Package | Description |
---|---|
com.compomics.util.experiment.identification.identification_parameters |
Parameters settings for the spectrum identification algorithms.
|
com.compomics.util.experiment.identification.identification_parameters.tool_specific |
Parameters settings for the search algorithms.
|
com.compomics.util.gui.parameters.identification_parameters |
GUI classes for parameters, settings and preferences used for identification.
|
com.compomics.util.gui.parameters.identification_parameters.algorithm_settings |
Search algorithm settings dialogs.
|
Modifier and Type | Method and Description |
---|---|
IdentificationAlgorithmParameter |
SearchParameters.getIdentificationAlgorithmParameter(int algorithmID)
Returns the algorithm specific parameters, null if not found.
|
Modifier and Type | Method and Description |
---|---|
HashMap<Integer,IdentificationAlgorithmParameter> |
SearchParameters.getAlgorithmSpecificParameters()
Returns the algorithm specific parameters in a map: algorithm as indexed
in the Advocate class > parameters.
|
Modifier and Type | Method and Description |
---|---|
boolean |
IdentificationAlgorithmParameter.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
Indicates whether another identificationAlgorithmParameter has the same
parameters.
|
void |
SearchParameters.setIdentificationAlgorithmParameter(int algorithmID,
IdentificationAlgorithmParameter identificationAlgorithmParameter)
Adds identification algorithm specific parameters.
|
Modifier and Type | Class and Description |
---|---|
class |
AndromedaParameters
The Andromeda specific parameters.
|
class |
CometParameters
The Comet specific parameters.
|
class |
DirecTagParameters
The DirecTag 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 |
TideParameters
The Tide specific parameters.
|
class |
XtandemParameters
The X!Tandem specific parameters.
|
Modifier and Type | Method and Description |
---|---|
boolean |
XtandemParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter) |
boolean |
TideParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter) |
boolean |
PNovoParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter) |
boolean |
PepnovoParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter) |
boolean |
OmssaParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter) |
boolean |
NovorParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter) |
boolean |
MyriMatchParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter) |
boolean |
MsgfParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter) |
boolean |
MsAmandaParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter) |
boolean |
DirecTagParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter) |
boolean |
CometParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter) |
boolean |
AndromedaParameters.equals(IdentificationAlgorithmParameter identificationAlgorithmParameter) |
Modifier and Type | Method and Description |
---|---|
IdentificationAlgorithmParameter |
AlgorithmSettingsDialog.getParameters()
Returns the parameters as set by the user.
|
Modifier and Type | Method and Description |
---|---|
AlgorithmSettingsDialog |
SpectrumMatchingSettingsDialog.getAlgorithmSettingsDialog(IdentificationAlgorithmParameter identificationAlgorithmParameter)
Returns the dialog to use to edit the given parameters.
|
Modifier and Type | Method and Description |
---|---|
IdentificationAlgorithmParameter |
XTandemSettingsDialog.getParameters() |
IdentificationAlgorithmParameter |
TideSettingsDialog.getParameters() |
IdentificationAlgorithmParameter |
PNovoSettingsDialog.getParameters() |
IdentificationAlgorithmParameter |
OmssaSettingsDialog.getParameters() |
IdentificationAlgorithmParameter |
NovorSettingsDialog.getParameters() |
IdentificationAlgorithmParameter |
MyriMatchSettingsDialog.getParameters() |
IdentificationAlgorithmParameter |
MsgfSettingsDialog.getParameters() |
IdentificationAlgorithmParameter |
MsAmandaSettingsDialog.getParameters() |
IdentificationAlgorithmParameter |
DirecTagSettingsDialog.getParameters() |
IdentificationAlgorithmParameter |
CometSettingsDialog.getParameters() |
IdentificationAlgorithmParameter |
AndromedaSettingsDialog.getParameters() |
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