Uses of Package
com.compomics.util.preferences

Packages that use com.compomics.util.preferences
com.compomics.software.dialogs   
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.gui.gene_mapping   
com.compomics.util.gui.spectrum This package contains GUI classes related to Spectrum and Chromatogram visualization. 
com.compomics.util.preferences   
com.compomics.util.preferences.gui   
 

Classes in com.compomics.util.preferences used by com.compomics.software.dialogs
UtilitiesUserPreferences
          Utilities user preferences will be serialized in the user folder and provide useful information to all compomics software, well as soon as they use it of course.
 

Classes in com.compomics.util.preferences used by com.compomics.util.experiment.biology
ModificationProfile
          This class stores the information about the modification preferences (colors, names) used for the selected project.
 

Classes in com.compomics.util.preferences used by com.compomics.util.experiment.identification
ModificationProfile
          This class stores the information about the modification preferences (colors, names) used for the selected project.
 

Classes in com.compomics.util.preferences used by com.compomics.util.gui.gene_mapping
GenePreferences
          Contains methods for downloading gene and GO mappings.
 

Classes in com.compomics.util.preferences used by com.compomics.util.gui.spectrum
ModificationProfile
          This class stores the information about the modification preferences (colors, names) used for the selected project.
 

Classes in com.compomics.util.preferences used by com.compomics.util.preferences
GenePreferences
          Contains methods for downloading gene and GO mappings.
IdFilter
          This class achieves a pre-filtering of the identifications for PeptideShaker.
ModificationProfile
          This class stores the information about the modification preferences (colors, names) used for the selected project.
UtilitiesUserPreferences
          Utilities user preferences will be serialized in the user folder and provide useful information to all compomics software, well as soon as they use it of course.
 

Classes in com.compomics.util.preferences used by com.compomics.util.preferences.gui
IdFilter
          This class achieves a pre-filtering of the identifications for PeptideShaker.
ProcessingPreferences
          This class groups the user preferences for the initial PeptideShaker processing.
PTMScoringPreferences
          This class contains the PTM scoring preferences.
 



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