com.compomics.util.experiment

Class ShotgunProtocol

java.lang.Object

com.compomics.util.experiment.ShotgunProtocol

All Implemented Interfaces:

Serializable

public class ShotgunProtocol
extends Object
implements Serializable

Generic class gathering information on a shotgun proteomics protocol.

Author:

Marc Vaudel

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
ShotgunProtocol()

Method Summary

Modifier and Type	Method and Description
void	addLabel(String ptmName, boolean complete) Adds a label.
ArrayList<String>	getEnrichedPtms() Returns the PTMs used for enrichment.
Enzyme	getEnzyme() Returns the enzyme used for digestion.
FragmentationMethod	getFragmentationMethod() Returns the fragmentation method.
HashMap<String,Boolean>	getLabellingPtms() Returns the PTMs used for labeling in a map: name of the PTM - boolean indicating whether the labeling is complete.
Double	getMs1Resolution() Returns the MS1 mass resolution.
Double	getMs2Resolution() Returns the MS2 resolution.
static ShotgunProtocol	inferProtocolFromSearchSettings(SearchParameters searchParameters) Backward compatibility inferring the protocol from search settings.
boolean	isMs1ResolutionPpm() Indicates whether the MS1 resolution is in ppm.
boolean	isMs2ResolutionPpm() Indicates whether the MS2 resolution is in ppm.
void	setEnrichedPtms(ArrayList<String> enrichedPtms) Sets the PTMs used for enrichment.
void	setEnzyme(Enzyme enzyme) Sets the enzyme used for digestion.
void	setFragmentationMethod(FragmentationMethod fragmentationMethod) Sets the fragmentation method.
void	setMs1Resolution(Double ms1Resolution) Sets the MS1 mass resolution.
void	setMs1ResolutionPpm(boolean ms1ResolutionPpm) Sets whether the MS1 resolution is in ppm.
void	setMs2Resolution(Double ms2Resolution) Sets the MS2 resolution.
void	setMs2ResolutionPpm(boolean ms2ResolutionPpm) Sets whether the MS2 resolution is in ppm.

Methods inherited from class java.lang.Object

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

Constructor Detail

ShotgunProtocol

public ShotgunProtocol()

Method Detail

getEnzyme

public Enzyme getEnzyme()

Returns the enzyme used for digestion.

Returns:

the enzyme used for digestion

setEnzyme

public void setEnzyme(Enzyme enzyme)

Sets the enzyme used for digestion.

Parameters:

enzyme - the enzyme used for digestion

getEnrichedPtms

public ArrayList<String> getEnrichedPtms()

Returns the PTMs used for enrichment. Null if no enrichment.

Returns:

the PTMs used for enrichment

setEnrichedPtms

public void setEnrichedPtms(ArrayList<String> enrichedPtms)

Sets the PTMs used for enrichment.

Parameters:

enrichedPtms - the PTMs used for enrichment

getMs1Resolution

public Double getMs1Resolution()

Returns the MS1 mass resolution.

Returns:

the MS1 mass resolution

setMs1Resolution

public void setMs1Resolution(Double ms1Resolution)

Sets the MS1 mass resolution.

Parameters:

ms1Resolution - the MS1 mass resolution

isMs1ResolutionPpm

public boolean isMs1ResolutionPpm()

Indicates whether the MS1 resolution is in ppm.

Returns:

a boolean indicating whether the MS1 resolution is in ppm

setMs1ResolutionPpm

public void setMs1ResolutionPpm(boolean ms1ResolutionPpm)

Sets whether the MS1 resolution is in ppm.

Parameters:

ms1ResolutionPpm - a boolean indicating whether the MS1 resolution is in ppm

getFragmentationMethod

public FragmentationMethod getFragmentationMethod()

Returns the fragmentation method.

Returns:

the fragmentation method

setFragmentationMethod

public void setFragmentationMethod(FragmentationMethod fragmentationMethod)

Sets the fragmentation method.

Parameters:

fragmentationMethod - the fragmentation method

getMs2Resolution

public Double getMs2Resolution()

Returns the MS2 resolution.

Returns:

the MS2 resolution

setMs2Resolution

public void setMs2Resolution(Double ms2Resolution)

Sets the MS2 resolution.

Parameters:

ms2Resolution - the MS2 resolution

isMs2ResolutionPpm

public boolean isMs2ResolutionPpm()

Indicates whether the MS2 resolution is in ppm.

Returns:

a boolean indicating whether the MS2 resolution is in ppm

setMs2ResolutionPpm

public void setMs2ResolutionPpm(boolean ms2ResolutionPpm)

Sets whether the MS2 resolution is in ppm.

Parameters:

ms2ResolutionPpm - a boolean indicating whether the MS2 resolution is in ppm

addLabel

public void addLabel(String ptmName,
                     boolean complete)

Adds a label.

Parameters:

ptmName - the name of the modification used for the label

complete - boolean indicating whether the labeling is complete (true) or partial (false)

getLabellingPtms

public HashMap<String,Boolean> getLabellingPtms()

Returns the PTMs used for labeling in a map: name of the PTM - boolean indicating whether the labeling is complete.

Returns:

the PTMs used for labeling

inferProtocolFromSearchSettings

public static ShotgunProtocol inferProtocolFromSearchSettings(SearchParameters searchParameters)

Backward compatibility inferring the protocol from search settings.

Parameters:

searchParameters - the search settings where to take the information from

Returns:

the inferred protocol