All Classes
Packages
com.compomics.cli.enzymes
com.compomics.cli.fasta
com.compomics.cli.identification_parameters
com.compomics.cli.modifications
com.compomics.cli.paths
com.compomics.cli.peptide_mapper
com.compomics.scripts_marc
com.compomics.software
com.compomics.software.autoupdater
com.compomics.software.cli
com.compomics.software.dialogs
com.compomics.software.log
com.compomics.software.settings
com.compomics.software.settings.gui
com.compomics.util
com.compomics.util.db
com.compomics.util.db.components
com.compomics.util.db.interfaces
com.compomics.util.db.object
com.compomics.util.db.object.objects
com.compomics.util.enumeration
com.compomics.util.examples
com.compomics.util.exceptions
com.compomics.util.exceptions.exception_handlers
com.compomics.util.experiment
com.compomics.util.experiment.biology.aminoacids
com.compomics.util.experiment.biology.aminoacids.impl
com.compomics.util.experiment.biology.aminoacids.sequence
com.compomics.util.experiment.biology.atoms
com.compomics.util.experiment.biology.atoms.impl
com.compomics.util.experiment.biology.enzymes
com.compomics.util.experiment.biology.genes
com.compomics.util.experiment.biology.genes.ensembl
com.compomics.util.experiment.biology.genes.go
com.compomics.util.experiment.biology.ions
com.compomics.util.experiment.biology.ions.impl
com.compomics.util.experiment.biology.modifications
com.compomics.util.experiment.biology.proteins
com.compomics.util.experiment.biology.taxonomy
com.compomics.util.experiment.biology.taxonomy.mappings
com.compomics.util.experiment.biology.variants
com.compomics.util.experiment.biology.variants.amino_acids
com.compomics.util.experiment.filtering
com.compomics.util.experiment.identification
com.compomics.util.experiment.identification.amino_acid_tags
com.compomics.util.experiment.identification.features
com.compomics.util.experiment.identification.filtering
com.compomics.util.experiment.identification.filtering.items
com.compomics.util.experiment.identification.identification_parameters
com.compomics.util.experiment.identification.matches
com.compomics.util.experiment.identification.matches_iterators
com.compomics.util.experiment.identification.modification
com.compomics.util.experiment.identification.modification.mapping
com.compomics.util.experiment.identification.modification.scores
com.compomics.util.experiment.identification.peptide_fragmentation
com.compomics.util.experiment.identification.peptide_fragmentation.models
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_configuration.features.generic
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation
com.compomics.util.experiment.identification.peptide_inference
com.compomics.util.experiment.identification.peptide_shaker
com.compomics.util.experiment.identification.protein_inference
com.compomics.util.experiment.identification.protein_inference.fm_index
com.compomics.util.experiment.identification.protein_sequences
com.compomics.util.experiment.identification.protein_sequences.digestion
com.compomics.util.experiment.identification.protein_sequences.digestion.iterators
com.compomics.util.experiment.identification.psm_scoring
com.compomics.util.experiment.identification.psm_scoring.psm_scores
com.compomics.util.experiment.identification.spectrum_annotation
com.compomics.util.experiment.identification.spectrum_annotation.simple_annotators
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators
com.compomics.util.experiment.identification.spectrum_assumptions
com.compomics.util.experiment.identification.utils
com.compomics.util.experiment.identification.validation
com.compomics.util.experiment.io.biology.protein
com.compomics.util.experiment.io.biology.protein.converters
com.compomics.util.experiment.io.biology.protein.iterators
com.compomics.util.experiment.io.identification
com.compomics.util.experiment.io.identification.idfilereaders
com.compomics.util.experiment.io.identification.writers
com.compomics.util.experiment.io.mass_spectrometry
com.compomics.util.experiment.io.mass_spectrometry.apl
com.compomics.util.experiment.io.mass_spectrometry.cms
com.compomics.util.experiment.io.mass_spectrometry.mgf
com.compomics.util.experiment.io.mass_spectrometry.ms2
com.compomics.util.experiment.io.mass_spectrometry.mzml
com.compomics.util.experiment.io.parameters
com.compomics.util.experiment.io.temp
com.compomics.util.experiment.mass_spectrometry
com.compomics.util.experiment.mass_spectrometry.indexes
com.compomics.util.experiment.mass_spectrometry.proteowizard
com.compomics.util.experiment.mass_spectrometry.spectra
com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser
com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.gui
com.compomics.util.experiment.mass_spectrometry.utils
com.compomics.util.experiment.normalization
com.compomics.util.experiment.patient
com.compomics.util.experiment.personalization
com.compomics.util.experiment.quantification
com.compomics.util.experiment.quantification.reporterion
com.compomics.util.experiment.quantification.spectrumcounting
com.compomics.util.experiment.refinement_parameters
com.compomics.util.experiment.units
com.compomics.util.general
com.compomics.util.general.servlet
com.compomics.util.gui
com.compomics.util.gui.atoms
com.compomics.util.gui.enzymes
com.compomics.util.gui.error_handlers
com.compomics.util.gui.error_handlers.notification
com.compomics.util.gui.events
com.compomics.util.gui.export.graphics
com.compomics.util.gui.export.report
com.compomics.util.gui.file_handling
com.compomics.util.gui.filtering
com.compomics.util.gui.genes
com.compomics.util.gui.interfaces
com.compomics.util.gui.isotopic_calculator
com.compomics.util.gui.modification
com.compomics.util.gui.parameters
com.compomics.util.gui.parameters.identification
com.compomics.util.gui.parameters.identification.advanced
com.compomics.util.gui.parameters.identification.algorithm
com.compomics.util.gui.parameters.identification.pride
com.compomics.util.gui.parameters.identification.search
com.compomics.util.gui.parameters.proteowizard
com.compomics.util.gui.parameters.tools
com.compomics.util.gui.protein
com.compomics.util.gui.renderers
com.compomics.util.gui.spectrum
com.compomics.util.gui.tablemodels
com.compomics.util.gui.utils
com.compomics.util.gui.utils.user_choice
com.compomics.util.gui.utils.user_choice.list_choosers
com.compomics.util.gui.variants.aa_substitutions
com.compomics.util.gui.waiting.waitinghandlers
com.compomics.util.interfaces
com.compomics.util.io
com.compomics.util.io.compression
com.compomics.util.io.compression.SectionGzWriter
com.compomics.util.io.export
com.compomics.util.io.export.features
com.compomics.util.io.export.features.peptideshaker
com.compomics.util.io.export.features.reporter
com.compomics.util.io.export.styles
com.compomics.util.io.export.writers
com.compomics.util.io.export.xml
com.compomics.util.io.file
com.compomics.util.io.file.filefilters
com.compomics.util.io.flat
com.compomics.util.io.flat.readers
com.compomics.util.io.ftp
com.compomics.util.io.json
com.compomics.util.io.json.adapter
com.compomics.util.io.json.marshallers
com.compomics.util.junit
com.compomics.util.math
com.compomics.util.math.clustering
com.compomics.util.math.clustering.settings
com.compomics.util.math.matrix
com.compomics.util.math.roc
com.compomics.util.math.statistics
com.compomics.util.math.statistics.distributions
com.compomics.util.math.statistics.linear_regression
com.compomics.util.math.statistics.linear_regression.filters
com.compomics.util.math.statistics.linear_regression.regressions
com.compomics.util.memory
com.compomics.util.messages
com.compomics.util.nucleotide
com.compomics.util.parameters
com.compomics.util.parameters.identification
com.compomics.util.parameters.identification.advanced
com.compomics.util.parameters.identification.search
com.compomics.util.parameters.identification.tool_specific
com.compomics.util.parameters.peptide_shaker
com.compomics.util.parameters.quantification.spectrum_counting
com.compomics.util.parameters.searchgui
com.compomics.util.parameters.tools
com.compomics.util.pdbfinder
com.compomics.util.pdbfinder.das.readers
com.compomics.util.pdbfinder.pdb
com.compomics.util.pride
com.compomics.util.pride.prideobjects
com.compomics.util.pride.prideobjects.webservice
com.compomics.util.pride.prideobjects.webservice.file
com.compomics.util.pride.prideobjects.webservice.query
com.compomics.util.pride.validation
com.compomics.util.protein
com.compomics.util.sun
com.compomics.util.threading
com.compomics.util.waiting