PeptideShaker 3.0.12 API

Packages

Package	Description
eu.isas.peptideshaker	PeptideShaker main calculations and jar wrapper.
eu.isas.peptideshaker.cmd	Command line usage.
eu.isas.peptideshaker.export	Exporting data from PeptideShaker.
eu.isas.peptideshaker.export.sections	Export sections.
eu.isas.peptideshaker.fileimport	Import of search results.
eu.isas.peptideshaker.followup	Export for follow-up analysis.
eu.isas.peptideshaker.gui	GUI dialogs and helper classes.
eu.isas.peptideshaker.gui.export	GUI export dialogs.
eu.isas.peptideshaker.gui.filtering	GUI filtering dialogs.
eu.isas.peptideshaker.gui.parameters	Preferences dialogs.
eu.isas.peptideshaker.gui.pride	GUI classes for exporting to PRIDE.
eu.isas.peptideshaker.gui.protein_inference	Protein inference dialogs.
eu.isas.peptideshaker.gui.protein_sequence	Protein sequence annotation.
eu.isas.peptideshaker.gui.start	Getting started dialog.
eu.isas.peptideshaker.gui.tablemodels	Table models.
eu.isas.peptideshaker.gui.tabpanels	Main GUI panels.
eu.isas.peptideshaker.parameters	Parameter settings.
eu.isas.peptideshaker.preferences	Preferences settings.
eu.isas.peptideshaker.processing	Classes used to create PeptideShaker projects.
eu.isas.peptideshaker.protein_inference	Protein inference classes.
eu.isas.peptideshaker.ptm	PTM scoring classes.
eu.isas.peptideshaker.recalibration	Spectrum recalibration.
eu.isas.peptideshaker.scoring	Identification scoring.
eu.isas.peptideshaker.scoring.maps	Target decoy maps.
eu.isas.peptideshaker.scoring.maps.specific	Specific target decoy maps.
eu.isas.peptideshaker.scoring.psm_scoring	PSM scoring.
eu.isas.peptideshaker.scoring.targetdecoy	Target/decoy related classes.
eu.isas.peptideshaker.stirred	Classes used to create stirred projects.
eu.isas.peptideshaker.stirred.modules	Modules for stirred mode.
eu.isas.peptideshaker.utils	Various utilities classes.
eu.isas.peptideshaker.validation	Matches validation.