Uses of Class
com.compomics.util.experiment.identification.SearchParameters

Packages that use SearchParameters
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.gui.searchsettings   
com.compomics.util.preferences   
com.compomics.util.pride   
 

Uses of SearchParameters in com.compomics.util.experiment.biology
 

Methods in com.compomics.util.experiment.biology with parameters of type SearchParameters
 ArrayList<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.
 

Uses of SearchParameters in com.compomics.util.experiment.identification
 

Methods in com.compomics.util.experiment.identification that return SearchParameters
static SearchParameters SearchParameters.getIdentificationParameters(File file)
          Loads the identification parameters from a serialized file.
 SearchParameters SearchParametersInputBean.getSearchParameters()
          Returns the search parameters.
 

Methods in com.compomics.util.experiment.identification with parameters of type SearchParameters
 boolean SearchParameters.equals(SearchParameters otherSearchParameters)
          Returns true of the search parameter objects have identical settings.
static void SearchParameters.saveIdentificationParameters(SearchParameters identificationParameters, File file)
          Saves the identification parameters to a serialized file.
 

Uses of SearchParameters in com.compomics.util.experiment.io.identifications
 

Methods in com.compomics.util.experiment.io.identifications that return SearchParameters
static SearchParameters IdentificationParametersReader.getSearchParameters(Properties aProps, File userModsFile)
          Deprecated. Conversion methods which converts an old school set of identification properties into a SearchParameters instance.
 

Uses of SearchParameters in com.compomics.util.gui.searchsettings
 

Methods in com.compomics.util.gui.searchsettings that return SearchParameters
 SearchParameters SearchSettingsDialogParent.getSearchParameters()
          Returns the search parameters.
 SearchParameters SearchSettingsDialog.getSearchParameters()
          Returns a SearchParameters instance based on the user input in the GUI.
 

Methods in com.compomics.util.gui.searchsettings with parameters of type SearchParameters
 void SearchSettingsDialogParent.setSearchParameters(SearchParameters searchParameters)
          Set the search parameters.
 

Constructors in com.compomics.util.gui.searchsettings with parameters of type SearchParameters
SearchSettingsDialog(JFrame parentFrame, SearchSettingsDialogParent searchSettingsDialogParent, SearchParameters searchParameters, Image normalIcon, Image waitingIcon, boolean setVisible, boolean modal)
          Creates a new SearchSettingsDialog.
 

Uses of SearchParameters in com.compomics.util.preferences
 

Methods in com.compomics.util.preferences with parameters of type SearchParameters
 void AnnotationPreferences.setPreferencesFromSearchParamaers(SearchParameters searchParameters)
          Updates the annotation parameters based on the search parameters
 

Uses of SearchParameters in com.compomics.util.pride
 

Methods in com.compomics.util.pride with parameters of type SearchParameters
static PtmToPrideMap PtmToPrideMap.loadPtmToPrideMap(SearchParameters searchParameters)
          Loads the PRIDE to PTM map from the user folder or creates a new one if the file is not present.
 



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