDeltaMass(double measuredMZ, boolean ppm)
          Returns the precursor mass error (in ppm or Da).
 double getEValue()
          Returns the e-value assigned by the advocate.
 String getFile()
          Returns the file.
 Charge getIdentificationCharge()
          Returns the charge used for identification.
 Peptide getPeptide()
          Get the theoretic peptide.
 IonMatch getPrecursorMatch(Peak precursorPeak)
          Returns the ion match.
 int getRank()
          Get the identification rank.
 boolean isDecoy()
          Is the identification decoy?
 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 eValue,
                         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
eValue - the e-value
identificationFile - the identification file
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

getC13

public int getC13(double measuredMZ)
Returns the distance in Da between the experimental mass and theoretic mass, image of the error between the precursor mass and the peptide monoisotopic mass (typically for the C13 option).

Parameters:
measuredMZ - the precursor m/z
Returns:
the distance in Da between the experimental mass and theoretic mass

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. If an error of more than 1 Da it will be substracted from the error. The C13 error can be retrieved by the function getC13().

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)

getEValue

public double getEValue()
Returns the e-value assigned by the advocate.

Returns:
the e-value

getFile

public String getFile()
Returns the file.

Returns:
the idenitfication file

isDecoy

public boolean isDecoy()
Is the identification decoy?

Returns:
a boolean indicating if the identification is a decoy one

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.


getPrecursorMatch

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

Parameters:
precursorPeak -
Returns:
the ion match


Copyright © 2012. All Rights Reserved.