Uses of Package
com.compomics.util.parameters.identification.search

Packages that use com.compomics.util.parameters.identification.search

Package	Description
com.compomics.util.experiment.biology.aminoacids.sequence	Classes related to the handling of protein sequences.
com.compomics.util.experiment.biology.ions	Experiment classes related to ions.
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.features	Classes for the generation of identification features.
com.compomics.util.experiment.identification.filtering	Classes for the filtering of identification objects.
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_fragmentation.models.ms2pip.features_generation	This package contains the classes needed to generate ms2pip features.
com.compomics.util.experiment.identification.protein_inference.fm_index	Protein sequence database indexing classes based on Burrows-Wheeler transform.
com.compomics.util.experiment.identification.protein_sequences.digestion	This package contains classes used to digest protein sequences into peptides.
com.compomics.util.experiment.identification.psm_scoring	Main PSM scoring class.
com.compomics.util.experiment.identification.psm_scoring.psm_scores	Main PTM scoring classes.
com.compomics.util.experiment.identification.spectrum_annotation	Classes used for ms2 spectrum annotation.
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators	This package contains implementations of the SpectrumAnnotator allowing the annotation of all ions.
com.compomics.util.experiment.identification.utils	This package contains utilities classes to handle identification objects.
com.compomics.util.experiment.io.identification	Experiment identification classes.
com.compomics.util.experiment.io.identification.idfilereaders	Experiment classes related to reading search engine files.
com.compomics.util.experiment.io.mass_spectrometry	Classes for the handling of mass spectrometry files.
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.gui.parameters.identification.advanced	Dialogs for advanced identification parameters.
com.compomics.util.gui.parameters.identification.algorithm	Search algorithm settings dialogs.
com.compomics.util.gui.parameters.identification.search	Dialogs for search parameters.
com.compomics.util.gui.spectrum	Spectrum and Chromatogram visualization GUI classes.
com.compomics.util.parameters.identification	Identification parameters.
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.
com.compomics.util.pride	Objects related to mapping to PRIDE.

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

Class	Description
ModificationParameters	This class stores the information about the modification parameters (usage, colors, names).

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

Class	Description
ModificationParameters	This class stores the information about the modification parameters (usage, colors, names).

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

Class	Description
ModificationParameters	This class stores the information about the modification parameters (usage, colors, names).
SearchParameters	This class groups the parameters used for identification.

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

Class	Description
DigestionParameters	This class groups the parameters for the digestion of proteins.
ModificationParameters	This class stores the information about the modification parameters (usage, colors, names).

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

Class	Description
ModificationParameters	This class stores the information about the modification parameters (usage, colors, names).

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

Class	Description
DigestionParameters	This class groups the parameters for the digestion of proteins.

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

Class	Description
DigestionParameters	This class groups the parameters for the digestion of proteins.
ModificationParameters	This class stores the information about the modification parameters (usage, colors, names).
SearchParameters	This class groups the parameters used for identification.

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

Class	Description
ModificationParameters	This class stores the information about the modification parameters (usage, colors, names).

Classes in com.compomics.util.parameters.identification.search used by com.compomics.util.experiment.identification.modification.mapping

Class	Description
SearchParameters	This class groups the parameters used for identification.

Classes in com.compomics.util.parameters.identification.search used by com.compomics.util.experiment.identification.modification.scores

Class	Description
ModificationParameters	This class stores the information about the modification parameters (usage, colors, names).

Classes in com.compomics.util.parameters.identification.search used by com.compomics.util.experiment.identification.modification.search_engine_mapping

Class	Description
SearchParameters	This class groups the parameters used for identification.

Classes in com.compomics.util.parameters.identification.search used by com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation

Class	Description
ModificationParameters	This class stores the information about the modification parameters (usage, colors, names).

Classes in com.compomics.util.parameters.identification.search used by com.compomics.util.experiment.identification.protein_inference.fm_index

Class	Description
SearchParameters	This class groups the parameters used for identification.

Classes in com.compomics.util.parameters.identification.search used by com.compomics.util.experiment.identification.protein_sequences.digestion

Class	Description
DigestionParameters	This class groups the parameters for the digestion of proteins.

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

Class	Description
ModificationParameters	This class stores the information about the modification parameters (usage, colors, names).

Classes in com.compomics.util.parameters.identification.search used by com.compomics.util.experiment.identification.psm_scoring.psm_scores

Class	Description
ModificationParameters	This class stores the information about the modification parameters (usage, colors, names).

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

Class	Description
ModificationParameters	This class stores the information about the modification parameters (usage, colors, names).
SearchParameters	This class groups the parameters used for identification.

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

Class	Description
ModificationParameters	This class stores the information about the modification parameters (usage, colors, names).

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

Class	Description
ModificationParameters	This class stores the information about the modification parameters (usage, colors, names).
SearchParameters	This class groups the parameters used for identification.

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

Class	Description
SearchParameters	This class groups the parameters used for identification.

Classes in com.compomics.util.parameters.identification.search used by com.compomics.util.experiment.io.identification.idfilereaders

Class	Description
SearchParameters	This class groups the parameters used for identification.

Classes in com.compomics.util.parameters.identification.search used by com.compomics.util.experiment.io.mass_spectrometry

Class	Description
SearchParameters	This class groups the parameters used for identification.

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

Class	Description
SearchParameters	This class groups the parameters used for identification.

Classes in com.compomics.util.parameters.identification.search used by com.compomics.util.gui.modification

Class	Description
ModificationParameters	This class stores the information about the modification parameters (usage, colors, names).

Classes in com.compomics.util.parameters.identification.search used by com.compomics.util.gui.parameters.identification.advanced

Class	Description
SearchParameters	This class groups the parameters used for identification.

Classes in com.compomics.util.parameters.identification.search used by com.compomics.util.gui.parameters.identification.algorithm

Class	Description
ModificationParameters	This class stores the information about the modification parameters (usage, colors, names).

Classes in com.compomics.util.parameters.identification.search used by com.compomics.util.gui.parameters.identification.search

Class	Description
SearchParameters	This class groups the parameters used for identification.

Classes in com.compomics.util.parameters.identification.search used by com.compomics.util.gui.spectrum

Class	Description
ModificationParameters	This class stores the information about the modification parameters (usage, colors, names).

Classes in com.compomics.util.parameters.identification.search used by com.compomics.util.parameters.identification

Class	Description
SearchParameters	This class groups the parameters used for identification.

Classes in com.compomics.util.parameters.identification.search used by com.compomics.util.parameters.identification.search

Class	Description
DigestionParameters	This class groups the parameters for the digestion of proteins.
DigestionParameters.CleavageParameter	Enum for the different types of digestion.
DigestionParameters.Specificity	Enum for the different types of enzyme specificity.
ModificationParameters	This class stores the information about the modification parameters (usage, colors, names).
SearchParameters	This class groups the parameters used for identification.
SearchParameters.MassAccuracyType	Possible mass accuracy types.

Classes in com.compomics.util.parameters.identification.search used by com.compomics.util.parameters.identification.tool_specific

Class	Description
DigestionParameters	This class groups the parameters for the digestion of proteins.
ModificationParameters	This class stores the information about the modification parameters (usage, colors, names).

Classes in com.compomics.util.parameters.identification.search used by com.compomics.util.pride

Class	Description
SearchParameters	This class groups the parameters used for identification.