Uses of Class
com.compomics.util.experiment.biology.proteins.Peptide

Packages that use Peptide 
Package Description
com.compomics.util.experiment.biology.ions
Experiment classes related to ions.
com.compomics.util.experiment.biology.proteins
Classes related to proteins.
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.matches
Experiment classes related to matches.
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
Classes related to protein inference.
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.simple_annotators
This package contains implementations of the SimpleAnnotator allowing the annotation of specific sets of ions.
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.spectrum_assumptions
Implementations of the SpectrumIdentificationAssumption.
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.gui.spectrum
Spectrum and Chromatogram visualization GUI classes.