Uses of Package
com.compomics.util.experiment.io.biology.protein

Packages that use com.compomics.util.experiment.io.biology.protein 
Package Description
com.compomics.cli.fasta
Command line for the handling of fasta files.
com.compomics.util.experiment.biology.genes
Classes related to genes.
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.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.peptide_inference
Classes related to peptide inference.
com.compomics.util.experiment.identification.protein_inference
Classes related to protein 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.protein_sequences
Protein sequence handling related classes.
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.biology.protein
Experiment IO classes for biological resources.
com.compomics.util.experiment.io.biology.protein.converters
Fasta file converters.
com.compomics.util.experiment.io.biology.protein.iterators
Fasta file iterators.
com.compomics.util.experiment.io.identification.writers
Writer for identification results.
com.compomics.util.experiment.quantification.spectrumcounting
Experiment classes related to spectrum counting.
com.compomics.util.gui.genes
Dialogs for the handling of genes.
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.search
Dialogs for search parameters.
com.compomics.util.gui.protein
GUI class related to protein sequence formatting.
com.compomics.util.gui.spectrum
Spectrum and Chromatogram visualization GUI classes.
com.compomics.util.nucleotide
Useful objects for modeling and handling nucleotides.
com.compomics.util.parameters.identification
Identification parameters.
com.compomics.util.parameters.identification.advanced
Advanced Identification parameters.
com.compomics.util.protein
Classes concerning useful Objects and their operations for modeling and handling proteins.