Packages

• com.compomics.software
• com.compomics.software.autoupdater
• com.compomics.software.dialogs
• 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.enumeration
• com.compomics.util.examples
• com.compomics.util.exceptions
• com.compomics.util.exceptions.exception_handlers
• com.compomics.util.experiment
• com.compomics.util.experiment.biology
• com.compomics.util.experiment.biology.aminoacids
• com.compomics.util.experiment.biology.atoms
• 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.mutations
• com.compomics.util.experiment.biology.taxonomy
• com.compomics.util.experiment.biology.taxonomy.mappings
• com.compomics.util.experiment.filtering
• com.compomics.util.experiment.identification
• com.compomics.util.experiment.identification.amino_acid_tags
• com.compomics.util.experiment.identification.amino_acid_tags.matchers
• com.compomics.util.experiment.identification.filtering
• com.compomics.util.experiment.identification.identification_parameters
• com.compomics.util.experiment.identification.identification_parameters.tool_specific
• com.compomics.util.experiment.identification.identifications
• com.compomics.util.experiment.identification.matches
• com.compomics.util.experiment.identification.matches_iterators
• com.compomics.util.experiment.identification.parameters_cli
• com.compomics.util.experiment.identification.protein_inference.proteintree
• com.compomics.util.experiment.identification.protein_sequences
• com.compomics.util.experiment.identification.psm_scoring
• com.compomics.util.experiment.identification.psm_scoring.psm_scores
• com.compomics.util.experiment.identification.ptm
• com.compomics.util.experiment.identification.ptm.ptmscores
• com.compomics.util.experiment.identification.spectrum_annotation
• com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators
• com.compomics.util.experiment.identification.spectrum_assumptions
• com.compomics.util.experiment.io
• com.compomics.util.experiment.io.identifications
• com.compomics.util.experiment.io.identifications.idfilereaders
• com.compomics.util.experiment.io.massspectrometry
• com.compomics.util.experiment.io.massspectrometry.export
• com.compomics.util.experiment.massspectrometry
• com.compomics.util.experiment.massspectrometry.proteowizard
• com.compomics.util.experiment.massspectrometry.proteowizard.gui
• 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.refinementparameters
• 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.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.filehandling
• com.compomics.util.gui.genes
• com.compomics.util.gui.interfaces
• com.compomics.util.gui.isotopic_calculator
• com.compomics.util.gui.parameters
• com.compomics.util.gui.parameters.identification_parameters
• com.compomics.util.gui.parameters.identification_parameters.algorithm_settings
• com.compomics.util.gui.protein
• com.compomics.util.gui.ptm
• 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.waiting.waitinghandlers
• com.compomics.util.interfaces
• com.compomics.util.io
• com.compomics.util.io.compression
• com.compomics.util.io.export
• com.compomics.util.io.export.styles
• com.compomics.util.io.export.writers
• com.compomics.util.io.filefilters
• com.compomics.util.io.json
• com.compomics.util.io.json.adapter
• com.compomics.util.io.json.marshallers
• com.compomics.util.junit
• com.compomics.util.maps
• 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.pdbfinder
• com.compomics.util.pdbfinder.das.readers
• com.compomics.util.pdbfinder.pdb
• com.compomics.util.preferences
• 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.protein_sequences_manager
• com.compomics.util.protein_sequences_manager.enums
• com.compomics.util.protein_sequences_manager.gui
• com.compomics.util.protein_sequences_manager.gui.preferences
• com.compomics.util.protein_sequences_manager.gui.sequences_import
• com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy
• com.compomics.util.sun
• com.compomics.util.waiting