Uses of Package
com.compomics.util.experiment.biology.modifications

Packages that use com.compomics.util.experiment.biology.modifications

Package	Description
com.compomics.cli.modifications	Command line for the handling of modifications.
com.compomics.util.experiment.biology.modifications
com.compomics.util.experiment.biology.proteins	Classes related to proteins.
com.compomics.util.experiment.identification.amino_acid_tags	Amino Acid Tag classes.
com.compomics.util.experiment.identification.modification	Modification mapping and localization.
com.compomics.util.experiment.identification.modification.mapping	Mapping between search engine and Utilities modifications.
com.compomics.util.experiment.identification.modification.scores	PTM scores.
com.compomics.util.experiment.identification.modification.search_engine_mapping	Mapping between search engine and Utilities modifications.
com.compomics.util.experiment.identification.peptide_inference	Classes related to peptide inference.
com.compomics.util.experiment.identification.protein_inference.fm_index	Protein sequence database indexing classes based on Burrows-Wheeler transform.
com.compomics.util.experiment.identification.utils	This package contains utilities classes to handle identification objects.
com.compomics.util.experiment.io.identification.writers	Writer for identification results.
com.compomics.util.experiment.io.parameters	Experiment IO classes relative to the handling of parameters.
com.compomics.util.gui.modification	PTM GUI dialogs.
com.compomics.util.parameters.identification.search	Identification parameters relative to the search.
com.compomics.util.parameters.identification.tool_specific	Parameters settings for the search algorithms.

Classes in com.compomics.util.experiment.biology.modifications used by com.compomics.cli.modifications

Class	Description
Modification	This class models a peptide or protein modification.

Classes in com.compomics.util.experiment.biology.modifications used by com.compomics.util.experiment.biology.modifications

Class	Description
Modification	This class models a peptide or protein modification.
ModificationCategory	Enum for the different modification categories supported.
ModificationFactory	This factory will load Modification from an XML file and provide them on demand as standard class.
ModificationProvider	Interface for a modification provider.
ModificationType	Enum for the different types of modifications supported.

Classes in com.compomics.util.experiment.biology.modifications used by com.compomics.util.experiment.biology.proteins

Class	Description
Modification	This class models a peptide or protein modification.

Classes in com.compomics.util.experiment.biology.modifications used by com.compomics.util.experiment.identification.amino_acid_tags

Class	Description
Modification	This class models a peptide or protein modification.

Classes in com.compomics.util.experiment.biology.modifications used by com.compomics.util.experiment.identification.modification

Class	Description
Modification	This class models a peptide or protein modification.

Classes in com.compomics.util.experiment.biology.modifications used by com.compomics.util.experiment.identification.modification.mapping

Class	Description
ModificationProvider	Interface for a modification provider.

Classes in com.compomics.util.experiment.biology.modifications used by com.compomics.util.experiment.identification.modification.scores

Class	Description
Modification	This class models a peptide or protein modification.
ModificationProvider	Interface for a modification provider.

Classes in com.compomics.util.experiment.biology.modifications used by com.compomics.util.experiment.identification.modification.search_engine_mapping

Class	Description
ModificationProvider	Interface for a modification provider.

Classes in com.compomics.util.experiment.biology.modifications used by com.compomics.util.experiment.identification.peptide_inference

Class	Description
ModificationProvider	Interface for a modification provider.

Classes in com.compomics.util.experiment.biology.modifications used by com.compomics.util.experiment.identification.protein_inference.fm_index

Class	Description
Modification	This class models a peptide or protein modification.

Classes in com.compomics.util.experiment.biology.modifications used by com.compomics.util.experiment.identification.utils

Class	Description
Modification	This class models a peptide or protein modification.
ModificationProvider	Interface for a modification provider.

Classes in com.compomics.util.experiment.biology.modifications used by com.compomics.util.experiment.io.identification.writers

Class	Description
ModificationProvider	Interface for a modification provider.

Classes in com.compomics.util.experiment.biology.modifications used by com.compomics.util.experiment.io.parameters

Class	Description
ModificationProvider	Interface for a modification provider.

Classes in com.compomics.util.experiment.biology.modifications used by com.compomics.util.gui.modification

Class	Description
Modification	This class models a peptide or protein modification.

Classes in com.compomics.util.experiment.biology.modifications used by com.compomics.util.parameters.identification.search

Class	Description
Modification	This class models a peptide or protein modification.

Classes in com.compomics.util.experiment.biology.modifications used by com.compomics.util.parameters.identification.tool_specific

Class	Description
ModificationCategory	Enum for the different modification categories supported.