All Classes

Class	Description
AnnotationPanel	This tab contains the basic protein annotation and links to other protein resources.
BestMatchSelection	This class contains the method for PSM best hit selection.
CLIExportMethods	This class groups standard methods used by the different command line interfaces.
DatabaseHelpDialog	Dialog to help the user select the correct database.
DisplayFeaturesGenerator	This class creates the display features needed for the GUI.
DisplayParameters	This class contains the display preferences for the current project.
DisplayPreferencesDialog	DisplayPreferencesDialog.
FastaExport	Export proteins in the FASTA format.
FastaExport.ExportType	Enum of the different types of export implemented.
FeaturesExportDialog	Dialog for exporting identification features.
FileImporter	This class is responsible for the import of identifications.
FiltersDialog	Displays the filters used for star/hide items.
FollowUpCLI	Command line interface to run follow-up analysis on psdb files.
FollowUpCLIInputBean	This class is a simple bean wrapping the CLI parameters provided in an Options instance.
FollowUpCLIParams	Enum class specifying the Command Line Parameters for follow up analysis.
FollowUpExportDialog	This class allows generating exports for follow up analysis.
FractionDetailsDialog	A dialog where the order of the fractions can be decided.
GettingStartedDialog	A dialog containing basic information on how to use PeptideShaker.
GOEAPanel	The PeptideShaker GO Enrichment Analysis tab.
GroupSimplification	This class handles the simplification of redundant groups based on the protein inference settings.
IdentificationParametersCLI	The SearchParametersCLI allows creating search parameters files using command line arguments.
IdImporter	This class imports the ids from a file.
IdToSpectrumFileMappingDialog	A dialog for selecting missing mgf files.
ImageIconPanel	This class extends JPanel to be able to display an ImageIcon object inside a JPanel.
InclusionListExport	This class exports identifications in an inclusion list.
InclusionListExport.ExportFormat	Enum of the different types of export implemented.
InclusionListExport.PeptideFilterType	Enum of the peptide filters implemented.
InclusionListExportDialog	Dialog for setting the inclusion list export settings.
InputMap	This class contains basic information about the hits as imported from the various search engine result files.
JumpToPanel	A Jump To panel for use in the menu bar in the main frame.
JumpToPanel.JumpType	Enum of the types of data to jump to.
MatchesValidator	This class validates the quality of identification matches.
MatchValidationDialog	This class displays information about the validation of a match.
MatchValidationDialog.MatchType	Type of match selected.
MethodsSectionDialog	A dialog for drafting the methods section for a publication based on PeptideShaker results.
ModificationDialog	A dialog for mapping unknown modifications to the list of supported modifications.
ModificationLocalizationScorer	This class scores the PSM PTMs using the scores implemented in compomics utilities.
ModificationSiteInferenceDialog	This dialog allows the user to verify/update the modification site.
ModificationsPanel	The Modifications tab.
ModificationSpecificMap	Modification specific target decoy map.
MzidCLI	Command line interface to export mzid files from psdb files.
MzidCLIInputBean	This class is a simple bean wrapping the CLI parameters provided in an Options instance.
MzidCLIParams	Enum class specifying the Command Line Parameters for mzid export.
MzIdentMLExport	The class that takes care of converting the data to mzIdentML.
MzIdentMLExportDialog	A dialog where the user can export the project to mzIdentML.
NewDialog	A dialog for selecting the files to load.
OverviewPanel	The overview panel displaying the proteins, the peptides and the spectra.
PathSettingsCLI	Allows the user to set the path settings in command line.
PathSettingsCLIInputBean	Parses the command line and retrieves the user input.
PathSettingsCLIParams	Enum of the command line parameters for path setting.
PeptideChecker	This class checks that the peptide to protein mapping is compatible with the modification status of the peptide.
PeptideFractionTableModel	This table model shows a fraction view of the peptides given in the constructor
PeptideShaker	This class will be responsible for the identification import and the associated calculations.
PeptideShakerCLI	A command line interface to run PeptideShaker.
PeptideShakerCLIInputBean	This class is a simple bean wrapping the CLI parameters provided in an Options instance.
PeptideShakerCLIParams	Enum class specifying the Command Line Parameters for PeptideShaker.
PeptideShakerGUI	The main PeptideShaker frame.
PeptideShakerIdentificationParametersCLIParams	This class provides the parameters which can be used for the identification parameters cli in PeptideShaker.
PeptideShakerMethods	This class generates the text needed to for the identification section of the methods section of a paper.
PeptideShakerParameters	This class stores parameters for a PeptideShaker project.
PeptideShakerPathParameters	This class sets the path preferences for the files to read/write.
PeptideShakerPathParameters.PeptideShakerPathKey	Enum of the paths which can be set in PeptideShaker.
PeptideShakerWrapper	A wrapper class used to start the jar file with parameters.
PeptideShakerZipFileChecker	A wrapper class used to check if the jar file is attempted started from within an unzipped zip file.
PeptideTableModel	Table model for a set of peptide matches.
PepXmlExport	Export to PepXML.
PrideDataTypeSelectionDialog	A dialog for selecting if public or private data is to be loaded.
PrideFreeTextSearchDialog	A dialog for using PRIDE free text search via https://www.ebi.ac.uk/pride/archive/simpleSearch.
PridePrivateDataDialog	A dialog for getting the PRIDE private project access information from the user.
PrideReshakeGUI	Frame for talking to the PRIDE Archive web service to select projects for reshaking.
PrideReshakeSetupDialog	Dialog for setting up the PRIDE Reshake.
PrideSearchParametersDialog	Display the extracted search settings to the user.
ProgenesisExport	This class exports identifications for post-processing with Non-Linear Progenesis.
ProgenesisExport.ExportType	Enum of the different types of export implemented.
ProjectDetails	This class contains the details about a project.
ProjectDetailsDialog	This dialog displays the project properties.
ProjectExport	This class takes care of exporting the entire project as a single file.
ProjectParametersDialog	A dialog where the user can edit the PeptideShaker preferences.
ProjectsFilterDialog	A dialog displaying various filters that can be applied to the PRIDE project table.
Properties	This class provides the PeptideShaker version number.
ProteinAnnotations	This class generates the tooltips for a ProteinSequencePanel.
ProteinFractionsPanel	Displays information about which fractions the peptides and proteins were detected in.
ProteinFractionTableModel	This table model displays the protein confidence in every fraction.
ProteinGoTableModel	Model for a the GO mappings protein table.
ProteinInference	This class groups the methods for protein inference.
ProteinInference.GroupSimplificationOption
ProteinInferenceDialog	This dialog allows the user to resolve manually some protein inference issues.
ProteinInferenceGraphLegendDialog	Dialog for displaying the protein inference graph legend.
ProteinInferenceGraphPanel	A panel to display protein inference graphs.
ProteinInferenceGraphSelectionDialog	Dialog for displaying the selected nodes in a ProteinInferenceGraphPanel.
ProteinInferencePeptideLevelDialog	A simple dialog for showing the list of proteins a given peptide can map to.
ProteinProcessor	Scores modification localization on proteins, estimates spectrum counting and summary statistics values.
ProteinSequencePanel	This class can be used to create a protein sequence plot.
ProteinSequencePanelParent	An interface implemented by parents of ProteinSequencePanel plots/charts.
ProteinStructurePanel	The Protein Structure tab.
ProteinTableModel	Model for the protein table.
ProteoformExport	Export for PathwayMatcher.
PsAnnotationFeature	This class lists the annotation export features.
PsAnnotationSection	This class outputs the annotation related export features.
PsdbExporter	This class exports a PeptideShaker project as pdsb file.
PsdbParent	Implementing this abstract class allows interacting with a psdb files.
PSExportFactory	The PeptideShaker export factory
PsExportStyle	This class contains the style for a PeptideShaker excel export.
PsFragmentFeature	This class lists the fragment identification features.
PsFragmentSection	This class outputs the PSM related export features.
PsIdentificationAlgorithmMatchesFeature	This class lists the Algorithm identification features.
PsIdentificationAlgorithmMatchesSection	This report section contains the results of the identification algorithms.
PsInputFilterFeature	This enum lists the export features related to the import features.
PsInputFilterSection	This class outputs the annotation related export features.
PSMaps	This class contains all scoring maps from PeptideShaker and will be used to store the information.
PsmFirstHitRunnable	This class tries to find a best hit per search engine for each spectrum match.
PsmImporter	This class can be used to import PSMs from search engine results.
PsmImportRunnable	Runnable for the import of PSMs.
PsmProcessor	Iterates the spectrum matches and saves assumption probabilities, selects best hits, scores modification localization, and refines protein mapping accordingly.
PsmProcessorRunnable	This class processes PSMs.
PsmScorer	This class scores peptide spectrum matches.
PsmTableModel	Table model for a set of peptide to spectrum matches.
PsPeptideFeature	This class lists the peptide identification features.
PsPeptideSection	This class outputs the peptide related export features.
PsProjectFeature	This class lists the PSM identification features.
PsProjectSection	This class outputs the project related export features.
PsProteinFeature	This class lists the protein identification features.
PsProteinSection	This class outputs the protein related export features.
PsPsmFeature	This class lists the PSM identification features.
PsPsmSection	This class outputs the PSM level export features.
PsPtmScoringFeature	This enum groups the export features related to PTM scoring.
PsPtmScoringSection	This class outputs the project related export features.
PsSearchFeature	This class lists the export features linked to the spectrum identification.
PsSearchParametersSection	This class outputs the search parameters related export features.
PsSpectrumCountingFeature	This class lists all the export features related to the spectrum counting.
PsSpectrumCountingSection	This class outputs the spectrum counting related export features.
PsValidationFeature	This enum lists the export features linked to the validation process.
PsValidationSection	This class outputs the validation related export features.
PsZipUtils	This class contains information and methods to zip and unzip files from PeptideShaker.
PtmSelectionDialog	PTM location dialog for the Progenesis export.
QCPanel	This panel will display QC statistics for the current project.
RecalibrationExporter	This class exports recalibrated spectra.
ReportCLI	This class performs the command line export of reports in command line.
ReportCLIInputBean	This class is a simple bean wrapping the CLI parameters provided in an Options instance.
ReportCLIParams	This class provides the available reports as command line parameters.
ResidueAnnotation	Annotation for a given protein residue.
RunMzDeviation	This class computes the mz deviations for a a given run (i.e.
SaveDialog	A dialog for displaying the various save/export options.
SimpleSpecificMap	Specific target decoy map where the highest value with enough values is kept.
SpecificTargetDecoyMap	This stores target decoy maps grouped by file and category.
SpectrumColorsDialog	Dialog for user selection of spectrum annotation colors.
SpectrumCountingSettingsDialog	SpectrumCountingSettingsDialog.
SpectrumExporter	This class can be used to export spectra.
SpectrumExporter.ExportType	Enum of the different types of export implemented.
SpectrumIdentificationPanel	The Spectrum ID panel.
SpectrumRecalibrator	This class recalibrates spectra.
StarHider	This class provides information whether a hit should be hidden or starred.
Stirred	This class imports the results of a search engine from SearchGUI in the utilities model.
StirredCLI	Command line to manage the modifications.
StirredOptions	Enum class specifying the ModificationsCLI parameters.
StirredOptionsBean	This class parses the parameters from an ModificationsCLI.
StirRunnable	This class scores the modification localization.
TagMapper	This class can be used to map tags to proteins.
TargetDecoyMap	This map contains the information of a target/decoy strategy.
TargetDecoyPoint	This class represents a target/decoy hit in its simplest form.
TargetDecoyResults	This class will compile Target/decoy results of a certain target/decoy map according to user's validation criteria
TargetDecoySeries	This class will contain the PEP, FDR and FNR values of a target decoy map directly available for plotting.
TieBreaker	This class breaks ties between equally scoring peptides.
Tips	This class provides the tips of the day.
UnipeptExport	Export peptide sequences to the Unipept web interface.
UserParameters	In this class are stored the user preferences for PeptideShaker.
UserPreferencesParent	Implementing this class will give you access to the saved user preferences.
ValidationPanel	This panel displays statistical information about the dataset.
WelcomeDialog	A simple welcome dialog with the option to open an existing project or create a new one.