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.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.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.

Classes in com.compomics.util.experiment.io.biology.protein used by com.compomics.cli.fasta

Class	Description
FastaParameters	The parameters used to parse a FASTA file.

Classes in com.compomics.util.experiment.io.biology.protein used by com.compomics.util.experiment.biology.genes

Class	Description
FastaSummary	This class parses a FASTA file and gathers summary statistics.
ProteinDetailsProvider	Interface for a class able to provide metadata on proteins.
SequenceProvider	Interface for a class able to retrieve the sequence of a given protein.

Classes in com.compomics.util.experiment.io.biology.protein used by com.compomics.util.experiment.biology.ions

Class	Description
SequenceProvider	Interface for a class able to retrieve the sequence of a given protein.

Classes in com.compomics.util.experiment.io.biology.protein used by com.compomics.util.experiment.biology.proteins

Class	Description
SequenceProvider	Interface for a class able to retrieve the sequence of a given protein.

Classes in com.compomics.util.experiment.io.biology.protein used by com.compomics.util.experiment.identification.features

Class	Description
SequenceProvider	Interface for a class able to retrieve the sequence of a given protein.

Classes in com.compomics.util.experiment.io.biology.protein used by com.compomics.util.experiment.identification.filtering

Class	Description
ProteinDetailsProvider	Interface for a class able to provide metadata on proteins.
SequenceProvider	Interface for a class able to retrieve the sequence of a given protein.

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

Class	Description
SequenceProvider	Interface for a class able to retrieve the sequence of a given protein.

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

Class	Description
SequenceProvider	Interface for a class able to retrieve the sequence of a given protein.

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

Class	Description
SequenceProvider	Interface for a class able to retrieve the sequence of a given protein.

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

Class	Description
SequenceProvider	Interface for a class able to retrieve the sequence of a given protein.

Classes in com.compomics.util.experiment.io.biology.protein used by com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation

Class	Description
SequenceProvider	Interface for a class able to retrieve the sequence of a given protein.

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

Class	Description
SequenceProvider	Interface for a class able to retrieve the sequence of a given protein.

Classes in com.compomics.util.experiment.io.biology.protein used by com.compomics.util.experiment.identification.protein_inference

Class	Description
SequenceProvider	Interface for a class able to retrieve the sequence of a given protein.

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

Class	Description
FastaParameters	The parameters used to parse a FASTA file.
Header	This class represents the header for a Protein instance.
ProteinDatabase	Enum of the supported protein databases.
ProteinDetailsProvider	Interface for a class able to provide metadata on proteins.
SequenceProvider	Interface for a class able to retrieve the sequence of a given protein.

Classes in com.compomics.util.experiment.io.biology.protein used by com.compomics.util.experiment.identification.protein_sequences

Class	Description
SequenceProvider	Interface for a class able to retrieve the sequence of a given protein.

Classes in com.compomics.util.experiment.io.biology.protein used by com.compomics.util.experiment.identification.psm_scoring

Class	Description
SequenceProvider	Interface for a class able to retrieve the sequence of a given protein.

Classes in com.compomics.util.experiment.io.biology.protein used by com.compomics.util.experiment.identification.psm_scoring.psm_scores

Class	Description
SequenceProvider	Interface for a class able to retrieve the sequence of a given protein.

Classes in com.compomics.util.experiment.io.biology.protein used by com.compomics.util.experiment.identification.spectrum_annotation

Class	Description
SequenceProvider	Interface for a class able to retrieve the sequence of a given protein.

Classes in com.compomics.util.experiment.io.biology.protein used by com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators

Class	Description
SequenceProvider	Interface for a class able to retrieve the sequence of a given protein.

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

Class	Description
FastaParameters	The parameters used to parse a FASTA file.
SequenceProvider	Interface for a class able to retrieve the sequence of a given protein.

Classes in com.compomics.util.experiment.io.biology.protein used by com.compomics.util.experiment.io.biology.protein

Class	Description
FastaParameters	The parameters used to parse a FASTA file.
FastaSummary	This class parses a FASTA file and gathers summary statistics.
Header	This class represents the header for a Protein instance.
ProteinDatabase	Enum of the supported protein databases.

Classes in com.compomics.util.experiment.io.biology.protein used by com.compomics.util.experiment.io.biology.protein.converters

Class	Description
FastaParameters	The parameters used to parse a FASTA file.
FastaSummary	This class parses a FASTA file and gathers summary statistics.

Classes in com.compomics.util.experiment.io.biology.protein used by com.compomics.util.experiment.io.biology.protein.iterators

Class	Description
Header	This class represents the header for a Protein instance.
ProteinIterator	Interface for a protein iterator.

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

Class	Description
FastaSummary	This class parses a FASTA file and gathers summary statistics.
ProteinDetailsProvider	Interface for a class able to provide metadata on proteins.
SequenceProvider	Interface for a class able to retrieve the sequence of a given protein.

Classes in com.compomics.util.experiment.io.biology.protein used by com.compomics.util.experiment.quantification.spectrumcounting

Class	Description
SequenceProvider	Interface for a class able to retrieve the sequence of a given protein.

Classes in com.compomics.util.experiment.io.biology.protein used by com.compomics.util.gui.genes

Class	Description
ProteinDetailsProvider	Interface for a class able to provide metadata on proteins.

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

Class	Description
SequenceProvider	Interface for a class able to retrieve the sequence of a given protein.

Classes in com.compomics.util.experiment.io.biology.protein used by com.compomics.util.gui.parameters.identification.advanced

Class	Description
FastaSummary	This class parses a FASTA file and gathers summary statistics.

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

Class	Description
FastaParameters	The parameters used to parse a FASTA file.

Classes in com.compomics.util.experiment.io.biology.protein used by com.compomics.util.gui.protein

Class	Description
FastaParameters	The parameters used to parse a FASTA file.

Classes in com.compomics.util.experiment.io.biology.protein used by com.compomics.util.gui.spectrum

Class	Description
SequenceProvider	Interface for a class able to retrieve the sequence of a given protein.

Classes in com.compomics.util.experiment.io.biology.protein used by com.compomics.util.nucleotide

Class	Description
Header	This class represents the header for a Protein instance.

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

Class	Description
FastaParameters	The parameters used to parse a FASTA file.

Classes in com.compomics.util.experiment.io.biology.protein used by com.compomics.util.parameters.identification.advanced

Class	Description
FastaSummary	This class parses a FASTA file and gathers summary statistics.

Classes in com.compomics.util.experiment.io.biology.protein used by com.compomics.util.protein

Class	Description
Header	This class represents the header for a Protein instance.