Package | Description |
---|---|
com.compomics.util.experiment.biology |
This package contains experiement classes related to biological entities.
|
com.compomics.util.experiment.identification |
This package contains experiment classes related to identifications.
|
com.compomics.util.experiment.io.identifications | |
com.compomics.util.preferences |
Modifier and Type | Method and Description |
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java.util.ArrayList<java.lang.String> |
PTMFactory.loadBackedUpModifications(SearchParameters searchParameters,
boolean overwrite)
Verifies that the modifications backed-up in the search parameters are
loaded and alerts the user in case conflicts are found.
|
Modifier and Type | Method and Description |
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static SearchParameters |
SearchParameters.getIdentificationParameters(java.io.File file)
Loads the identification parameters from a serialized file.
|
Modifier and Type | Method and Description |
---|---|
boolean |
SearchParameters.equals(SearchParameters otherSearchParameters)
Returns true of the search parameter objects have identical settings.
|
static void |
SearchParameters.saveIdentificationParameters(SearchParameters identificationParameters,
java.io.File file)
Saves the identification parameters to a serialized file.
|
Modifier and Type | Method and Description |
---|---|
static SearchParameters |
IdentificationParametersReader.getSearchParameters(java.util.Properties aProps,
java.io.File userModsFile)
Deprecated.
Conversion methods which converts an old school set of identification
properties into a SearchParameters instance.
|
Modifier and Type | Method and Description |
---|---|
void |
AnnotationPreferences.setPreferencesFromSearchParamaers(SearchParameters searchParameters)
Updates the annotation parameters based on the search parameters
|
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