Package com.compomics.util.experiment.identification.spectrum_annotation

Class NeutralLossesMap

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap

All Implemented Interfaces:

Serializable

public class NeutralLossesMap
extends ExperimentObject

This class contains the informations relative to the accounting of neutral losses

Author:

Marc Vaudel

See Also:

• Serialized Form

Field Summary

Fields inherited from class com.compomics.util.experiment.personalization.ExperimentObject

NO_KEY

Constructor Summary

Constructors

Constructor	Description
NeutralLossesMap()	Constructor.

Method Summary

Modifier and Type	Method	Description
void	addNeutralLoss(NeutralLoss neutralLoss, int bStart, int yStart)	Adds a new neutral loss to the map.
void	addNeutralLoss(String neutralLossName, int bStart, int yStart)	Adds a new neutral loss to the map.
void	clearNeutralLosses()	Clears the mapping.
NeutralLossesMap	clone()
boolean	containsLoss(String neutralLossName)	Returns a boolean indicating whether a loss is implemented in the mapping.
ArrayList<String>	getAccountedNeutralLosses()	Returns an arraylist of the names of the implemented neutral losses.
Integer	getForwardStart(String neutralLossName)	Returns the amino acid where a neutral loss should start being accounted for when predicting b ions (counting from N-terminus, first aa is 1).
int	getRewindStart(String neutralLossName)	Returns the amino acid where a neutral loss should start being accounted for when predicting b ions (counting from N-terminus, first aa is 1).
boolean	isEmpty()	Returns a boolean indicating if the mapping is empty.
void	makeSequenceIndependant()	Makes the neutral losses sequence independent.

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject

addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

NeutralLossesMap

public NeutralLossesMap()

Constructor.

Method Details

addNeutralLoss

public void addNeutralLoss(NeutralLoss neutralLoss,
 int bStart,
 int yStart)

Adds a new neutral loss to the map.

Parameters:

neutralLoss - the new neutral loss

bStart - the amino acid position where the neutral loss should start being accounted starting from the N-terminus (first is 1)

yStart - the amino acid position where the neutral loss should start being accounted starting from the C-terminus (first is 1)

addNeutralLoss

public void addNeutralLoss(String neutralLossName,
 int bStart,
 int yStart)

Adds a new neutral loss to the map.

Parameters:

neutralLossName - the new neutral loss name

bStart - the amino acid position where the neutral loss should start being accounted starting from the N-terminus (first is 1)

yStart - the amino acid position where the neutral loss should start being accounted starting from the C-terminus (first is 1)

clearNeutralLosses

public void clearNeutralLosses()

Clears the mapping.

makeSequenceIndependant

public void makeSequenceIndependant()

Makes the neutral losses sequence independent.

isEmpty

public boolean isEmpty()

Returns a boolean indicating if the mapping is empty.

Returns:

a boolean indicating if the mapping is empty

getAccountedNeutralLosses

public ArrayList<String> getAccountedNeutralLosses()

Returns an arraylist of the names of the implemented neutral losses.

Returns:

an arraylist of the names of the implemented neutral losses

getForwardStart

public Integer getForwardStart(String neutralLossName)

Returns the amino acid where a neutral loss should start being accounted for when predicting b ions (counting from N-terminus, first aa is 1).

Parameters:

neutralLossName - the name of the neutral loss of interest

Returns:

the first amino acid where to account for the neutral loss

getRewindStart

public int getRewindStart(String neutralLossName)

Returns the amino acid where a neutral loss should start being accounted for when predicting b ions (counting from N-terminus, first aa is 1).

Parameters:

neutralLossName - the name of the neutral loss of interest

Returns:

the first amino acid where to account for the neutral loss

containsLoss

public boolean containsLoss(String neutralLossName)

Returns a boolean indicating whether a loss is implemented in the mapping.

Parameters:

neutralLossName - the name of the neutral loss of interest

Returns:

a boolean indicating whether a loss is implemented in the mapping

clone

public NeutralLossesMap clone()

Overrides:

clone in class Object