Uses of Package
com.compomics.util.preferences

Packages that use com.compomics.util.preferences

Package	Description
com.compomics.software.dialogs	Dialogs for starting compomics-utilities tools and setting their Java options.
com.compomics.util.experiment.biology	Experiment classes related to biological entities.
com.compomics.util.experiment.biology.genes	Classes related to genes.
com.compomics.util.experiment.identification	Experiment classes related to identifications.
com.compomics.util.experiment.identification.amino_acid_tags	Amino Acid Tag classes.
com.compomics.util.experiment.identification.amino_acid_tags.matchers	Tag matching classes.
com.compomics.util.experiment.identification.filtering	Classes for the filtering of identification objects.
com.compomics.util.experiment.identification.identification_parameters	Parameters settings for the spectrum identification algorithms.
com.compomics.util.experiment.identification.matches	Experiment classes related to matches.
com.compomics.util.experiment.identification.parameters_cli	Identification search parameters.
com.compomics.util.experiment.identification.protein_inference.proteintree	Protein sequence database indexing classes.
com.compomics.util.experiment.identification.psm_scoring	Main PSM scoring class.
com.compomics.util.experiment.identification.ptm.ptmscores	PTM scores.
com.compomics.util.experiment.identification.spectrum_annotation	Classes used for ms2 spectrum annotation.
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators	Spectrum annotation.
com.compomics.util.experiment.io.identifications	Experiment identification classes.
com.compomics.util.experiment.io.identifications.idfilereaders	Experiment classes related to reading search engine files.
com.compomics.util.gui	Basic GUI classes.
com.compomics.util.gui.error_handlers	Help handlers.
com.compomics.util.gui.export.graphics	Exporting of graphics.
com.compomics.util.gui.parameters	GUI classes for parameters, settings and preferences.
com.compomics.util.gui.parameters.identification_parameters	GUI classes for parameters, settings and preferences used for identification.
com.compomics.util.preferences	Utilities preferences classes.
com.compomics.util.protein_sequences_manager.gui	GUI classes used for the management of FASTA files.

Classes in com.compomics.util.preferences used by com.compomics.software.dialogs

Class and Description
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

Class and Description
SequenceMatchingPreferences The sequence matching options.

Classes in com.compomics.util.preferences used by com.compomics.util.experiment.biology.genes

Class and Description
GenePreferences Contains methods for downloading gene and GO mappings.

Classes in com.compomics.util.preferences used by com.compomics.util.experiment.identification

Class and Description
SequenceMatchingPreferences The sequence matching options.

Classes in com.compomics.util.preferences used by com.compomics.util.experiment.identification.amino_acid_tags

Class and Description
SequenceMatchingPreferences The sequence matching options.

Classes in com.compomics.util.preferences used by com.compomics.util.experiment.identification.amino_acid_tags.matchers

Class and Description
SequenceMatchingPreferences The sequence matching options.

Classes in com.compomics.util.preferences used by com.compomics.util.experiment.identification.filtering

Class and Description
SequenceMatchingPreferences The sequence matching options.

Classes in com.compomics.util.preferences used by com.compomics.util.experiment.identification.identification_parameters

Class and Description
IdentificationParameters Generic class grouping the parameters used for protein identification.
MarshallableParameter Interface for a parameter which can be marshalled as .par file.
MarshallableParameter.Type Enum of the type of parameter which can be encountered in a .par file.

Classes in com.compomics.util.preferences used by com.compomics.util.experiment.identification.matches

Class and Description
SequenceMatchingPreferences The sequence matching options.

Classes in com.compomics.util.preferences used by com.compomics.util.experiment.identification.parameters_cli

Class and Description
IdentificationParameters Generic class grouping the parameters used for protein identification.

Classes in com.compomics.util.preferences used by com.compomics.util.experiment.identification.protein_inference.proteintree

Class and Description
SequenceMatchingPreferences The sequence matching options.

Classes in com.compomics.util.preferences used by com.compomics.util.experiment.identification.psm_scoring

Class and Description
IdentificationParameters Generic class grouping the parameters used for protein identification.

Classes in com.compomics.util.preferences used by com.compomics.util.experiment.identification.ptm.ptmscores

Class and Description
SequenceMatchingPreferences The sequence matching options.

Classes in com.compomics.util.preferences used by com.compomics.util.experiment.identification.spectrum_annotation

Class and Description
SequenceMatchingPreferences The sequence matching options.

Classes in com.compomics.util.preferences used by com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators

Class and Description
SequenceMatchingPreferences The sequence matching options.

Classes in com.compomics.util.preferences used by com.compomics.util.experiment.io.identifications

Class and Description
SequenceMatchingPreferences The sequence matching options.

Classes in com.compomics.util.preferences used by com.compomics.util.experiment.io.identifications.idfilereaders

Class and Description
SequenceMatchingPreferences The sequence matching options.

Classes in com.compomics.util.preferences used by com.compomics.util.gui

Class and Description
LastSelectedFolder Convenience class keeping class of the last selected folders.

Classes in com.compomics.util.preferences used by com.compomics.util.gui.error_handlers

Class and Description
LastSelectedFolder Convenience class keeping class of the last selected folders.

Classes in com.compomics.util.preferences used by com.compomics.util.gui.export.graphics

Class and Description
LastSelectedFolder Convenience class keeping class of the last selected folders.

Classes in com.compomics.util.preferences used by com.compomics.util.gui.parameters

Class and Description
IdentificationParameters Generic class grouping the parameters used for protein identification.
LastSelectedFolder Convenience class keeping class of the last selected folders.
ProcessingPreferences ProcessingPreferences.
PSProcessingPreferences Deprecated. replaced by utilities processing preferences and fraction preferences

Classes in com.compomics.util.preferences used by com.compomics.util.gui.parameters.identification_parameters

Class and Description
FractionSettings Settings for the handling of fractions.
GenePreferences Contains methods for downloading gene and GO mappings.
IdentificationParameters Generic class grouping the parameters used for protein identification.
IdMatchValidationPreferences Generic class grouping the identification matches validation preferences.
LastSelectedFolder Convenience class keeping class of the last selected folders.
ProteinInferencePreferences Generic class grouping the protein inference preferences.
PsmScoringPreferences Generic class for peptide spectrum match scoring.
PTMScoringPreferences This class contains the PTM localization scoring preferences.
SequenceMatchingPreferences The sequence matching options.
ValidationQCPreferences This class lists the criteria used for quality control of the validated matches.

Classes in com.compomics.util.preferences used by com.compomics.util.preferences

Class and Description
FractionSettings Settings for the handling of fractions.
GenePreferences Contains methods for downloading gene and GO mappings.
IdentificationParameters Generic class grouping the parameters used for protein identification.
IdMatchValidationPreferences Generic class grouping the identification matches validation preferences.
LastSelectedFolder Convenience class keeping class of the last selected folders.
MarshallableParameter Interface for a parameter which can be marshalled as .par file.
MarshallableParameter.Type Enum of the type of parameter which can be encountered in a .par file.
ProcessingPreferences.ProcessingType Class indicating the type of processing.
ProteinInferencePreferences Generic class grouping the protein inference preferences.
PsmScoringPreferences Generic class for peptide spectrum match scoring.
PTMScoringPreferences This class contains the PTM localization scoring preferences.
SearchGuiOutputOption This enum lists the possible output options.
SequenceMatchingPreferences The sequence matching options.
SequenceMatchingPreferences.MatchingType The different types of amino acid matching.
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.
ValidationQCPreferences This class lists the criteria used for quality control of the validated matches.

Classes in com.compomics.util.preferences used by com.compomics.util.protein_sequences_manager.gui

Class and Description
LastSelectedFolder Convenience class keeping class of the last selected folders.