All Classes and Interfaces

Class	Description
CLIExportMethods	This class groups standard methods used by the different command line interfaces.
ClusterBuilder	Methods for building clusters based on a reporter project.
ClusterClassKey	Key for a cluster class.
ClusteringSettings	Settings for the clustering.
ClusteringSettingsDialog	Clustering settings dialog.
CorrectionMatrix	A correction matrix contains the deisotoping coefficients as well as the labels to be corrected.
Deisotoper	This class takes care of the deisotoping of reporter ion intensities.
DisplayPreferences	Reporter display preferences.
IdentificationParametersCLI	The SearchParametersCLI allows creating search parameters files using command line arguments.
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.
LabellingEfficiencyDialog	Labeling efficiency dialog.
MethodSettingsDialog	Dialog for setting the reporter method details.
NewDialog	This panel will be used to load the necessary files and settings to start the analysis.
NormalizationSettings	Settings used for the normalization.
NormalizationSettingsDialog	The preferences dialog.
NormalizationType	Enum for the different normalization types supported.
Normalizer	Normalizes the ratios according to the NormalizationSettings.
OverviewPanel	The Overview tab.
PathSettingsCLI	Allows the user to set the path settings in command line.
PathSettingsCLIInputBean	Parses the command line and retrieves the user input.
PathSettingsCLIParams	Parameters for the path settings command line.
PeptideClusterClassKey	Key for the class of a peptide cluster.
PeptideQuantificationDetails	This class contains the quantitative information at the peptide level.
PeptideTableModel	Model for the peptide table.
ProjectDetails	This class contains the reporter details on the project.
ProjectImporter	Imports a project from a psdb file.
ProjectSaver	This class can be used to save the Reporter projects in a psdb file.
Properties	This class contains many of the properties that are used during the use of the tool, but that are not stored in the UserProperties.prop file between each run of the program.
ProteinClusterClassKey	Key for the class of a protein cluster.
ProteinPtmQuantificationDetails	This class contains the quantitative information at the GO level.
ProteinQuantificationDetails	This class contains the quantitative information at the protein level.
ProteinRatioType	Enum for the protein ratio types.
ProteinTableModel	Model for the protein table.
PsmClusterClassKey	Key for the class of a PSM cluster.
PsmQuantificationDetails	This class contains the quantitative information at the PSM level.
PsmTableModel	Model for the PSM table.
QuantificationFeaturesCache	The quantification features cache stores quantification features.
QuantificationFeaturesGenerator	The quantification features generator provides various quantification features.
QuantificationFilter	This class indicates whether identification features or ratios are valid according to the user settings.
RatioEstimationSettings	Settings for the estimation of a peptide or protein ratio.
RatioEstimationSettingsDialog	The preferences dialog.
RatioEstimator	This class estimates ratios at the peptide and protein level.
ReagentOrderDialog	Dialog for altering the reagent order.
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.
ReportDialog	This dialog allows the user to select, add and edit reports.
Reporter	Reporter performs reporter ion based quantification on MS2/MS3 spectra.
ReporterCLI	Command line interface for reporter.
ReporterCLIInputBean	This class is used to verify that a command line is valid and parse its parameters.
ReporterCLIParameters	Command line option parameters for ReporterCLI.
ReporterExportFactory	The reporter export factory manages the reports available from Reporter.
ReporterGUI	The main Reporter GUI.
ReporterIonSelectionSettings	Preferences for the reporter ions selection in spectra.
ReporterIonSelectionSettingsDialog	The preferences dialog.
ReporterIonsLocationType	Enum of the possible spectrum reporter ions locations.
ReporterMerger	Merging Reporter protein reports.
ReporterPathPreferences	This class sets the path preferences for the files to read/write.
ReporterPathPreferences.ReporterPathKey	Enum of the paths which can be set in Reporter.
ReporterPeptideSection	This class outputs the peptide related quantification export features.
ReporterPreferences	This class contains the quantification options set by the user.
ReporterProteinSection	This class outputs the protein related export features.
ReporterPsmSection	This class outputs the PSM level quantification export features.
ReporterReportStyle	This class contains the style for a Reporter Excel export.
ReporterSettings	This class contains the reporter settings for this project.
ReporterSettingsDialog	The preferences dialog.
ReporterWrapper	A wrapper class used to start the jar file with parameters.
ReporterZipFileChecker	A wrapper class used to check if the jar file is attempted started from within an unzipped zip file.
SpectrumMerger	Merging of MS2 and MS3 data from Fusion instruments to merge the reporters from HCD MS3 with the identification from CID MS2.
SpectrumQuantificationDetails	This class contains the quantitative information at the spectrum level.
WelcomeDialog	A simple welcome dialog with the option to open an existing project or create a new one.