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.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.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.