Uses of Interface
com.compomics.util.gui.parameters.identification.IdentificationAlgorithmParameter

Packages that use IdentificationAlgorithmParameter

Package	Description
com.compomics.util.gui.parameters.identification	GUI classes for parameters, settings and preferences used for identification.
com.compomics.util.gui.parameters.identification.algorithm	Search algorithm settings dialogs.
com.compomics.util.parameters.identification.search	Identification parameters relative to the search.
com.compomics.util.parameters.identification.tool_specific	Parameters settings for the search algorithms.

Uses of IdentificationAlgorithmParameter in com.compomics.util.gui.parameters.identification

Methods in com.compomics.util.gui.parameters.identification that return IdentificationAlgorithmParameter

Modifier and Type	Method	Description
IdentificationAlgorithmParameter	AlgorithmParametersDialog.getParameters()	Returns the parameters as set by the user.

Methods in com.compomics.util.gui.parameters.identification with parameters of type IdentificationAlgorithmParameter

Modifier and Type	Method	Description
boolean	IdentificationAlgorithmParameter.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)	Indicates whether another identificationAlgorithmParameter has the same parameters.

Uses of IdentificationAlgorithmParameter in com.compomics.util.gui.parameters.identification.algorithm

Methods in com.compomics.util.gui.parameters.identification.algorithm that return IdentificationAlgorithmParameter

Modifier and Type	Method	Description
IdentificationAlgorithmParameter	AndromedaParametersDialog.getParameters()
IdentificationAlgorithmParameter	CometParametersDialog.getParameters()
IdentificationAlgorithmParameter	DirecTagParametersDialog.getParameters()
IdentificationAlgorithmParameter	MetaMorpheusParametersDialog.getParameters()
IdentificationAlgorithmParameter	MsAmandaParametersDialog.getParameters()
IdentificationAlgorithmParameter	MsgfParametersDialog.getParameters()
IdentificationAlgorithmParameter	MyriMatchParametersDialog.getParameters()
IdentificationAlgorithmParameter	NovorParametersDialog.getParameters()
IdentificationAlgorithmParameter	OmssaParametersDialog.getParameters()
IdentificationAlgorithmParameter	PepNovoParametersDialog.getParameters()
IdentificationAlgorithmParameter	PNovoParametersDialog.getParameters()
IdentificationAlgorithmParameter	SageParametersDialog.getParameters()
IdentificationAlgorithmParameter	TideParametersDialog.getParameters()
IdentificationAlgorithmParameter	XTandemParametersDialog.getParameters()

Uses of IdentificationAlgorithmParameter in com.compomics.util.parameters.identification.search

Methods in com.compomics.util.parameters.identification.search that return IdentificationAlgorithmParameter

Modifier and Type	Method	Description
IdentificationAlgorithmParameter	SearchParameters.getIdentificationAlgorithmParameter(int algorithmID)	Returns the algorithm specific parameters, null if not found.

Methods in com.compomics.util.parameters.identification.search that return types with arguments of type IdentificationAlgorithmParameter

Modifier and Type	Method	Description
HashMap<Integer,IdentificationAlgorithmParameter>	SearchParameters.getAlgorithmSpecificParameters()	Returns the algorithm specific parameters in a map: algorithm as indexed in the Advocate class > parameters.

Methods in com.compomics.util.parameters.identification.search with parameters of type IdentificationAlgorithmParameter

Modifier and Type	Method	Description
void	SearchParameters.setIdentificationAlgorithmParameter(int algorithmID, IdentificationAlgorithmParameter identificationAlgorithmParameter)	Adds identification algorithm specific parameters.

Uses of IdentificationAlgorithmParameter in com.compomics.util.parameters.identification.tool_specific

Classes in com.compomics.util.parameters.identification.tool_specific that implement IdentificationAlgorithmParameter

Modifier and Type	Class	Description
class	AndromedaParameters	The Andromeda specific parameters.
class	CometParameters	The Comet specific parameters.
class	DirecTagParameters	The DirecTag specific parameters.
class	MetaMorpheusParameters	The MetaMorpheus specific parameters.
class	MsAmandaParameters	The MS Amanda specific parameters.
class	MsgfParameters	The MS-GF+ specific parameters.
class	MyriMatchParameters	The MyriMatch specific parameters.
class	NovorParameters	Novor specific parameters.
class	OmssaParameters	The OMSSA specific parameters.
class	PepnovoParameters	PepNovo specific parameters.
class	PNovoParameters	pNovo specific parameters.
class	SageParameters	The Sage specific parameters.
class	TideParameters	The Tide specific parameters.
class	XtandemParameters	The X!Tandem specific parameters.

Methods in com.compomics.util.parameters.identification.tool_specific with parameters of type IdentificationAlgorithmParameter

Modifier and Type	Method	Description
boolean	AndromedaParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
boolean	CometParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
boolean	DirecTagParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
boolean	MetaMorpheusParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
boolean	MsAmandaParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
boolean	MsgfParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
boolean	MyriMatchParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
boolean	NovorParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
boolean	OmssaParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
boolean	PepnovoParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
boolean	PNovoParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
boolean	SageParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
boolean	TideParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
boolean	XtandemParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)