All Classes and Interfaces
Class
Description
This tab contains the basic protein annotation and links to other protein
resources.
This class contains the method for PSM best hit selection.
This class groups standard methods used by the different command line
interfaces.
Dialog to help the user select the correct database.
Export for RT prediction using DeepLC.
Utils for the export and import of ms2pip results.
This class creates the display features needed for the GUI.
This class contains the display preferences for the current project.
DisplayPreferencesDialog.
This class is a convenience class to have a DefaultJsonConverter with the
ExportFactory interfaces.
Utils for exports.
Export proteins in the FASTA format.
Enum of the different types of export implemented.
Dialog for exporting identification features.
This class is responsible for the import of identifications.
Displays the filters used for star/hide items.
Command line interface to run follow-up analysis on psdb files.
This class is a simple bean wrapping the CLI parameters provided in an
Options instance.
Enum class specifying the Command Line Parameters for follow up analysis.
This class allows generating exports for follow up analysis.
A dialog where the order of the fractions can be decided.
A dialog containing basic information on how to use PeptideShaker.
The PeptideShaker GO Enrichment Analysis tab.
This class handles the simplification of redundant groups based on the
protein inference settings.
The SearchParametersCLI allows creating search parameters files using command
line arguments.
This class imports the ids from a file.
A dialog for selecting missing mgf files.
This class extends JPanel to be able to display an ImageIcon object inside a
JPanel.
This class exports identifications in an inclusion list.
Enum of the different types of export implemented.
Enum of the peptide filters implemented.
Dialog for setting the inclusion list export settings.
This class contains basic information about the hits as imported from the
various search engine result files.
A Jump To panel for use in the menu bar in the main frame.
Enum of the types of data to jump to.
This class validates the quality of identification matches.
This class displays information about the validation of a match.
Type of match selected.
A dialog for drafting the methods section for a publication based on
PeptideShaker results.
A dialog for mapping unknown modifications to the list of supported
modifications.
This class scores the PSM PTMs using the scores implemented in compomics
utilities.
This dialog allows the user to verify/update the modification site.
The Modifications tab.
Modification specific target decoy map.
Export training files for ms2pip.
Utils for the export and import of ms2pip results.
Command line interface to export mzid files from psdb files.
This class is a simple bean wrapping the CLI parameters provided in an
Options instance.
Enum class specifying the Command Line Parameters for mzid export.
The class that takes care of converting the data to mzIdentML.
A dialog where the user can export the project to mzIdentML.
A dialog for selecting the files to load.
The overview panel displaying the proteins, the peptides and the spectra.
Allows the user to set the path settings in command line.
Parses the command line and retrieves the user input.
Enum of the command line parameters for path setting.
Export for peak intensities.
This class checks that the peptide to protein mapping is compatible with the
modification status of the peptide.
This table model shows a fraction view of the peptides given in the
constructor
This class will be responsible for the identification import and the
associated calculations.
A command line interface to run PeptideShaker.
This class is a simple bean wrapping the CLI parameters provided in an
Options instance.
Enum class specifying the Command Line Parameters for PeptideShaker.
The main PeptideShaker frame.
This class provides the parameters which can be used for the identification
parameters cli in PeptideShaker.
This class generates the text needed to for the identification section of the
methods section of a paper.
This class stores parameters for a PeptideShaker project.
This class sets the path preferences for the files to read/write.
Enum of the paths which can be set in PeptideShaker.
A wrapper class used to start the jar file with parameters.
A wrapper class used to check if the jar file is attempted started from
within an unzipped zip file.
Table model for a set of peptide matches.
Export to PepXML.
Export for Percolator.
Utils for the export and import of Percolator results.
A dialog for selecting if public or private data is to be loaded.
A dialog for using PRIDE free text search via
https://www.ebi.ac.uk/pride/archive/simpleSearch.
A dialog for getting the PRIDE private project access information from the
user.
Frame for talking to the PRIDE Archive web service to select projects for
reshaking.
Dialog for setting up the PRIDE Reshake.
Display the extracted search settings to the user.
This class exports identifications for post-processing with Non-Linear
Progenesis.
Enum of the different types of export implemented.
This class contains the details about a project.
This dialog displays the project properties.
This class takes care of exporting the entire project as a single file.
A dialog where the user can edit the PeptideShaker preferences.
A dialog displaying various filters that can be applied to the PRIDE project
table.
This class provides the PeptideShaker version number.
This class generates the tooltips for a ProteinSequencePanel.
Displays information about which fractions the peptides and proteins were
detected in.
This table model displays the protein confidence in every fraction.
Model for a the GO mappings protein table.
This class groups the methods for protein inference.
This dialog allows the user to resolve manually some protein inference
issues.
Dialog for displaying the protein inference graph legend.
A panel to display protein inference graphs.
Dialog for displaying the selected nodes in a ProteinInferenceGraphPanel.
A simple dialog for showing the list of proteins a given peptide can map to.
Scores modification localization on proteins, estimates spectrum counting and
summary statistics values.
This class can be used to create a protein sequence plot.
An interface implemented by parents of ProteinSequencePanel plots/charts.
The Protein Structure tab.
Model for the protein table.
Export for PathwayMatcher.
This class outputs the annotation related export features.
This class exports a PeptideShaker project as pdsb file.
Implementing this abstract class allows interacting with a psdb files.
The PeptideShaker export factory.
This class contains the style for a PeptideShaker excel export.
This class outputs the PSM related export features.
This report section contains the results of the identification algorithms.
This class outputs the annotation related export features.
This class contains all scoring maps from PeptideShaker and will be used to
store the information.
This class tries to find a best hit per search engine for each spectrum
match.
Export for PSM identifications.
This class can be used to import PSMs from search engine results.
Runnable for the import of PSMs.
Iterates the spectrum matches and saves assumption probabilities, selects
best hits, scores modification localization, and refines protein mapping
accordingly.
This class processes PSMs.
This class scores peptide spectrum matches.
Table model for a set of peptide to spectrum matches.
This class outputs the peptide related export features.
This class outputs the project related export features.
This class outputs the protein related export features.
This class outputs the PSM level export features.
This class outputs the project related export features.
This class outputs the search parameters related export features.
This class outputs the spectrum counting related export features.
This class outputs the validation related export features.
This class contains information and methods to zip and unzip files from
PeptideShaker.
PTM location dialog for the Progenesis export.
This panel will display QC statistics for the current project.
This class exports recalibrated spectra.
This class performs the command line export of reports in command line.
This class is a simple bean wrapping the CLI parameters provided in an
Options instance.
This class provides the available reports as command line parameters.
Annotation for a given protein residue.
This class computes the mz deviations for a a given run (i.e.
A dialog for displaying the various save/export options.
Specific target decoy map where the highest value with enough values is kept.
This stores target decoy maps grouped by file and category.
Dialog for user selection of spectrum annotation colors.
SpectrumCountingSettingsDialog.
This class can be used to export spectra.
Enum of the different types of export implemented.
The Spectrum ID panel.
This class recalibrates spectra.
This class provides information whether a hit should be hidden or starred.
This class imports the results of a search engine from SearchGUI in the
utilities model.
Command line to manage the modifications.
Enum class specifying the ModificationsCLI parameters.
This class parses the parameters from an ModificationsCLI.
This class scores the modification localization.
This class can be used to map tags to proteins.
This map contains the information of a target/decoy strategy.
This class represents a target/decoy hit in its simplest form.
This class will compile Target/decoy results of a certain target/decoy map
according to user's validation criteria
This class will contain the PEP, FDR and FNR values of a target decoy map
directly available for plotting.
This class breaks ties between equally scoring peptides.
This class provides the tips of the day.
Export peptide sequences to the Unipept web interface.
In this class are stored the user preferences for PeptideShaker.
Implementing this class will give you access to the saved user preferences.
This panel displays statistical information about the dataset.
A simple welcome dialog with the option to open an existing project or create
a new one.