com.compomics.util.experiment.identification.identification_parameters.tool_specific

Class NovorParameters

java.lang.Object

com.compomics.util.experiment.identification.identification_parameters.tool_specific.NovorParameters

All Implemented Interfaces:

IdentificationAlgorithmParameter, Serializable

public class NovorParameters
extends Object
implements IdentificationAlgorithmParameter

Novor specific parameters.

Author:

Harald Barsnes

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
NovorParameters() Constructor.

Method Summary

Modifier and Type	Method and Description
boolean	equals(IdentificationAlgorithmParameter identificationAlgorithmParameter) Indicates whether another identificationAlgorithmParameter has the same parameters.
Advocate	getAlgorithm() Returns the identification algorithm.
String	getFragmentationMethod() Returns the fragmentation method.
String	getMassAnalyzer() Returns the mass analyzer.
HashMap<String,String>	getNovorPtmMap() Returns the Novor to utilities PTM map.
String	getUtilitiesPtmName(String novorPtmShortName) Returns the utilities PTM name corresponding to the given Novor PTM short name.
void	setFragmentationMethod(String fragmentationMethod) Set the fragmentation method.
void	setMassAnalyzer(String massAnalyzer) Set the mass analyzer.
void	setNovorPtmMap(HashMap<String,String> novorPtmMap) Set the Novor to utilities PTM map.
String	toString(boolean html) Returns the parameters as a string.

Methods inherited from class java.lang.Object

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

Constructor Detail

NovorParameters

public NovorParameters()

Constructor.

Method Detail

getAlgorithm

public Advocate getAlgorithm()

Description copied from interface: IdentificationAlgorithmParameter

Returns the identification algorithm.

Specified by:

getAlgorithm in interface IdentificationAlgorithmParameter

Returns:

the identification algorithm

equals

public boolean equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)

Description copied from interface: IdentificationAlgorithmParameter

Indicates whether another identificationAlgorithmParameter has the same parameters.

Specified by:

equals in interface IdentificationAlgorithmParameter

Parameters:

identificationAlgorithmParameter - the other identificationAlgorithmParameter

Returns:

true if the algorithm and parameters are the same

toString

public String toString(boolean html)

Description copied from interface: IdentificationAlgorithmParameter

Returns the parameters as a string.

Specified by:

toString in interface IdentificationAlgorithmParameter

Parameters:

html - use HTML formatting

Returns:

the parameters as a string

getFragmentationMethod

public String getFragmentationMethod()

Returns the fragmentation method.

Returns:

the fragmentation method

setFragmentationMethod

public void setFragmentationMethod(String fragmentationMethod)

Set the fragmentation method.

Parameters:

fragmentationMethod - the fragmentation method to set

getMassAnalyzer

public String getMassAnalyzer()

Returns the mass analyzer.

Returns:

the mass analyzer

setMassAnalyzer

public void setMassAnalyzer(String massAnalyzer)

Set the mass analyzer.

Parameters:

massAnalyzer - the mass analyzer to set

getNovorPtmMap

public HashMap<String,String> getNovorPtmMap()

Returns the Novor to utilities PTM map. Null if not set.

Returns:

the Novor to utilities PTM map, null if not set

setNovorPtmMap

public void setNovorPtmMap(HashMap<String,String> novorPtmMap)

Set the Novor to utilities PTM map.

Parameters:

novorPtmMap - the novorPtmMap to set

getUtilitiesPtmName

public String getUtilitiesPtmName(String novorPtmShortName)

Returns the utilities PTM name corresponding to the given Novor PTM short name. Null if not found.

Parameters:

novorPtmShortName - the Novor PTM short name

Returns:

the utilities PTM name