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, double measuredMass, double eValue, String identificationFile)
          Constructor for a peptide assumption
 
Method Summary
 void addAnnotation(IonMatch ionMatch)
          add a fragment ion annotation
 int getAdvocate()
          get the used advocate
 HashSet<IonMatch> getAnnotations()
          retrieves all fragment ion annotation
 int getC13()
          Returns the number of 1Da intervals between the measured mass and the theoretical mass
 double getDeltaMass(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
 double getMeasuredMass()
          Returns the measured precursor mass according to the search engine
 Peptide getPeptide()
          get the theoretic peptide
 int getRank()
          Get the identification rank
 boolean isDecoy()
          is the identification decoy?
 
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,
                         double measuredMass,
                         double eValue,
                         String identificationFile)
Constructor for a peptide assumption

Parameters:
aPeptide - the theoretic peptide
rank - the identification rank
advocate - the advocate used
measuredMass - the precursor measured mass
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

getMeasuredMass

public double getMeasuredMass()
Returns the measured precursor mass according to the search engine

Returns:
the measured precursor mass according to the search engine

getC13

public int getC13()
Returns the number of 1Da intervals between the measured mass and the theoretical mass

Returns:
the number of 1Da intervals between the measured mass and the theoretical mass

getDeltaMass

public double getDeltaMass(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.

Parameters:
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

addAnnotation

public void addAnnotation(IonMatch ionMatch)
add a fragment ion annotation

Parameters:
ionMatch - an ion match

getAnnotations

public HashSet<IonMatch> getAnnotations()
retrieves all fragment ion annotation

Returns:
all fragment ion annotations

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


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